Starting phenix.real_space_refine on Tue Sep 15 04:45:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6drj_7999/09_2026/6drj_7999.cif Found real_map, /net/cci-nas-00/data/ceres_data/6drj_7999/09_2026/6drj_7999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6drj_7999/09_2026/6drj_7999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6drj_7999/09_2026/6drj_7999.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6drj_7999/09_2026/6drj_7999.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6drj_7999/09_2026/6drj_7999.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6drj_7999/09_2026/6drj_7999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6drj_7999/09_2026/6drj_7999.map" } resolution = 3.3 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= 0.031 sd= 0.778 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 Ca 4 9.91 5 P 8 5.49 5 S 148 5.16 5 C 22956 2.51 5 N 6328 2.21 5 O 6072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.15s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35516 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1266, 8842 Classifications: {'peptide': 1266} Incomplete info: {'truncation_to_alanine': 410} Link IDs: {'PTRANS': 51, 'TRANS': 1214} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1434 Unresolved non-hydrogen angles: 1799 Unresolved non-hydrogen dihedrals: 1150 Unresolved non-hydrogen chiralities: 102 Planarities with less than four sites: {'GLU:plan': 71, 'ASN:plan1': 19, 'ARG:plan': 28, 'ASP:plan': 43, 'GLN:plan1': 25, 'HIS:plan': 13, 'PHE:plan': 12, 'TYR:plan': 4, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 902 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' CA': 1, 'APR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 12.63, per 1000 atoms: 0.36 Number of scatterers: 35516 At special positions: 0 Unit cell: (152.508, 151.434, 173.988, 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) Ca 4 19.99 S 148 16.00 P 8 15.00 O 6072 8.00 N 6328 7.00 C 22956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A1012 " - pdb=" SG CYS A1024 " distance=2.02 Simple disulfide: pdb=" SG CYS B1012 " - pdb=" SG CYS B1024 " distance=2.02 Simple disulfide: pdb=" SG CYS C1012 " - pdb=" SG CYS C1024 " distance=2.02 Simple disulfide: pdb=" SG CYS D1012 " - pdb=" SG CYS D1024 " distance=2.02 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: 3.06 Conformation dependent library (CDL) restraints added in 1.4 seconds 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9592 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 24 sheets defined 56.0% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 39 through 45 removed outlier: 4.216A pdb=" N TRP A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 159 through 177 removed outlier: 3.727A pdb=" N LYS A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 206 removed outlier: 3.657A pdb=" N ALA A 197 " --> pdb=" O HIS A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 removed outlier: 3.573A pdb=" N LYS A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.573A pdb=" N LEU A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 343 Processing helix chain 'A' and resid 351 through 363 Processing helix chain 'A' and resid 371 through 388 removed outlier: 4.775A pdb=" N GLN A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N MET A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 419 removed outlier: 3.593A pdb=" N ALA A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 438 removed outlier: 4.300A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 434 " --> pdb=" O ARG A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 449 removed outlier: 3.760A pdb=" N ALA A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER A 446 " --> pdb=" O ASP A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 removed outlier: 3.530A pdb=" N LEU A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) Proline residue: A 462 - end of helix removed outlier: 3.600A pdb=" N GLY A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 482 removed outlier: 3.584A pdb=" N GLU A 481 " --> pdb=" O ARG A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 490 Processing helix chain 'A' and resid 494 through 502 removed outlier: 3.515A pdb=" N GLU A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 516 Processing helix chain 'A' and resid 535 through 548 removed outlier: 3.741A pdb=" N VAL A 539 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU A 542 " --> pdb=" O HIS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 604 removed outlier: 4.169A pdb=" N LEU A 598 " --> pdb=" O PRO A 594 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 599 " --> pdb=" O GLY A 595 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 600 " --> pdb=" O ARG A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 616 removed outlier: 4.206A pdb=" N GLU A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 638 removed outlier: 3.864A pdb=" N LEU A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 672 removed outlier: 3.802A pdb=" N SER A 670 " --> pdb=" O SER A 666 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP A 671 " --> pdb=" O GLU A 667 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP A 672 " --> pdb=" O CYS A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 680 Processing helix chain 'A' and resid 685 through 688 removed outlier: 3.751A pdb=" N GLY A 688 " --> pdb=" O PRO A 685 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 685 through 688' Processing helix chain 'A' and resid 692 through 699 removed outlier: 3.942A pdb=" N ALA A 699 " --> pdb=" O LEU A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 removed outlier: 3.532A pdb=" N ILE A 705 " --> pdb=" O ASP A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 720 removed outlier: 3.671A pdb=" N GLN A 711 " --> pdb=" O HIS A 707 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A 720 " --> pdb=" O GLN A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 737 removed outlier: 3.726A pdb=" N VAL A 731 " --> pdb=" O PRO A 727 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 732 " --> pdb=" O HIS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 4.251A pdb=" N ILE A 741 " --> pdb=" O PHE A 737 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR A 742 " --> pdb=" O PHE