Starting phenix.real_space_refine on Thu Mar 5 02:50:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zjs_74340/03_2026/9zjs_74340_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zjs_74340/03_2026/9zjs_74340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zjs_74340/03_2026/9zjs_74340_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zjs_74340/03_2026/9zjs_74340_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zjs_74340/03_2026/9zjs_74340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zjs_74340/03_2026/9zjs_74340.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 80 5.16 5 C 11474 2.51 5 N 2932 2.21 5 O 3302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17796 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 9139 Classifications: {'peptide': 1117} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 40, 'TRANS': 1076} Chain breaks: 10 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 8593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 8593 Classifications: {'peptide': 1047} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 1012} Chain breaks: 17 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.23, per 1000 atoms: 0.24 Number of scatterers: 17796 At special positions: 0 Unit cell: (111.54, 124.74, 149.16, 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 80 16.00 P 6 15.00 Mg 2 11.99 O 3302 8.00 N 2932 7.00 C 11474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 710.1 milliseconds 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4148 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 11 sheets defined 63.8% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 421 through 433 removed outlier: 3.688A pdb=" N THR A 425 " --> pdb=" O PRO A 422 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS A 426 " --> pdb=" O ASP A 423 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 428 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ASP A 429 " --> pdb=" O LYS A 426 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N PHE A 430 " --> pdb=" O HIS A 427 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 431 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 450 through 457 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 475 through 483 Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 517 through 529 Processing helix chain 'A' and resid 554 through 568 removed outlier: 3.546A pdb=" N GLU A 558 " --> pdb=" O ASP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 592 Processing helix chain 'A' and resid 597 through 604 removed outlier: 4.353A pdb=" N ILE A 601 " --> pdb=" O HIS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 620 Processing helix chain 'A' and resid 642 through 649 removed outlier: 3.776A pdb=" N MET A 649 " --> pdb=" O GLU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 686 removed outlier: 3.625A pdb=" N GLY A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 699 removed outlier: 3.803A pdb=" N PHE A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER A 697 " --> pdb=" O ASN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 724 Processing helix chain 'A' and resid 743 through 754 Processing helix chain 'A' and resid 769 through 783 Processing helix chain 'A' and resid 804 through 822 removed outlier: 4.320A pdb=" N TYR A 808 " --> pdb=" O GLN A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 845 Processing helix chain 'A' and resid 858 through 876 Processing helix chain 'A' and resid 878 through 881 Processing helix chain 'A' and resid 882 through 890 Processing helix chain 'A' and resid 893 through 906 removed outlier: 3.513A pdb=" N ILE A 897 " --> pdb=" O ASN A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 928 Processing helix chain 'A' and resid 935 through 943 Processing helix chain 'A' and resid 955 through 961 Processing helix chain 'A' and resid 962 through 965 Processing helix chain 'A' and resid 985 through 1001 Processing helix chain 'A' and resid 1003 through 1014 Processing helix chain 'A' and resid 1015 through 1020 removed outlier: 4.223A pdb=" N THR A1020 " --> pdb=" O LEU A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1034 Processing helix chain 'A' and resid 1052 through 1063 Processing helix chain 'A' and resid 1063 through 1078 removed outlier: 3.685A pdb=" N VAL A1067 " --> pdb=" O GLY A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1095 removed outlier: 3.703A pdb=" N CYS A1085 " --> pdb=" O ASN A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1113 Processing helix chain 'A' and resid 1116 through 1138 Processing helix chain 'A' and resid 1145 through 1173 Processing helix chain 'A' and resid 1194 through 1212 removed outlier: 3.769A pdb=" N GLN A1198 " --> pdb=" O ILE A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1218 removed outlier: 6.292A pdb=" N PHE A1216 " --> pdb=" O LEU A1213 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP A1218 " --> pdb=" O PRO A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1233 Processing helix chain 'A' and resid 1244 through 1258 removed outlier: 3.995A pdb=" N ASN A1252 " --> pdb=" O LEU A1248 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR A1253 " --> pdb=" O ALA A1249 " (cutoff:3.500A) Proline residue: A1255 - end of helix Processing helix chain 'A' and resid 1259 through 1277 Processing helix chain 'A' and resid 1285 through 1307 Processing helix chain 'A' and resid 1325 through 1339 Processing helix chain 'A' and resid 1343 through 1349 removed outlier: 3.504A pdb=" N GLU A1349 " --> pdb=" O SER A1345 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1352 No H-bonds generated for 'chain 'A' and resid 1350 through 1352' Processing helix chain 'A' and resid 1354 through 1375 Processing helix chain 'A' and resid 1381 through 1399 removed outlier: 3.597A pdb=" N LYS A1385 " --> pdb=" O GLN A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1423 Proline residue: A1421 - end of helix Processing helix chain 'A' and resid 1429 through 1439 Processing helix chain 'A' and resid 1453 through 1468 Processing helix chain 'A' and resid 1469 through 1472 Processing helix chain 'A' and resid 1487 through 1490 Processing helix chain 'A' and resid 1495 through 1501 Processing helix chain 'A' and resid 1510 through 1515 Processing helix chain 'A' and resid 1520 through 1527 removed outlier: 3.844A pdb=" N LEU A1526 " --> pdb=" O LYS A1522 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 400 Processing helix chain 'B' and resid 421 through 427 removed outlier: 3.781A pdb=" N HIS B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 434 Processing helix chain 'B' and resid 445 through 450 Processing helix chain 'B' and resid 453 through 458 Processing helix chain 'B' and resid 465 through 471 removed outlier: 4.256A pdb=" N TYR B 469 " --> pdb=" O PHE B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 483 Processing helix chain 'B' and resid 509 through 517 Processing helix chain 'B' and resid 517 through 529 Processing helix chain 'B' and resid 554 through 568 removed outlier: 3.606A pdb=" N GLU B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 600 through 603 Processing helix chain 'B' and resid 610 through 621 removed outlier: 3.685A pdb=" N LEU B 621 " --> pdb=" O THR B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 649 Processing helix chain 'B' and resid 664 through 669 removed outlier: 4.034A pdb=" N LYS B 669 " --> pdb=" O LEU B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 686 Processing helix chain 'B' and resid 690 through 699 removed outlier: 3.683A pdb=" N PHE B 694 " --> pdb=" O SER