A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 765 removed outlier: 3.603A pdb=" N GLU A 752 " --> pdb=" O PHE A 748 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 758 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 807 removed outlier: 4.526A pdb=" N MET A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 833 removed outlier: 3.694A pdb=" N TYR A 814 " --> pdb=" O GLN A 810 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER A 819 " --> pdb=" O TRP A 815 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 863 removed outlier: 3.909A pdb=" N LEU A 845 " --> pdb=" O TRP A 841 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU A 846 " --> pdb=" O ARG A 842 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR A 847 " --> pdb=" O GLU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 878 removed outlier: 3.882A pdb=" N MET A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 900 Processing helix chain 'A' and resid 904 through 931 removed outlier: 3.686A pdb=" N PHE A 908 " --> pdb=" O SER A 904 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR A 909 " --> pdb=" O ASP A 905 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE A 910 " --> pdb=" O THR A 906 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 912 " --> pdb=" O PHE A 908 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET A 927 " --> pdb=" O CYS A 923 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE A 930 " --> pdb=" O LEU A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 972 removed outlier: 4.231A pdb=" N ILE A 940 " --> pdb=" O LEU A 936 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A 941 " --> pdb=" O GLY A 937 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE A 942 " --> pdb=" O PRO A 938 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG A 945 " --> pdb=" O ILE A 941 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRP A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 987 removed outlier: 3.576A pdb=" N ILE A 982 " --> pdb=" O ARG A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 994 removed outlier: 3.555A pdb=" N TYR A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 994 " --> pdb=" O PRO A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1002 removed outlier: 3.719A pdb=" N ILE A1002 " --> pdb=" O PHE A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1053 removed outlier: 3.623A pdb=" N THR A1040 " --> pdb=" O PRO A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1072 removed outlier: 3.720A pdb=" N LEU A1058 " --> pdb=" O LEU A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1092 removed outlier: 3.794A pdb=" N TYR A1083 " --> pdb=" O LYS A1079 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS A1087 " --> pdb=" O TYR A1083 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU A1088 " --> pdb=" O GLU A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1114 removed outlier: 3.647A pdb=" N SER A1103 " --> pdb=" O PHE A1099 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A1106 " --> pdb=" O LEU A1102 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A1112 " --> pdb=" O PHE A1108 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A1113 " --> pdb=" O ILE A1109 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A1114 " --> pdb=" O ARG A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1157 removed outlier: 3.821A pdb=" N GLU A1134 " --> pdb=" O GLN A1130 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU A1135 " --> pdb=" O THR A1131 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER A1150 " --> pdb=" O ASN A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1183 removed outlier: 3.623A pdb=" N ARG A1162 " --> pdb=" O SER A1158 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS A1164 " --> pdb=" O GLU A1160 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A1168 " --> pdb=" O HIS A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1368 through 1378 Processing helix chain 'A' and resid 1382 through 1388 Processing helix chain 'A' and resid 1427 through 1433 Processing helix chain 'A' and resid 1456 through 1471 removed outlier: 4.201A pdb=" N GLU A1461 " --> pdb=" O SER A1457 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A1462 " --> pdb=" O TYR A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1474 No H-bonds generated for 'chain 'A' and resid 1472 through 1474' Processing helix chain 'B' and resid 39 through 45 removed outlier: 4.216A pdb=" N TRP B 43 " --> pdb=" O SER B 39 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 136 Processing helix chain 'B' and resid 159 through 177 removed outlier: 3.726A pdb=" N LYS B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR B 177 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 206 removed outlier: 3.658A pdb=" N ALA B 197 " --> pdb=" O HIS B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 removed outlier: 3.574A pdb=" N LYS B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.574A pdb=" N LEU B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN B 314 " --> pdb=" O PRO B 310 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASN B 322 " --> pdb=" O ASN B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 343 Processing helix chain 'B' and resid 351 through 363 Processing helix chain 'B' and resid 371 through 388 removed outlier: 4.776A pdb=" N GLN B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N MET B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 419 removed outlier: 3.594A pdb=" N ALA B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 438 removed outlier: 4.300A pdb=" N GLU B 433 " --> pdb=" O GLU B 429 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 434 " --> pdb=" O ARG B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 449 removed outlier: 3.760A pdb=" N ALA B 444 " --> pdb=" O ARG B 440 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER B 446 " --> pdb=" O ASP B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 removed outlier: 3.530A pdb=" N LEU B 460 " --> pdb=" O THR B 456 " (cutoff:3.500A) Proline residue: B 462 - end of helix removed outlier: 3.599A pdb=" N GLY B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 482 removed outlier: 3.584A pdb=" N GLU B 481 " --> pdb=" O ARG B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 490 Processing helix chain 'B' and resid 494 through 