B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 722 removed outlier: 4.351A pdb=" N GLU B 712 " --> pdb=" O ARG B 708 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG B 713 " --> pdb=" O ASP B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 770 through 782 Processing helix chain 'B' and resid 805 through 822 Processing helix chain 'B' and resid 840 through 845 Processing helix chain 'B' and resid 861 through 873 Processing helix chain 'B' and resid 878 through 881 Processing helix chain 'B' and resid 882 through 890 Processing helix chain 'B' and resid 893 through 906 removed outlier: 4.397A pdb=" N ILE B 897 " --> pdb=" O ASN B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 928 removed outlier: 3.704A pdb=" N TYR B 927 " --> pdb=" O LEU B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 943 Processing helix chain 'B' and resid 956 through 961 Processing helix chain 'B' and resid 962 through 965 Processing helix chain 'B' and resid 985 through 1000 removed outlier: 3.546A pdb=" N LYS B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 998 " --> pdb=" O GLU B 994 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR B1000 " --> pdb=" O LEU B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1014 Processing helix chain 'B' and resid 1015 through 1019 Processing helix chain 'B' and resid 1023 through 1036 Processing helix chain 'B' and resid 1052 through 1063 Processing helix chain 'B' and resid 1063 through 1076 removed outlier: 3.942A pdb=" N VAL B1067 " --> pdb=" O GLY B1063 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS B1076 " --> pdb=" O LEU B1072 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1095 Processing helix chain 'B' and resid 1098 through 1113 removed outlier: 3.549A pdb=" N ALA B1102 " --> pdb=" O ASP B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1138 removed outlier: 3.812A pdb=" N SER B1120 " --> pdb=" O ASN B1116 " (cutoff:3.500A) Processing helix chain 'B' and resid 1147 through 1172 Processing helix chain 'B' and resid 1194 through 1213 Processing helix chain 'B' and resid 1221 through 1232 Processing helix chain 'B' and resid 1244 through 1278 removed outlier: 3.939A pdb=" N TYR B1253 " --> pdb=" O ALA B1249 " (cutoff:3.500A) Proline residue: B1255 - end of helix removed outlier: 4.929A pdb=" N LYS B1261 " --> pdb=" O LEU B1257 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE B1262 " --> pdb=" O THR B1258 " (cutoff:3.500A) Processing helix chain 'B' and resid 1286 through 1308 Processing helix chain 'B' and resid 1324 through 1339 Processing helix chain 'B' and resid 1343 through 1349 Processing helix chain 'B' and resid 1350 through 1353 Processing helix chain 'B' and resid 1354 through 1375 removed outlier: 4.847A pdb=" N SER B1360 " --> pdb=" O GLU B1356 " (cutoff:3.500A) Processing helix chain 'B' and resid 1381 through 1399 removed outlier: 3.755A pdb=" N LYS B1385 " --> pdb=" O GLN B1381 " (cutoff:3.500A) Processing helix chain 'B' and resid 1407 through 1420 Processing helix chain 'B' and resid 1429 through 1440 Processing helix chain 'B' and resid 1449 through 1451 No H-bonds generated for 'chain 'B' and resid 1449 through 1451' Processing helix chain 'B' and resid 1452 through 1461 Processing helix chain 'B' and resid 1495 through 1501 removed outlier: 3.601A pdb=" N CYS B1501 " --> pdb=" O LYS B1497 " (cutoff:3.500A) Processing helix chain 'B' and resid 1510 through 1514 Processing helix chain 'B' and resid 1516 through 1519 Processing helix chain 'B' and resid 1520 through 1527 Processing helix chain 'B' and resid 1557 through 1561 Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 464 removed outlier: 6.330A pdb=" N ASN A 462 " --> pdb=" O TRP A 491 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N PHE A 493 " --> pdb=" O ASN A 462 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N HIS A 464 " --> pdb=" O PHE A 493 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 490 " --> pdb=" O PHE A 437 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N TYR A 413 " --> pdb=" O PHE A 437 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 439 " --> pdb=" O TYR A 413 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 415 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLU A 441 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR A 417 " --> pdb=" O GLU A 441 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN A 412 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL A 542 " --> pdb=" O GLN A 412 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE A 414 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU A 544 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL A 416 " --> pdb=" O LEU A 544 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 631 through 632 Processing sheet with id=AA3, first strand: chain 'A' and resid 653 through 655 removed outlier: 4.299A pdb=" N CYS A 760 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG A 759 " --> pdb=" O LEU A 795 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU A 797 " --> pdb=" O ARG A 759 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA A 761 " --> pdb=" O LEU A 797 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N ASP A 799 " --> pdb=" O ALA A 761 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 794 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU A 833 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 796 " --> pdb=" O LEU A 833 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N CYS A 835 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A 798 " --> pdb=" O CYS A 835 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N ARG A 837 " --> pdb=" O VAL A 798 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS A 731 " --> pdb=" O ILE A 832 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASN A 834 " --> pdb=" O LYS A 731 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE A 733 " --> pdb=" O ASN A 834 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N MET A 836 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU A 735 " --> pdb=" O MET A 836 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 933 through 934 Processing sheet with id=AA5, first strand: chain 'A' and resid 1278 through 1280 Processing sheet with id=AA6, first strand: chain 'A' and resid 1492 through 1494 removed outlier: 3.513A pdb=" N PHE A1481 " --> pdb=" O PHE A1576 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU A1574 " --> pdb=" O LEU A1483 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1492 through 1494 removed outlier: 3.513A pdb=" N PHE A1481 " --> pdb=" O PHE A1576 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU A1574 " --> pdb=" O LEU A1483 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER A1571 " --> pdb=" O ILE A1586 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE A1586 " --> pdb=" O SER A1571 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR A1554 " --> pdb=" O ALA A1583 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N ASP A1585 " --> pdb=" O THR A1554 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 462 through 464 removed outlier: 6.463A pdb=" N ASN B 462 " --> pdb=" O TRP B 491 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N PHE B 493 " --> pdb=" O ASN B 462 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N HIS B 464 " --> pdb=" O PHE B 493 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR B 413 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N LEU B 440 " --> pdb=" O TYR B 413 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU B 415 