502 removed outlier: 3.515A pdb=" N GLU B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 516 Processing helix chain 'B' and resid 535 through 548 removed outlier: 3.741A pdb=" N VAL B 539 " --> pdb=" O CYS B 535 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU B 542 " --> pdb=" O HIS B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 604 removed outlier: 4.169A pdb=" N LEU B 598 " --> pdb=" O PRO B 594 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE B 599 " --> pdb=" O GLY B 595 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 600 " --> pdb=" O ARG B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 616 removed outlier: 4.206A pdb=" N GLU B 616 " --> pdb=" O GLU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 638 removed outlier: 3.865A pdb=" N LEU B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 672 removed outlier: 3.803A pdb=" N SER B 670 " --> pdb=" O SER B 666 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP B 671 " --> pdb=" O GLU B 667 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP B 672 " --> pdb=" O CYS B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 680 Processing helix chain 'B' and resid 685 through 688 removed outlier: 3.751A pdb=" N GLY B 688 " --> pdb=" O PRO B 685 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 685 through 688' Processing helix chain 'B' and resid 692 through 699 removed outlier: 3.942A pdb=" N ALA B 699 " --> pdb=" O LEU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 706 removed outlier: 3.532A pdb=" N ILE B 705 " --> pdb=" O ASP B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 720 removed outlier: 3.671A pdb=" N GLN B 711 " --> pdb=" O HIS B 707 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 720 " --> pdb=" O GLN B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 737 removed outlier: 3.726A pdb=" N VAL B 731 " --> pdb=" O PRO B 727 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 732 " --> pdb=" O HIS B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 4.252A pdb=" N ILE B 741 " --> pdb=" O PHE B 737 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR B 742 " --> pdb=" O PHE B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 765 removed outlier: 3.603A pdb=" N GLU B 752 " --> pdb=" O PHE B 748 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 758 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU B 759 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 807 removed outlier: 4.527A pdb=" N MET B 803 " --> pdb=" O SER B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 833 removed outlier: 3.694A pdb=" N TYR B 814 " --> pdb=" O GLN B 810 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER B 819 " --> pdb=" O TRP B 815 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 863 removed outlier: 3.909A pdb=" N LEU B 845 " --> pdb=" O TRP B 841 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU B 846 " --> pdb=" O ARG B 842 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR B 847 " --> pdb=" O GLU B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 878 removed outlier: 3.882A pdb=" N MET B 876 " --> pdb=" O ARG B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 900 Processing helix chain 'B' and resid 904 through 931 removed outlier: 3.686A pdb=" N PHE B 908 " --> pdb=" O SER B 904 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR B 909 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE B 910 " --> pdb=" O THR B 906 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 912 " --> pdb=" O PHE B 908 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET B 927 " --> pdb=" O CYS B 923 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE B 929 " --> pdb=" O ARG B 925 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE B 930 " --> pdb=" O LEU B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 972 removed outlier: 4.231A pdb=" N ILE B 940 " --> pdb=" O LEU B 936 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE B 941 " --> pdb=" O GLY B 937 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE B 942 " --> pdb=" O PRO B 938 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG B 945 " --> pdb=" O ILE B 941 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP B 960 " --> pdb=" O LEU B 956 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 987 removed outlier: 3.576A pdb=" N ILE B 982 " --> pdb=" O ARG B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 994 removed outlier: 3.555A pdb=" N TYR B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE B 994 " --> pdb=" O PRO B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1002 removed outlier: 3.718A pdb=" N ILE B1002 " --> pdb=" O PHE B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1053 removed outlier: 3.623A pdb=" N THR B1040 " --> pdb=" O PRO B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1053 through 1072 removed outlier: 3.721A pdb=" N LEU B1058 " --> pdb=" O LEU B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1092 removed outlier: 3.794A pdb=" N TYR B1083 " --> pdb=" O LYS B1079 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS B1087 " --> pdb=" O TYR B1083 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU B1088 " --> pdb=" O GLU B1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1114 removed outlier: 3.647A pdb=" N SER B1103 " --> pdb=" O PHE B1099 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B1106 " --> pdb=" O LEU B1102 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B1112 " --> pdb=" O PHE B1108 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE B1113 " --> pdb=" O ILE B1109 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B1114 " --> pdb=" O ARG B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1157 removed outlier: 3.821A pdb=" N GLU B1134 " --> pdb=" O GLN B1130 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU B1135 " --> pdb=" O THR B1131 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER B1150 " --> pdb=" O ASN B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1158 through 1183 removed outlier: 3.623A pdb=" N ARG B1162 " --> pdb=" O SER B1158 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS B1164 " --> pdb=" O GLU B1160 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU B1168 " --> pdb=" O HIS B1164 " (cutoff:3.500A) Processing helix chain 'B' and resid 1368 