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLN B 412 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL B 542 " --> pdb=" O GLN B 412 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE B 414 " --> pdb=" O VAL B 542 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 544 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL B 416 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU B 574 " --> pdb=" O PHE B 539 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL B 541 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ILE B 576 " --> pdb=" O VAL B 541 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHE B 543 " --> pdb=" O ILE B 576 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 653 through 654 removed outlier: 6.742A pdb=" N VAL B 794 " --> pdb=" O ILE B 831 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEU B 833 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B 796 " --> pdb=" O LEU B 833 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N CYS B 835 " --> pdb=" O LEU B 796 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL B 798 " --> pdb=" O CYS B 835 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N ARG B 837 " --> pdb=" O VAL B 798 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU B 735 " --> pdb=" O MET B 836 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N HIS B 734 " --> pdb=" O ILE B 851 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL B 853 " --> pdb=" O HIS B 734 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR B 736 " --> pdb=" O VAL B 853 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 933 through 934 removed outlier: 3.508A pdb=" N ILE B 933 " --> pdb=" O VAL B 981 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1492 through 1494 removed outlier: 3.846A pdb=" N PHE B1481 " --> pdb=" O PHE B1576 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU B1574 " --> pdb=" O LEU B1483 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LYS B1569 " --> pdb=" O ILE B1588 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE B1588 " --> pdb=" O LYS B1569 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER B1571 " --> pdb=" O ILE B1586 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE B1586 " --> pdb=" O SER B1571 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ALA B1583 " --> pdb=" O PRO B1552 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR B1554 " --> pdb=" O ALA B1583 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N ASP B1585 " --> pdb=" O THR B1554 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLU B1542 " --> pdb=" O GLN B1531 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N GLN B1531 " --> pdb=" O GLU B1542 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2793 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: 3.79 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5615 1.34 - 1.46: 2943 1.46 - 1.58: 9482 1.58 - 1.69: 9 1.69 - 1.81: 114 Bond restraints: 18163 Sorted by residual: bond pdb=" N GLY A1532 " pdb=" CA GLY A1532 " ideal model delta sigma weight residual 1.443 1.478 -0.035 8.60e-03 1.35e+04 1.66e+01 bond pdb=" N VAL B 460 " pdb=" CA VAL B 460 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.07e-02 8.73e+03 1.13e+01 bond pdb=" N ILE B 434 " pdb=" CA ILE B 434 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.19e-02 7.06e+03 1.09e+01 bond pdb=" CA SER A 490 " pdb=" CB SER A 490 " ideal model delta sigma weight residual 1.526 1.478 0.048 1.53e-02 4.27e+03 9.98e+00 bond pdb=" N ILE A 533 " pdb=" CA ILE A 533 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.49e+00 ... (remaining 18158 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 23677 1.70 - 3.40: 704 3.40 - 5.10: 74 5.10 - 6.80: 11 6.80 - 8.50: 5 Bond angle restraints: 24471 Sorted by residual: angle pdb=" N PHE A1017 " pdb=" CA PHE A1017 " pdb=" CB PHE A1017 " ideal model delta sigma weight residual 110.42 102.95 7.47 1.62e+00 3.81e-01 2.13e+01 angle pdb=" N VAL B 451 " pdb=" CA VAL B 451 " pdb=" C VAL B 451 " ideal model delta sigma weight residual 113.53 109.16 4.37 9.80e-01 1.04e+00 1.99e+01 angle pdb=" N ILE B1284 " pdb=" CA ILE B1284 " pdb=" C ILE B1284 " ideal model delta sigma weight residual 112.12 108.38 3.74 8.40e-01 1.42e+00 1.98e+01 angle pdb=" N GLU A 826 " pdb=" CA GLU A 826 " pdb=" C GLU A 826 " ideal model delta sigma weight residual 113.41 108.04 5.37 1.22e+00 6.72e-01 1.94e+01 angle pdb=" CA GLY B 496 " pdb=" C GLY B 496 " pdb=" O GLY B 496 " ideal model delta sigma weight residual 122.39 118.39 4.00 9.30e-01 1.16e+00 1.85e+01 ... (remaining 24466 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 9752 18.04 - 36.07: 970 36.07 - 54.11: 208 54.11 - 72.14: 94 72.14 - 90.18: 13 Dihedral angle restraints: 11037 sinusoidal: 4659 harmonic: 6378 Sorted by residual: dihedral pdb=" CA ARG A 515 " pdb=" C ARG A 515 " pdb=" N GLU A 516 " pdb=" CA GLU A 516 " ideal model delta harmonic sigma weight residual -180.00 -160.58 -19.42 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CB GLU A 866 " pdb=" CG GLU A 866 " pdb=" CD GLU A 866 " pdb=" OE1 GLU A 866 " ideal model delta sinusoidal sigma weight residual 0.00 -90.18 90.18 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU B 974 " pdb=" CG GLU B 974 " pdb=" CD GLU B 974 " pdb=" OE1 GLU B 974 " ideal model delta sinusoidal sigma weight residual 0.00 84.97 -84.97 1 3.00e+01 1.11e-03 9.73e+00 ... (remaining 11034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2615 0.111 - 0.222: 70 0.222 - 0.333: 2 0.333 - 0.444: 0 0.444 - 0.555: 1 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CG LEU B1036 " pdb=" CB LEU B1036 " pdb=" CD1 LEU B1036 " pdb=" CD2 LEU B1036 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.69e+00 chirality pdb=" C2' ATP A1602 " pdb=" C1' ATP A1602 " pdb=" C3' ATP A1602 " pdb=" O2' ATP A1602 " both_signs ideal model delta sigma weight residual False -2.68 -2.99 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C3' ATP A1602 " pdb=" C2' ATP A1602 " pdb=" C4' ATP A1602 " pdb=" O3' ATP A1602 " both_signs ideal model delta sigma weight residual False -2.63 -2.88 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 2685 not shown) Planarity restraints: 3076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1533 " -0.268 9.50e-02 1.11e+02 1.20e-01 8.87e+00 pdb=" NE ARG A1533 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A1533 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A1533 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A1533 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1014 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C GLU A1014 " 0.042 2.00e-02 2.50e+03 pdb=" O GLU A1014 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A1015 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 930 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C ASP A 930 " -0.030 2.00e-02 2.50e+03 pdb=" O ASP A 930 " 0.011 2.00e-02 2.50e+03 pdb=" N THR A 931 " 0.010 2.00e-02 2.50e+03 ... (remaining 3073 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 66 2.46 - 3.07: 12796 3.07 - 3.68: 25587 3.68 - 4.29: 39570 4.29 - 4.90: 66032 Nonbonded interactions: 144051 Sorted by model distance: nonbonded pdb=" OG1 THR B 744 " pdb="MG MG B1602 " model vdw 1.846 2.170 nonbonded pdb="MG MG A1601 " pdb=" O1G ATP A1602 " model vdw 1.984 2.170 nonbonded pdb=" N GLU B 826 " pdb=" OE1 GLU B 826 " model vdw 2.091 3.120 nonbonded pdb=" N GLU A 503 " pdb=" OE1 GLU A 503 " model vdw 2.104 3.120 nonbonded pdb=" N ASP A 805 " pdb=" OD1 ASP A 805 " model vdw 2.138 3.120 ... (remaining 144046 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 390 through 472 or resid 475 through 595 or resid 600 thro \ ugh 623 or resid 643 through 722 or resid 733 through 767 or resid 769 through 7 \ 82 or resid 793 through 855 or resid 860 through 874 or resid 877 through 945 or \ resid 955 through 1036 or resid 1050 through 1076 or resid 1084 through 1138 or \ resid 1146 through 1172 or resid 1191 through 1232 or resid 1242 through 1308 o \ r resid 1324 through 1441 or resid 1455 or resid 1458 or resid 1463 or resid 146 \ 7 or resid 1469 or resid 1479 through 1588)) selection = (chain 'B' and (resid 390 through 1308 or resid 1324 through 1442 or resid 1445 \ or resid 1450 or resid 1452 or resid 1454 or resid 1479 through 1540 or resid 15 \ 52 through 1561 or resid 1570 through 1588)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.890 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: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.380 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 0.048 18163 Z= 0.312 Angle : 0.649 8.495 24471 Z= 0.429 Chirality : 0.046 0.555 2688 Planarity : 0.004 0.120 3076 Dihedral : 15.816 90.176 6889 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 23.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.94 % Allowed : 14.89 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.18), residues: 2106 helix: 2.04 (0.15), residues: 1215 sheet: -0.87 (0.36), residues: 181 loop : -0.34 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1562 TYR 0.027 0.002 TYR B1093 PHE 0.016 0.002 PHE A 758 TRP 0.012 0.001 TRP A1134 HIS 0.005 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00542 (18163) covalent geometry : angle 0.64904 (24471) hydrogen bonds : bond 0.15232 ( 956) hydrogen bonds : angle 6.11852 ( 2793) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 222 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 838 SER cc_start: 0.8982 (t) cc_final: 0.8778 (p) REVERT: A 888 MET cc_start: 0.9029 (mmm) cc_final: 0.8407 (mmm) REVERT: A 911 PHE cc_start: 0.8832 (m-80) cc_final: 0.8557 (m-10) REVERT: A 974 GLU cc_start: 0.8461 (pp20) cc_final: 0.7944 (pp20) REVERT: A 1254 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7685 (mt) REVERT: A 1483 LEU cc_start: 0.7905 (tp) cc_final: 0.7661 (tp) REVERT: A 1531 GLN cc_start: 0.7710 (mp10) cc_final: 0.7450 (mp10) REVERT: B 714 LEU cc_start: 0.8577 (tp) cc_final: 0.8306 (tp) REVERT: B 719 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7677 (tp40) REVERT: B 838 SER cc_start: 0.7723 (t) cc_final: 0.7146 (p) REVERT: B 908 GLN cc_start: 0.4000 (mm-40) cc_final: 0.3751 (mm-40) REVERT: B 960 MET cc_start: 0.7352 (mmm) cc_final: 0.6739 (mmm) REVERT: B 1030 ASP cc_start: 0.7976 (m-30) cc_final: 0.7738 (m-30) REVERT: B 1031 MET cc_start: 0.8331 (mmm) cc_final: 0.7565 (tmm) REVERT: B 1051 PHE cc_start: 0.7786 (m-80) cc_final: 0.7397 (m-80) REVERT: B 1202 GLU cc_start: 0.7659 (tp30) cc_final: 0.7418 (mm-30) REVERT: B 1254 ILE cc_start: 0.5656 (OUTLIER) cc_final: 0.5274 (mm) REVERT: B 1294 ARG cc_start: 0.7986 (mtm180) cc_final: 0.7427 (mtm180) outliers start: 58 outliers final: 41 residues processed: 261 average time/residue: 0.1497 time to fit residues: 58.6702 Evaluate side-chains 236 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 992 SER Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1074 SER Chi-restraints excluded: chain A residue 1138 ASN Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1147 ASP Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1405 VAL Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 584 GLN Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 719 GLN Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 836 MET Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 984 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1072 LEU Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1254 ILE Chi-restraints excluded: chain B residue 1258 THR Chi-restraints excluded: chain B residue 1306 ILE Chi-restraints excluded: chain B residue 1357 ASP Chi-restraints excluded: chain B residue 1420 GLN Chi-restraints excluded: chain B residue 1517 VAL Chi-restraints excluded: chain B residue 1578 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 chunk 77 optimal weight: 0.0670 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN A 804 GLN A1536 ASN B 427 HIS B 925 ASN B1252 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.149415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.105249 restraints weight = 28357.736| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.85 r_work: 0.3201 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18163 Z= 0.126 Angle : 0.518 10.382 24471 Z= 0.270 Chirality : 0.041 0.161 2688 Planarity : 0.003 0.037 3076 Dihedral : 7.944 88.009 2457 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.63 % Allowed : 12.97 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.18), residues: 2106 helix: 2.27 (0.15), residues: 1252 sheet: -0.23 (0.38), residues: 170 loop : -0.16 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 630 TYR 0.019 0.001 TYR A1093 PHE 0.014 0.001 PHE A 675 TRP 0.011 0.001 TRP B1440 HIS 0.005 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00280 (18163) covalent geometry : angle 0.51776 (24471) hydrogen bonds : bond 0.04438 ( 956) hydrogen bonds : angle 4.53177 ( 2793) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 229 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 671 LYS cc_start: 0.8881 (mttt) cc_final: 0.8566 (mttp) REVERT: A 751 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8982 (mp) REVERT: A 1121 ASP cc_start: 0.8426 (m-30) cc_final: 0.7778 (m-30) REVERT: A 1430 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7388 (mt-10) REVERT: A 1469 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7753 (ptmt) REVERT: B 538 LYS cc_start: 0.8276 (mmtt) cc_final: 0.8020 (mmpt) REVERT: B 838 SER cc_start: 0.7630 (t) cc_final: 0.7126 (p) REVERT: B 908 GLN cc_start: 0.3802 (mm-40) cc_final: 0.3499 (mm-40) REVERT: B 960 MET cc_start: 0.7707 (mmm) cc_final: 0.7101 (mmm) REVERT: B 1030 ASP cc_start: 0.8094 (m-30) cc_final: 0.7787 (m-30) REVERT: B 1031 MET cc_start: 0.8451 (mmm) cc_final: 0.7513 (tmm) REVERT: B 1105 TRP cc_start: 0.7003 (m100) cc_final: 0.5997 (m100) REVERT: B 1202 GLU cc_start: 0.7828 (tp30) cc_final: 0.7500 (mm-30) REVERT: B 1278 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7139 (tp) REVERT: B 1294 ARG cc_start: 0.7989 (mtm180) cc_final: 0.7393 (mtm180) REVERT: B 1399 GLN cc_start: 0.8631 (tt0) cc_final: 0.8341 (tt0) outliers start: 52 outliers final: 25 residues processed: 271 average time/residue: 0.1518 time to fit residues: 62.1212 Evaluate side-chains 210 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1282 ASN Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain A residue 1401 THR Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1469 LYS Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 931 THR Chi-restraints excluded: chain B residue 958 ASP Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 985 HIS Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1157 GLU Chi-restraints excluded: chain B residue 1278 LEU Chi-restraints excluded: chain B residue 1344 PHE Chi-restraints excluded: chain B residue 1408 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 153 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN A 804 GLN A 891 ASN ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.146015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.101950 restraints weight = 28524.849| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.63 r_work: 0.3163 