through 1378 Processing helix chain 'B' and resid 1382 through 1388 Processing helix chain 'B' and resid 1427 through 1433 Processing helix chain 'B' and resid 1456 through 1471 removed outlier: 4.202A pdb=" N GLU B1461 " --> pdb=" O SER B1457 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B1462 " --> pdb=" O TYR B1458 " (cutoff:3.500A) Processing helix chain 'B' and resid 1472 through 1474 No H-bonds generated for 'chain 'B' and resid 1472 through 1474' Processing helix chain 'C' and resid 39 through 45 removed outlier: 4.217A pdb=" N TRP C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 136 Processing helix chain 'C' and resid 159 through 177 removed outlier: 3.727A pdb=" N LYS C 172 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR C 177 " --> pdb=" O VAL C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 206 removed outlier: 3.657A pdb=" N ALA C 197 " --> pdb=" O HIS C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 removed outlier: 3.574A pdb=" N LYS C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 322 removed outlier: 3.574A pdb=" N LEU C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 343 Processing helix chain 'C' and resid 351 through 363 Processing helix chain 'C' and resid 371 through 388 removed outlier: 4.775A pdb=" N GLN C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N MET C 388 " --> pdb=" O ASP C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 419 removed outlier: 3.593A pdb=" N ALA C 408 " --> pdb=" O ASP C 404 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER C 417 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 438 removed outlier: 4.300A pdb=" N GLU C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU C 434 " --> pdb=" O ARG C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 449 removed outlier: 3.760A pdb=" N ALA C 444 " --> pdb=" O ARG C 440 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER C 446 " --> pdb=" O ASP C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 470 removed outlier: 3.530A pdb=" N LEU C 460 " --> pdb=" O THR C 456 " (cutoff:3.500A) Proline residue: C 462 - end of helix removed outlier: 3.600A pdb=" N GLY C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 482 removed outlier: 3.583A pdb=" N GLU C 481 " --> pdb=" O ARG C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 490 Processing helix chain 'C' and resid 494 through 502 removed outlier: 3.515A pdb=" N GLU C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 516 Processing helix chain 'C' and resid 535 through 548 removed outlier: 3.742A pdb=" N VAL C 539 " --> pdb=" O CYS C 535 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU C 542 " --> pdb=" O HIS C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 604 removed outlier: 4.169A pdb=" N LEU C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE C 599 " --> pdb=" O GLY C 595 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 600 " --> pdb=" O ARG C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 616 removed outlier: 4.207A pdb=" N GLU C 616 " --> pdb=" O GLU C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 638 removed outlier: 3.864A pdb=" N LEU C 626 " --> pdb=" O ILE C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 672 removed outlier: 3.802A pdb=" N SER C 670 " --> pdb=" O SER C 666 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP C 671 " --> pdb=" O GLU C 667 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP C 672 " --> pdb=" O CYS C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 680 Processing helix chain 'C' and resid 685 through 688 removed outlier: 3.750A pdb=" N GLY C 688 " --> pdb=" O PRO C 685 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 685 through 688' Processing helix chain 'C' and resid 692 through 699 removed outlier: 3.943A pdb=" N ALA C 699 " --> pdb=" O LEU C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 706 removed outlier: 3.532A pdb=" N ILE C 705 " --> pdb=" O ASP C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 720 removed outlier: 3.670A pdb=" N GLN C 711 " --> pdb=" O HIS C 707 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY C 720 " --> pdb=" O GLN C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 737 removed outlier: 3.725A pdb=" N VAL C 731 " --> pdb=" O PRO C 727 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C 732 " --> pdb=" O HIS C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 4.251A pdb=" N ILE C 741 " --> pdb=" O PHE C 737 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR C 742 " --> pdb=" O PHE C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 765 removed outlier: 3.603A pdb=" N GLU C 752 " --> pdb=" O PHE C 748 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 758 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 807 removed outlier: 4.526A pdb=" N MET C 803 " --> pdb=" O SER C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 808 through 833 removed outlier: 3.694A pdb=" N TYR C 814 " --> pdb=" O GLN C 810 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER C 819 " --> pdb=" O TRP C 815 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET C 832 " --> pdb=" O ALA C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 863 removed outlier: 3.909A pdb=" N LEU C 845 " --> pdb=" O TRP C 841 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU C 846 " --> pdb=" O ARG C 842 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR C 847 " --> pdb=" O GLU C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 879 removed outlier: 3.881A pdb=" N MET C 876 " --> pdb=" O ARG C 872 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS C 879 " --> pdb=" O LYS C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 900 Processing helix chain 'C' and resid 904 through 931 removed outlier: 3.687A pdb=" N PHE C 908 " --> pdb=" O SER C 904 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR C 909 " --> pdb=" O ASP C 905 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE C 910 " --> pdb=" O THR C 906 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS C 912 " --> pdb=" O PHE C 908 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET C 927 " --> pdb=" O CYS C 923 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE C 929 " --> pdb=" O ARG C 925 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE C 930 " --> pdb=" O LEU