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18163 Z= 0.194 Angle : 0.551 10.685 24471 Z= 0.287 Chirality : 0.043 0.189 2688 Planarity : 0.004 0.041 3076 Dihedral : 7.246 88.964 2389 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.84 % Allowed : 14.89 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.18), residues: 2106 helix: 1.99 (0.14), residues: 1253 sheet: -0.21 (0.37), residues: 178 loop : -0.15 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1562 TYR 0.026 0.002 TYR A1093 PHE 0.024 0.002 PHE A1344 TRP 0.010 0.001 TRP A1512 HIS 0.009 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00466 (18163) covalent geometry : angle 0.55069 (24471) hydrogen bonds : bond 0.04990 ( 956) hydrogen bonds : angle 4.52524 ( 2793) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 196 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 671 LYS cc_start: 0.9016 (mttt) cc_final: 0.8709 (mttp) REVERT: A 751 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9144 (mp) REVERT: A 911 PHE cc_start: 0.8781 (m-80) cc_final: 0.8533 (m-10) REVERT: A 954 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6452 (mt-10) REVERT: A 1469 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8010 (ptmt) REVERT: B 455 TYR cc_start: 0.7990 (t80) cc_final: 0.7735 (t80) REVERT: B 538 LYS cc_start: 0.8392 (mmtt) cc_final: 0.8164 (mmpt) REVERT: B 712 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7619 (tt0) REVERT: B 838 SER cc_start: 0.7817 (t) cc_final: 0.7363 (p) REVERT: B 908 GLN cc_start: 0.3917 (mm-40) cc_final: 0.3619 (mm-40) REVERT: B 960 MET cc_start: 0.7589 (mmm) cc_final: 0.7300 (mmm) REVERT: B 1030 ASP cc_start: 0.8114 (m-30) cc_final: 0.7858 (m-30) REVERT: B 1105 TRP cc_start: 0.7077 (m100) cc_final: 0.6175 (m100) REVERT: B 1202 GLU cc_start: 0.7826 (tp30) cc_final: 0.7605 (mm-30) REVERT: B 1278 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7346 (tp) REVERT: B 1294 ARG cc_start: 0.8112 (mtm180) cc_final: 0.7488 (mtm180) outliers start: 56 outliers final: 36 residues processed: 241 average time/residue: 0.1377 time to fit residues: 50.6770 Evaluate side-chains 217 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1282 ASN Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain A residue 1401 THR Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1469 LYS Chi-restraints excluded: chain A residue 1511 LEU Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 620 LYS Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 802 GLU Chi-restraints excluded: chain B residue 836 MET Chi-restraints excluded: chain B residue 931 THR Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 958 ASP Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1084 ILE Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1278 LEU Chi-restraints excluded: chain B residue 1344 PHE Chi-restraints excluded: chain B residue 1357 ASP Chi-restraints excluded: chain B residue 1408 VAL Chi-restraints excluded: chain B residue 1578 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 64 optimal weight: 2.9990 chunk 29 optimal weight: 0.0770 chunk 25 optimal weight: 5.9990 chunk 189 optimal weight: 20.0000 chunk 150 optimal weight: 0.0670 chunk 143 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A1198 GLN B 581 HIS B 985 HIS B1059 HIS ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 ASN ** B1399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.145756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.101483 restraints weight = 28570.050| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.83 r_work: 0.3145 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18163 Z= 0.190 Angle : 0.534 10.530 24471 Z= 0.277 Chirality : 0.042 0.140 2688 Planarity : 0.004 0.041 3076 Dihedral : 7.129 84.169 2389 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.39 % Allowed : 15.50 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.18), residues: 2106 helix: 1.95 (0.15), residues: 1249 sheet: -0.19 (0.37), residues: 178 loop : -0.19 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1488 TYR 0.025 0.002 TYR A1093 PHE 0.022 0.002 PHE A1344 TRP 0.011 0.001 TRP B 586 HIS 0.006 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00458 (18163) covalent geometry : angle 0.53432 (24471) hydrogen bonds : bond 0.04704 ( 956) hydrogen bonds : angle 4.42738 ( 2793) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 198 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 671 LYS cc_start: 0.8915 (mttt) cc_final: 0.8683 (mptt) REVERT: A 751 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9099 (mp) REVERT: A 954 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6384 (mt-10) REVERT: A 1388 PHE cc_start: 0.8787 (t80) cc_final: 0.8469 (t80) REVERT: A 1469 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7923 (ptmt) REVERT: B 455 TYR cc_start: 0.7929 (t80) cc_final: 0.7674 (t80) REVERT: B 538 LYS cc_start: 0.8411 (mmtt) cc_final: 0.8194 (mmpt) REVERT: B 620 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6824 (mtmm) REVERT: B 712 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7588 (tt0) REVERT: B 838 SER cc_start: 0.7772 (t) cc_final: 0.7281 (p) REVERT: B 866 GLU cc_start: 0.6088 (mm-30) cc_final: 0.5806 (mm-30) REVERT: B 908 GLN cc_start: 0.4115 (mm-40) cc_final: 0.3842 (mm-40) REVERT: B 960 MET cc_start: 0.7586 (mmm) cc_final: 0.7259 (mmm) REVERT: B 1030 ASP cc_start: 0.8088 (m-30) cc_final: 0.7795 (m-30) REVERT: B 1105 TRP cc_start: 0.7033 (m100) cc_final: 0.6089 (m100) REVERT: B 1202 GLU cc_start: 0.7797 (tp30) cc_final: 0.7465 (mm-30) REVERT: B 1278 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7366 (tp) REVERT: B 1294 ARG cc_start: 0.8073 (mtm180) cc_final: 0.7406 (mtm180) REVERT: B 1432 TYR cc_start: 0.7840 (m-80) cc_final: 0.7321 (m-80) outliers start: 67 outliers final: 43 residues processed: 247 average time/residue: 0.1399 time to fit residues: 52.3072 Evaluate side-chains 233 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 185 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1282 ASN Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1329 VAL Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain A residue 1401 THR Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1469 LYS Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 620 LYS Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 836 MET Chi-restraints excluded: chain B residue 872 ILE Chi-restraints excluded: chain B residue 906 LYS Chi-restraints excluded: chain B residue 931 THR Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 985 HIS Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1084 ILE Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1135 ILE Chi-restraints excluded: chain B residue 1157 GLU Chi-restraints excluded: chain B residue 1278 LEU Chi-restraints excluded: chain B residue 1344 PHE Chi-restraints excluded: chain B residue 1357 ASP Chi-restraints excluded: chain B residue 1408 VAL Chi-restraints excluded: chain B residue 1489 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 110 optimal weight: 7.9990 chunk 214 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 GLN A 804 GLN A 891 ASN B 899 ASN B 985 HIS B1086 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.147319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.103337 restraints weight = 28339.221| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.71 r_work: 0.3192 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18163 Z= 0.122 Angle : 0.485 10.119 24471 Z= 0.251 Chirality : 0.040 0.145 2688 Planarity : 0.003 0.039 3076 Dihedral : 6.720 82.911 2388 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.84 % Allowed : 15.91 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.18), residues: 2106 helix: 2.16 (0.15), residues: 1248 sheet: -0.23 (0.37), residues: 184 loop : -0.16 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1488 TYR 0.019 0.001 TYR A1093 PHE 0.023 0.001 PHE B 956 TRP 0.011 0.001 TRP B 586 HIS 0.009 0.001 HIS B 985 Details of bonding type rmsd covalent geometry : bond 0.00277 (18163) covalent geometry : angle 0.48530 (24471) hydrogen bonds : bond 0.03973 ( 956) hydrogen bonds : angle 4.20347 ( 2793) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 207 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 671 LYS cc_start: 0.8887 (mttt) cc_final: 0.8668 (mptt) REVERT: A 751 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8997 (mp) REVERT: A 954 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6344 (mt-10) REVERT: A 1121 ASP cc_start: 0.8416 (m-30) cc_final: 0.7769 (m-30) REVERT: A 1388 PHE cc_start: 0.8741 (t80) cc_final: 0.8446 (t80) REVERT: A 1427 GLN cc_start: 0.7143 (pt0) cc_final: 0.6878 (mp10) REVERT: A 1469 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7829 (ptmt) REVERT: B 455 TYR cc_start: 0.7924 (t80) cc_final: 0.7603 (t80) REVERT: B 478 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8449 (mp0) REVERT: B 712 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7596 (tt0) REVERT: B 838 SER cc_start: 0.7748 (t) cc_final: 0.7277 (p) REVERT: B 866 GLU cc_start: 0.6223 (mm-30) cc_final: 0.5805 (mm-30) REVERT: B 908 GLN cc_start: 0.4084 (mm-40) cc_final: 0.3809 (mm-40) REVERT: B 960 MET cc_start: 0.7571 (mmm) cc_final: 0.7300 (mmm) REVERT: B 1030 ASP cc_start: 0.8076 (m-30) cc_final: 0.7781 (m-30) REVERT: B 1105 TRP cc_start: 0.6933 (m100) cc_final: 0.6009 (m100) REVERT: B 1202 GLU cc_start: 0.7830 (tp30) cc_final: 0.7438 (mm-30) REVERT: B 1278 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7393 (tp) REVERT: B 1294 ARG cc_start: 0.8032 (mtm180) cc_final: 0.7384 (mtm180) outliers start: 56 outliers final: 38 residues processed: 247 average time/residue: 0.1390 time to fit residues: 51.8044 Evaluate side-chains 228 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 891 ASN Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1282 ASN Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain A residue 1401 THR Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1469 LYS Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 872 ILE Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 906 LYS Chi-restraints excluded: chain B residue 931 THR Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 944 ILE Chi-restraints excluded: chain B residue 985 HIS Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1084 ILE Chi-restraints excluded: chain B residue 1135 ILE Chi-restraints excluded: chain B residue 1157 GLU Chi-restraints excluded: chain B residue 1214 ILE Chi-restraints excluded: chain B residue 1278 LEU Chi-restraints excluded: chain B residue 1344 PHE Chi-restraints excluded: chain B residue 1357 ASP Chi-restraints excluded: chain B residue 1408 VAL Chi-restraints excluded: chain B residue 1489 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 172 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 83 optimal weight: 0.0670 chunk 94 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 159 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 891 ASN B 447 ASN B 985 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.148813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.105550 restraints weight = 28232.542| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.60 r_work: 0.3222 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 18163 Z= 0.099 Angle : 0.467 9.845 24471 Z= 0.240 Chirality : 0.039 0.139 2688 Planarity : 0.003 0.038 3076 Dihedral : 6.406 82.285 2387 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.68 % Allowed : 16.46 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.19), residues: 2106 helix: 2.28 (0.15), residues: 1250 sheet: 0.13 (0.38), residues: 178 loop : -0.08 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 459 TYR 0.017 0.001 TYR A1093 PHE 0.019 0.001 PHE A1371 TRP 0.010 0.001 TRP B 586 HIS 0.009 0.001 HIS B 985 Details of bonding type rmsd covalent geometry : bond 0.00217 (18163) covalent geometry : angle 0.46669 (24471) hydrogen bonds : bond 0.03566 ( 956) hydrogen bonds : angle 4.05551 ( 2793) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 208 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 671 LYS cc_start: 0.8971 (mttt) cc_final: 0.8722 (mptt) REVERT: A 751 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9017 (mp) REVERT: A 1073 GLU cc_start: 0.8715 (tp30) cc_final: 0.8352 (mm-30) REVERT: A 1121 ASP cc_start: 0.8677 (m-30) cc_final: 0.8075 (m-30) REVERT: A 1427 GLN cc_start: 0.7208 (pt0) cc_final: 0.6893 (mp10) REVERT: A 1469 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7807 (ptmt) REVERT: B 478 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8482 (mp0) REVERT: B 649 MET cc_start: 0.5629 (mmp) cc_final: 0.5280 (mmp) REVERT: B 712 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7631 (tt0) REVERT: B 838 SER cc_start: 0.7871 (t) cc_final: 0.7438 (p) REVERT: B 866 GLU cc_start: 0.6236 (mm-30) cc_final: 0.5801 (mm-30) REVERT: B 908 GLN cc_start: 0.3915 (mm-40) cc_final: 0.3629 (mm-40) REVERT: B 960 MET cc_start: 0.7486 (mmm) cc_final: 0.6852 (mmm) REVERT: B 1030 ASP cc_start: 0.8134 (m-30) cc_final: 0.7833 (m-30) REVERT: B 1105 TRP cc_start: 0.6867 (m100) cc_final: 0.5965 (m100) REVERT: B 1202 GLU cc_start: 0.7883 (tp30) cc_final: 0.7462 (mm-30) REVERT: B 1278 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7405 (tp) outliers start: 53 outliers final: 32 residues processed: 246 average time/residue: 0.1488 time to fit residues: 55.7626 Evaluate side-chains 226 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 891 ASN Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1282 ASN Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain A residue 1401 THR Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1469 LYS Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 872 ILE Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 931 THR Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 944 ILE Chi-restraints excluded: chain B residue 985 HIS Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1157 GLU Chi-restraints excluded: chain B residue 1214 ILE Chi-restraints excluded: chain B residue 1278 LEU Chi-restraints excluded: chain B residue 1408 VAL Chi-restraints excluded: chain B residue 1578 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 3 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 45 optimal weight: 0.0050 chunk 34 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 183 optimal weight: 0.0980 chunk 176 optimal weight: 10.0000 chunk 195 optimal weight: 3.9990 overall best weight: 1.