C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 972 removed outlier: 4.232A pdb=" N ILE C 940 " --> pdb=" O LEU C 936 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE C 941 " --> pdb=" O GLY C 937 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE C 942 " --> pdb=" O PRO C 938 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG C 945 " --> pdb=" O ILE C 941 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP C 960 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU C 972 " --> pdb=" O LYS C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 987 removed outlier: 3.576A pdb=" N ILE C 982 " --> pdb=" O ARG C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 994 removed outlier: 3.554A pdb=" N TYR C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 994 " --> pdb=" O PRO C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1002 removed outlier: 3.718A pdb=" N ILE C1002 " --> pdb=" O PHE C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1053 removed outlier: 3.623A pdb=" N THR C1040 " --> pdb=" O PRO C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1053 through 1072 removed outlier: 3.720A pdb=" N LEU C1058 " --> pdb=" O LEU C1054 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1092 removed outlier: 3.795A pdb=" N TYR C1083 " --> pdb=" O LYS C1079 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS C1087 " --> pdb=" O TYR C1083 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU C1088 " --> pdb=" O GLU C1084 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1114 removed outlier: 3.647A pdb=" N SER C1103 " --> pdb=" O PHE C1099 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE C1106 " --> pdb=" O LEU C1102 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL C1112 " --> pdb=" O PHE C1108 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C1114 " --> pdb=" O ARG C1110 " (cutoff:3.500A) Processing helix chain 'C' and resid 1129 through 1157 removed outlier: 3.821A pdb=" N GLU C1134 " --> pdb=" O GLN C1130 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU C1135 " --> pdb=" O THR C1131 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER C1150 " --> pdb=" O ASN C1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 1158 through 1183 removed outlier: 3.622A pdb=" N ARG C1162 " --> pdb=" O SER C1158 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS C1164 " --> pdb=" O GLU C1160 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU C1168 " --> pdb=" O HIS C1164 " (cutoff:3.500A) Processing helix chain 'C' and resid 1368 through 1378 Processing helix chain 'C' and resid 1382 through 1388 Processing helix chain 'C' and resid 1427 through 1433 Processing helix chain 'C' and resid 1456 through 1471 removed outlier: 4.201A pdb=" N GLU C1461 " --> pdb=" O SER C1457 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C1462 " --> pdb=" O TYR C1458 " (cutoff:3.500A) Processing helix chain 'C' and resid 1472 through 1474 No H-bonds generated for 'chain 'C' and resid 1472 through 1474' Processing helix chain 'D' and resid 39 through 45 removed outlier: 4.216A pdb=" N TRP D 43 " --> pdb=" O SER D 39 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 136 Processing helix chain 'D' and resid 159 through 177 removed outlier: 3.726A pdb=" N LYS D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR D 177 " --> pdb=" O VAL D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 206 removed outlier: 3.657A pdb=" N ALA D 197 " --> pdb=" O HIS D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 287 removed outlier: 3.573A pdb=" N LYS D 287 " --> pdb=" O LYS D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 322 removed outlier: 3.573A pdb=" N LEU D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN D 314 " --> pdb=" O PRO D 310 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN D 322 " --> pdb=" O ASN D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 343 Processing helix chain 'D' and resid 351 through 363 Processing helix chain 'D' and resid 371 through 388 removed outlier: 4.775A pdb=" N GLN D 383 " --> pdb=" O THR D 379 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N MET D 388 " --> pdb=" O ASP D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 419 removed outlier: 3.592A pdb=" N ALA D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER D 417 " --> pdb=" O LEU D 413 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER D 419 " --> pdb=" O LYS D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 438 removed outlier: 4.299A pdb=" N GLU D 433 " --> pdb=" O GLU D 429 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU D 434 " --> pdb=" O ARG D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 449 removed outlier: 3.761A pdb=" N ALA D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER D 446 " --> pdb=" O ASP D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 470 removed outlier: 3.530A pdb=" N LEU D 460 " --> pdb=" O THR D 456 " (cutoff:3.500A) Proline residue: D 462 - end of helix removed outlier: 3.600A pdb=" N GLY D 470 " --> pdb=" O SER D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 482 removed outlier: 3.584A pdb=" N GLU D 481 " --> pdb=" O ARG D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 490 Processing helix chain 'D' and resid 494 through 502 removed outlier: 3.515A pdb=" N GLU D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 516 Processing helix chain 'D' and resid 535 through 548 removed outlier: 3.742A pdb=" N VAL D 539 " --> pdb=" O CYS D 535 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU D 542 " --> pdb=" O HIS D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 604 removed outlier: 4.170A pdb=" N LEU D 598 " --> pdb=" O PRO D 594 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE D 599 " --> pdb=" O GLY D 595 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 600 " --> pdb=" O ARG D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 616 removed outlier: 4.206A pdb=" N GLU D 616 " --> pdb=" O GLU D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 638 removed outlier: 3.864A pdb=" N LEU D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 672 removed outlier: 3.802A pdb=" N SER D 670 " --> pdb=" O SER D 666 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP D 671 " --> pdb=" O GLU D 667 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP D 672 " --> pdb=" O CYS D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 680 Processing helix chain 'D' and resid 685 through 688 removed outlier: 3.750A pdb=" N GLY D 688 " --> pdb=" O PRO D 685 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 685 through 688' Processing helix chain 'D' and resid 692 through 699 removed outlier: 3.942A pdb=" N ALA D 699 " --> pdb=" O LEU D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 706 removed outlier: 3.532A pdb=" N ILE D 705 " --> pdb=" O ASP D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 720 removed outlier: 3.670A pdb=" N GLN D 711 " --> pdb=" O HIS D 707 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY D 720 " --> pdb=" O GLN D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 727 through 737 removed outlier: 3.726A pdb=" N VAL D 731 " --> pdb=" O PRO D 727 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU D 732 " --> pdb=" O HIS D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 743 removed outlier: 4.251A pdb=" N ILE D 741 " --> pdb=" O PHE D 737 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR D 742 " --> pdb=" O PHE D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 765 removed outlier: 3.602A pdb=" N GLU D 752 " --> pdb=" O PHE D 748 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA D 758 " --> pdb=" O ILE D 754 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU D 759 " --> pdb=" O GLN D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 799 through 807 removed outlier: 4.526A pdb=" N MET D 803 " --> pdb=" O SER D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 833 removed outlier: 3.694A pdb=" N TYR D 814 " --> pdb=" O GLN D 810 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER D 819 " --> pdb=" O TRP D 815 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET D 832 " --> pdb=" O ALA D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 863 removed outlier: 3.909A pdb=" N LEU D 845 " --> pdb=" O TRP D 841 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU D 846 " --> pdb=" O ARG D 842 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR D 847 " --> pdb=" O GLU D 843 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 878 removed outlier: 3.882A pdb=" N MET D 876 " --> pdb=" O ARG D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 881 through 900 Processing helix chain 'D' and resid 904 through 931 removed outlier: 3.686A pdb=" N PHE D 908 " --> pdb=" O SER D 904 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TYR D 909 " --> pdb=" O ASP D 905 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE D 910 " --> pdb=" O THR D 906 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS D 912 " --> pdb=" O PHE D 908 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET D 927 " --> pdb=" O CYS D 923 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE D 929 " --> pdb=" O ARG D 925 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE D 930 " --> pdb=" O LEU D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 936 through 972 removed outlier: 4.231A pdb=" N ILE D 940 " --> pdb=" O LEU D 936 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE D 941 " --> pdb=" O GLY D 937 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE D 942 " --> pdb=" O PRO D 938 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG D 945 " --> pdb=" O ILE D 941 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP D 960 " --> pdb=" O LEU D 956 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU D 972 " --> pdb=" O LYS D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 987 removed outlier: 3.576A pdb=" N ILE D 982 " --> pdb=" O ARG D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 994 removed outlier: 3.554A pdb=" N TYR D 991 " --> pdb=" O VAL D 987 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 994 " --> pdb=" O PRO D 990 " (cutoff:3.500A) Processing helix chain 'D' and resid 997 through 1002 removed outlier: 3.718A pdb=" N ILE D1002 " --> pdb=" O PHE D 998 " (cutoff:3.500A) Processing helix chain 'D' and resid 1036 through 1053 removed outlier: 3.623A pdb=" N THR D1040 " --> pdb=" O PRO D1036 " (cutoff:3.500A) Processing helix chain 'D' and resid 1053 through 1072 removed outlier: 3.720A pdb=" N LEU D1058 " --> pdb=" O LEU D1054 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1092 removed outlier: 3.793A pdb=" N TYR D1083 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS D1087 " --> pdb=" O TYR D1083 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU D1088 " --> pdb=" O GLU D1084 " (cutoff:3.500A) Processing helix chain 'D' and resid 1099 through 1114 removed outlier: 3.647A pdb=" N SER D1103 " --> pdb=" O PHE D1099 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE D1106 " --> pdb=" O LEU D1102 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL D1112 " --> pdb=" O PHE D1108 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE D1113 " --> pdb=" O ILE D1109 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU D1114 " --> pdb=" O ARG D1110 " (cutoff:3.500A) Processing helix chain 'D' and resid 1129 through 1157 removed outlier: 3.820A pdb=" N GLU D1134 " --> pdb=" O GLN D1130 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU D1135 " --> pdb=" O THR D1131 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER D1150 " --> pdb=" O ASN D1146 " (cutoff:3.500A) Processing helix chain 'D' and resid 1158 through 1183 removed outlier: 3.622A pdb=" N ARG D1162 " --> pdb=" O SER D1158 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N HIS D1164 " --> pdb=" O GLU D1160 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU D1168 " --> pdb=" O HIS D1164 " (cutoff:3.500A) Processing helix chain 'D' and resid 1368 through 1378 Processing helix chain 'D' and resid 1382 through 1388 Processing helix chain 'D' and resid 1427 through 1433 Processing helix chain 'D' and resid 1456 through 1471 removed outlier: 4.201A pdb=" N GLU D1461 " --> pdb=" O SER D1457 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA D1462 " --> pdb=" O TYR D1458 " (cutoff:3.500A) Processing helix chain 'D' and resid 1472 through 1474 No H-bonds generated for 'chain 'D' and resid 1472 through 1474' Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 107 removed outlier: 4.054A pdb=" N ASP A 105 " --> pdb=" O PHE A 236 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 117 through 120 removed outlier: 6.731A pdb=" N VAL A 214 " --> pdb=" O HIS A 259 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N LEU A 261 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY A 216 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL A 263 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA A 218 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU A 146 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL A 304 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N SER A 148 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N VAL A 328 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N CYS A 303 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLU A 330 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL A 305 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 683 through 684 removed outlier: 3.520A pdb=" N SER A 684 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 690 " --> pdb=" O SER A 684 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1356 through 1357 removed outlier: 5.495A pdb=" N PHE A1332 " --> pdb=" O LEU A1346 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N VAL A1348 " --> pdb=" O PRO A1330 " (cutoff:3.500A) removed outlier: 15.335A pdb=" N GLU A1350 " --> pdb=" O LEU A1328 " (cutoff:3.500A) removed outlier: 19.961A pdb=" N LEU A1328 " --> pdb=" O GLU A1350 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY A1323 " --> pdb=" O TRP A1410 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU A1412 " --> pdb=" O GLY A1323 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASN A1325 " --> pdb=" O GLU A1412 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N SER A1414 " --> pdb=" O ASN A1325 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE A1327 " --> pdb=" O SER A1414 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE A1416 " --> pdb=" O ILE A1327 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N HIS A1329 " --> pdb=" O ILE A1416 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU A1418 " --> pdb=" O HIS A1329 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE A1331 " --> pdb=" O LEU A1418 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL A1411 " --> pdb=" O VAL A1400 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1356 through 1357 removed outlier: 3.573A pdb=" N GLN A1445 " --> pdb=" O ALA A1347 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AA8, first strand: chain 'B' and resid 104 through 107 removed outlier: 4.055A pdb=" N ASP B 105 " --> pdb=" O PHE B 236 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 117 through 120 removed outlier: 6.730A pdb=" N VAL B 214 " --> pdb=" O HIS B 259 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N LEU B 261 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY B 216 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL B 263 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA B 218 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU B 146 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL B 304 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N SER B 148 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N VAL B 328 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N CYS B 303 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLU B 330 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL B 305 " --> pdb=" O GLU B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 683 through 684 removed outlier: 3.519A pdb=" N SER B 684 " --> pdb=" O SER B 690 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 690 " --> pdb=" O SER B 684 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 1356 through 1357 removed outlier: 5.496A pdb=" N PHE B1332 " --> pdb=" O LEU B1346 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N VAL B1348 " --> pdb=" O PRO B1330 " (cutoff:3.500A) removed outlier: 15.335A pdb=" N GLU B1350 " --> pdb=" O LEU B1328 " (cutoff:3.500A) removed outlier: 19.961A pdb=" N LEU B1328 " --> pdb=" O GLU B1350 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY B1323 " --> pdb=" O TRP B1410 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU B1412 " --> pdb=" O GLY B1323 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASN B1325 " --> pdb=" O GLU B1412 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N SER B1414 " --> pdb=" O ASN B1325 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE B1327 " --> pdb=" O SER B1414 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE B1416 " --> pdb=" O ILE B1327 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N HIS B1329 " --> pdb=" O ILE B1416 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU B1418 " --> pdb=" O HIS B1329 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE B1331 " --> pdb=" O LEU B1418 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL B1411 " --> pdb=" O VAL B1400 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1356 through 1357 removed outlier: 3.573A pdb=" N GLN B1445 " --> pdb=" O ALA B1347 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 49 through 51 Processing sheet with id=AB5, first strand: chain 'C' and resid 104 through 107 removed outlier: 4.053A pdb=" N ASP C 105 " --> pdb=" O PHE C 236 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 117 through 120 removed outlier: 6.731A pdb=" N VAL C 214 " --> pdb=" O HIS C 259 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N LEU C 261 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY C 216 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL C 263 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA C 218 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU C 146 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL C 304 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N SER C 148 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N VAL C 328 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N CYS C 303 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLU C 330 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL C 305 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 683 through 684 removed outlier: 3.519A pdb=" N SER C 684 " --> pdb=" O SER C 690 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER C 690 " --> pdb=" O SER C 684 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 1356 