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 891 ASN B 447 ASN ** B 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN B 985 HIS ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.147137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.103852 restraints weight = 28445.486| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.66 r_work: 0.3193 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18163 Z= 0.137 Angle : 0.492 9.421 24471 Z= 0.253 Chirality : 0.040 0.165 2688 Planarity : 0.003 0.039 3076 Dihedral : 6.387 82.652 2383 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.68 % Allowed : 16.41 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.18), residues: 2106 helix: 2.25 (0.15), residues: 1249 sheet: 0.20 (0.38), residues: 179 loop : -0.10 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 459 TYR 0.022 0.001 TYR A1093 PHE 0.033 0.001 PHE B 956 TRP 0.012 0.001 TRP A1518 HIS 0.009 0.001 HIS B 985 Details of bonding type rmsd covalent geometry : bond 0.00322 (18163) covalent geometry : angle 0.49193 (24471) hydrogen bonds : bond 0.03954 ( 956) hydrogen bonds : angle 4.13621 ( 2793) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 198 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 751 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9005 (mp) REVERT: A 911 PHE cc_start: 0.8568 (m-80) cc_final: 0.8166 (m-10) REVERT: A 954 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6135 (mt-10) REVERT: A 1121 ASP cc_start: 0.8428 (m-30) cc_final: 0.7809 (m-30) REVERT: A 1260 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8023 (mp) REVERT: A 1426 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.6723 (t80) REVERT: A 1427 GLN cc_start: 0.7171 (pt0) cc_final: 0.6883 (mp10) REVERT: A 1469 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7858 (ptmt) REVERT: B 478 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8463 (mp0) REVERT: B 649 MET cc_start: 0.5662 (mmp) cc_final: 0.5287 (mmp) REVERT: B 712 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7625 (tt0) REVERT: B 798 VAL cc_start: 0.8075 (OUTLIER) cc_final: 0.7807 (p) REVERT: B 838 SER cc_start: 0.7791 (t) cc_final: 0.7331 (p) REVERT: B 866 GLU cc_start: 0.6272 (mm-30) cc_final: 0.5825 (mm-30) REVERT: B 880 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6272 (pp20) REVERT: B 908 GLN cc_start: 0.4072 (mm-40) cc_final: 0.3799 (mm-40) REVERT: B 960 MET cc_start: 0.7657 (mmm) cc_final: 0.7178 (mmm) REVERT: B 1030 ASP cc_start: 0.8082 (m-30) cc_final: 0.7778 (m-30) REVERT: B 1105 TRP cc_start: 0.6848 (m100) cc_final: 0.5967 (m100) REVERT: B 1202 GLU cc_start: 0.7860 (tp30) cc_final: 0.7414 (mm-30) REVERT: B 1294 ARG cc_start: 0.8011 (mtm180) cc_final: 0.7328 (mtm180) outliers start: 53 outliers final: 38 residues processed: 238 average time/residue: 0.1390 time to fit residues: 51.0458 Evaluate side-chains 234 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 891 ASN Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1282 ASN Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain A residue 1401 THR Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1469 LYS Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 872 ILE Chi-restraints excluded: chain B residue 880 GLU Chi-restraints excluded: chain B residue 906 LYS Chi-restraints excluded: chain B residue 931 THR Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 944 ILE Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 985 HIS Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1157 GLU Chi-restraints excluded: chain B residue 1214 ILE Chi-restraints excluded: chain B residue 1408 VAL Chi-restraints excluded: chain B residue 1489 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 185 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 194 optimal weight: 0.0970 chunk 79 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 208 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 891 ASN B 447 ASN ** B 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN B 985 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.148812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.105128 restraints weight = 28268.079| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.54 r_work: 0.3225 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18163 Z= 0.099 Angle : 0.471 10.855 24471 Z= 0.241 Chirality : 0.039 0.152 2688 Planarity : 0.003 0.038 3076 Dihedral : 6.204 82.498 2383 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.33 % Allowed : 16.97 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.18), residues: 2106 helix: 2.32 (0.15), residues: 1249 sheet: 0.28 (0.38), residues: 179 loop : -0.06 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 459 TYR 0.017 0.001 TYR A1093 PHE 0.019 0.001 PHE A1371 TRP 0.011 0.001 TRP A1518 HIS 0.005 0.001 HIS B 985 Details of bonding type rmsd covalent geometry : bond 0.00216 (18163) covalent geometry : angle 0.47117 (24471) hydrogen bonds : bond 0.03524 ( 956) hydrogen bonds : angle 4.01525 ( 2793) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 751 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9028 (mp) REVERT: A 911 PHE cc_start: 0.8632 (m-80) cc_final: 0.8239 (m-10) REVERT: A 1073 GLU cc_start: 0.8722 (tp30) cc_final: 0.8353 (mm-30) REVERT: A 1121 ASP cc_start: 0.8676 (m-30) cc_final: 0.8076 (m-30) REVERT: A 1426 TYR cc_start: 0.7070 (OUTLIER) cc_final: 0.6637 (t80) REVERT: A 1427 GLN cc_start: 0.7222 (pt0) cc_final: 0.6862 (mp10) REVERT: A 1469 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7761 (ptmt) REVERT: B 478 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8474 (mp0) REVERT: B 649 MET cc_start: 0.5673 (mmp) cc_final: 0.5332 (mmp) REVERT: B 712 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7654 (tt0) REVERT: B 798 VAL cc_start: 0.8016 (OUTLIER) cc_final: 0.7803 (p) REVERT: B 838 SER cc_start: 0.7895 (t) cc_final: 0.7438 (p) REVERT: B 866 GLU cc_start: 0.6274 (mm-30) cc_final: 0.5823 (mm-30) REVERT: B 908 GLN cc_start: 0.3896 (mm-40) cc_final: 0.3611 (mm-40) REVERT: B 960 MET cc_start: 0.7586 (mmm) cc_final: 0.6723 (mmm) REVERT: B 1019 ASP cc_start: 0.7621 (m-30) cc_final: 0.7412 (m-30) REVERT: B 1030 ASP cc_start: 0.8129 (m-30) cc_final: 0.7819 (m-30) REVERT: B 1051 PHE cc_start: 0.7577 (m-80) cc_final: 0.7202 (m-80) REVERT: B 1105 TRP cc_start: 0.6825 (m100) cc_final: 0.5950 (m100) REVERT: B 1202 GLU cc_start: 0.7876 (tp30) cc_final: 0.7430 (mm-30) REVERT: B 1294 ARG cc_start: 0.8048 (mtm180) cc_final: 0.7503 (mtm180) outliers start: 46 outliers final: 32 residues processed: 238 average time/residue: 0.1333 time to fit residues: 49.0381 Evaluate side-chains 228 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1282 ASN Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1469 LYS Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 872 ILE Chi-restraints excluded: chain B residue 931 THR Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 944 ILE Chi-restraints excluded: chain B residue 985 HIS Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1157 GLU Chi-restraints excluded: chain B residue 1214 ILE Chi-restraints excluded: chain B residue 1408 VAL Chi-restraints excluded: chain B residue 1489 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 141 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 chunk 12 optimal weight: 0.0670 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN B 985 HIS ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.147375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.103950 restraints weight = 28199.762| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.59 r_work: 0.3200 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18163 Z= 0.134 Angle : 0.495 10.127 24471 Z= 0.254 Chirality : 0.040 0.142 2688 Planarity : 0.003 0.038 3076 Dihedral : 6.270 82.571 2383 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.23 % Allowed : 17.33 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.18), residues: 2106 helix: 2.27 (0.15), residues: 1250 sheet: 0.34 (0.38), residues: 179 loop : -0.08 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 459 TYR 0.022 0.001 TYR A1432 PHE 0.030 0.001 PHE B 956 TRP 0.009 0.001 TRP A1518 HIS 0.008 0.001 HIS B 985 Details of bonding type rmsd covalent geometry : bond 0.00313 (18163) covalent geometry : angle 0.49473 (24471) hydrogen bonds : bond 0.03866 ( 956) hydrogen bonds : angle 4.08012 ( 2793) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 751 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9030 (mp) REVERT: A 911 PHE cc_start: 0.8634 (m-80) cc_final: 0.8255 (m-10) REVERT: A 1073 GLU cc_start: 0.8761 (tp30) cc_final: 0.8412 (mm-30) REVERT: A 1121 ASP cc_start: 0.8697 (m-30) cc_final: 0.8093 (m-30) REVERT: A 1426 TYR cc_start: 0.7068 (OUTLIER) cc_final: 0.6614 (t80) REVERT: A 1427 GLN cc_start: 0.7223 (pt0) cc_final: 0.6866 (mp10) REVERT: A 1469 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7885 (ptmt) REVERT: B 478 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8475 (mp0) REVERT: B 649 MET cc_start: 0.5679 (mmp) cc_final: 0.5313 (mmp) REVERT: B 712 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7681 (tt0) REVERT: B 838 SER cc_start: 0.7933 (t) cc_final: 0.7463 (p) REVERT: B 866 GLU cc_start: 0.6278 (mm-30) cc_final: 0.5837 (mm-30) REVERT: B 880 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6336 (pp20) REVERT: B 908 GLN cc_start: 0.3920 (mm-40) cc_final: 0.3638 (mm-40) REVERT: B 960 MET cc_start: 0.7684 (mmm) cc_final: 0.7120 (mmm) REVERT: B 1030 ASP cc_start: 0.8116 (m-30) cc_final: 0.7819 (m-30) REVERT: B 1051 PHE cc_start: 0.7626 (m-80) cc_final: 0.7264 (m-80) REVERT: B 1105 TRP cc_start: 0.6827 (m100) cc_final: 0.5952 (m100) REVERT: B 1202 GLU cc_start: 0.7892 (tp30) cc_final: 0.7429 (mm-30) outliers start: 44 outliers final: 34 residues processed: 230 average time/residue: 0.1336 time to fit residues: 47.1062 Evaluate side-chains 229 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1282 ASN Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1469 LYS Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 872 ILE Chi-restraints excluded: chain B residue 880 GLU Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 931 THR Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 944 ILE Chi-restraints excluded: chain B residue 985 HIS Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1157 GLU Chi-restraints excluded: chain B residue 1214 ILE Chi-restraints excluded: chain B residue 1408 VAL Chi-restraints excluded: chain B residue 1489 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 84 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 122 optimal weight: 0.0770 chunk 213 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 181 optimal weight: 0.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 891 ASN B 447 ASN B 834 ASN ** B 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN B 985 HIS B1086 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.147514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.103926 restraints weight = 28162.224| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.78 r_work: 0.3191 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18163 Z= 0.125 Angle : 0.494 9.939 24471 Z= 0.253 Chirality : 0.039 0.138 2688 Planarity : 0.003 0.038 3076 Dihedral : 6.246 82.455 2383 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.33 % Allowed : 16.92 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.18), residues: 2106 helix: 2.27 (0.15), residues: 1250 sheet: 0.40 (0.38), residues: 179 loop : -0.07 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1188 TYR 0.020 0.001 TYR A1093 PHE 0.020 0.001 PHE A1388 TRP 0.009 0.001 TRP B 586 HIS 0.009 0.001 HIS B 985 Details of bonding type rmsd covalent geometry : bond 0.00289 (18163) covalent geometry : angle 0.49365 (24471) hydrogen bonds : bond 0.03791 ( 956) hydrogen bonds : angle 4.06964 ( 2793) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 751 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8989 (mp) REVERT: A 911 PHE cc_start: 0.8551 (m-80) cc_final: 0.8190 (m-10) REVERT: A 954 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6078 (mt-10) REVERT: A 1073 GLU cc_start: 0.8615 (tp30) cc_final: 0.8239 (mm-30) REVERT: A 1121 ASP cc_start: 0.8435 (m-30) cc_final: 0.7803 (m-30) REVERT: A 1426 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.6551 (t80) REVERT: A 1427 GLN cc_start: 0.7198 (pt0) cc_final: 0.6820 (mp10) REVERT: A 1469 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7834 (ptmt) REVERT: B 478 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8454 (mp0) REVERT: B 649 MET cc_start: 0.5694 (mmp) cc_final: 0.5337 (mmp) REVERT: B 712 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7664 (tt0) REVERT: B 838 SER cc_start: 0.7863 (t) cc_final: 0.7384 (p) REVERT: B 880 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.6320 (pp20) REVERT: B 908 GLN cc_start: 0.4045 (mm-40) cc_final: 0.3770 (mm-40) REVERT: B 960 MET cc_start: 0.7700 (mmm) cc_final: 0.6881 (mmm) REVERT: B 1030 ASP cc_start: 0.8063 (m-30) cc_final: 0.7767 (m-30) REVERT: B 1051 PHE cc_start: 0.7580 (m-80) cc_final: 0.7187 (m-80) REVERT: B 1105 TRP cc_start: 0.6779 (m100) cc_final: 0.5923 (m100) REVERT: B 1202 GLU cc_start: 0.7861 (tp30) cc_final: 0.7392 (mm-30) REVERT: B 1256 TYR cc_start: 0.6327 (t80) cc_final: 0.5671 (t80) REVERT: B 1294 ARG cc_start: 0.7835 (mtm180) cc_final: 0.7299 (mtm180) outliers start: 46 outliers final: 36 residues processed: 234 average time/residue: 0.1304 time to fit residues: 46.9230 Evaluate side-chains 232 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 891 ASN Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1282 ASN Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1469 LYS Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 872 ILE Chi-restraints excluded: chain B residue 880 GLU Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 906 LYS Chi-restraints excluded: chain B residue 931 THR Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 944 ILE Chi-restraints excluded: chain B residue 985 HIS Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1084 ILE Chi-restraints excluded: chain B residue 1157 GLU Chi-restraints excluded: chain B residue 1214 ILE Chi-restraints excluded: chain B residue 1408 VAL Chi-restraints excluded: chain B residue 1489 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 152 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 0.0370 chunk 154 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 167 optimal weight: 8.9990 chunk 172 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 overall best weight: 1.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN ** B 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.147532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.104168 restraints weight = 28367.898| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.66 r_work: 0.3199 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 18163 Z= 0.171 Angle : 0.863 59.123 24471 Z= 0.524 Chirality : 0.040 0.319 2688 Planarity : 0.004 0.081 3076 Dihedral : 6.284 82.455 2383 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.23 % Allowed : 16.87 % Favored : 80.90 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.18), residues: 2106 helix: 2.27 (0.15), residues: 1250 sheet: 0.40 (0.38), residues: 179 loop : -0.08 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1188 TYR 0.020 0.001 TYR A1093 PHE 0.020 0.001 PHE A1388 TRP 0.009 0.001 TRP B 586 HIS 0.121 0.002 HIS B 985 Details of bonding type rmsd covalent geometry : bond 0.00347 (18163) covalent geometry : angle 0.86270 (24471) hydrogen bonds : bond 0.03793 ( 956) hydrogen bonds : angle 4.07577 ( 2793) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5434.03 seconds wall clock time: 93 minutes 37.59 seconds (5617.59 seconds total)