through 1357 removed outlier: 5.496A pdb=" N PHE C1332 " --> pdb=" O LEU C1346 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N VAL C1348 " --> pdb=" O PRO C1330 " (cutoff:3.500A) removed outlier: 15.334A pdb=" N GLU C1350 " --> pdb=" O LEU C1328 " (cutoff:3.500A) removed outlier: 19.960A pdb=" N LEU C1328 " --> pdb=" O GLU C1350 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLY C1323 " --> pdb=" O TRP C1410 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU C1412 " --> pdb=" O GLY C1323 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASN C1325 " --> pdb=" O GLU C1412 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N SER C1414 " --> pdb=" O ASN C1325 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE C1327 " --> pdb=" O SER C1414 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE C1416 " --> pdb=" O ILE C1327 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N HIS C1329 " --> pdb=" O ILE C1416 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU C1418 " --> pdb=" O HIS C1329 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE C1331 " --> pdb=" O LEU C1418 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL C1411 " --> pdb=" O VAL C1400 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1356 through 1357 removed outlier: 3.573A pdb=" N GLN C1445 " --> pdb=" O ALA C1347 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 49 through 51 Processing sheet with id=AC2, first strand: chain 'D' and resid 104 through 107 removed outlier: 4.054A pdb=" N ASP D 105 " --> pdb=" O PHE D 236 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 117 through 120 removed outlier: 6.731A pdb=" N VAL D 214 " --> pdb=" O HIS D 259 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N LEU D 261 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY D 216 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL D 263 " --> pdb=" O GLY D 216 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA D 218 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU D 146 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL D 304 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N SER D 148 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N VAL D 328 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS D 303 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLU D 330 " --> pdb=" O CYS D 303 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL D 305 " --> pdb=" O GLU D 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 683 through 684 removed outlier: 3.520A pdb=" N SER D 684 " --> pdb=" O SER D 690 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER D 690 " --> pdb=" O SER D 684 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 1356 through 1357 removed outlier: 5.495A pdb=" N PHE D1332 " --> pdb=" O LEU D1346 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N VAL D1348 " --> pdb=" O PRO D1330 " (cutoff:3.500A) removed outlier: 15.334A pdb=" N GLU D1350 " --> pdb=" O LEU D1328 " (cutoff:3.500A) removed outlier: 19.960A pdb=" N LEU D1328 " --> pdb=" O GLU D1350 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY D1323 " --> pdb=" O TRP D1410 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU D1412 " --> pdb=" O GLY D1323 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASN D1325 " --> pdb=" O GLU D1412 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N SER D1414 " --> pdb=" O ASN D1325 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE D1327 " --> pdb=" O SER D1414 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE D1416 " --> pdb=" O ILE D1327 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N HIS D1329 " --> pdb=" O ILE D1416 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU D1418 " --> pdb=" O HIS D1329 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE D1331 " --> pdb=" O LEU D1418 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL D1411 " --> pdb=" O VAL D1400 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 1356 through 1357 removed outlier: 3.573A pdb=" N GLN D1445 " --> pdb=" O ALA D1347 " (cutoff:3.500A) 1792 hydrogen bonds defined for protein. 5364 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: 7.60 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 5584 1.29 - 1.42: 9660 1.42 - 1.55: 20860 1.55 - 1.68: 28 1.68 - 1.81: 224 Bond restraints: 36356 Sorted by residual: bond pdb=" C PRO A1268 " pdb=" O PRO A1268 " ideal model delta sigma weight residual 1.235 1.162 0.073 1.30e-02 5.92e+03 3.12e+01 bond pdb=" C PRO D1268 " pdb=" O PRO D1268 " ideal model delta sigma weight residual 1.235 1.163 0.073 1.30e-02 5.92e+03 3.11e+01 bond pdb=" C PRO C1268 " pdb=" O PRO C1268 " ideal model delta sigma weight residual 1.235 1.163 0.072 1.30e-02 5.92e+03 3.10e+01 bond pdb=" C PRO B1268 " pdb=" O PRO B1268 " ideal model delta sigma weight residual 1.235 1.163 0.072 1.30e-02 5.92e+03 3.08e+01 bond pdb=" C ARG B 608 " pdb=" O ARG B 608 " ideal model delta sigma weight residual 1.237 1.176 0.060 1.19e-02 7.06e+03 2.56e+01 ... (remaining 36351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 45956 1.95 - 3.90: 3143 3.90 - 5.85: 560 5.85 - 7.80: 161 7.80 - 9.75: 44 Bond angle restraints: 49864 Sorted by residual: angle pdb=" C GLU C 447 " pdb=" N ILE C 448 " pdb=" CA ILE C 448 " ideal model delta sigma weight residual 121.85 114.50 7.35 1.19e+00 7.06e-01 3.82e+01 angle pdb=" C GLU B 447 " pdb=" N ILE B 448 " pdb=" CA ILE B 448 " ideal model delta sigma weight residual 121.85 114.51 7.34 1.19e+00 7.06e-01 3.81e+01 angle pdb=" C GLU A 447 " pdb=" N ILE A 448 " pdb=" CA ILE A 448 " ideal model delta sigma weight residual 121.85 114.52 7.33 1.19e+00 7.06e-01 3.79e+01 angle pdb=" C GLU D 447 " pdb=" N ILE D 448 " pdb=" CA ILE D 448 " ideal model delta sigma weight residual 121.85 114.53 7.32 1.19e+00 7.06e-01 3.78e+01 angle pdb=" C GLY C 112 " pdb=" N GLN C 113 " pdb=" CA GLN C 113 " ideal model delta sigma weight residual 121.50 112.84 8.66 1.43e+00 4.89e-01 3.67e+01 ... (remaining 49859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 20156 17.50 - 35.01: 760 35.01 - 52.51: 168 52.51 - 70.01: 12 70.01 - 87.52: 20 Dihedral angle restraints: 21116 sinusoidal: 6356 harmonic: 14760 Sorted by residual: dihedral pdb=" CA ILE A1053 " pdb=" C ILE A1053 " pdb=" N LEU A1054 " pdb=" CA LEU A1054 " ideal model delta harmonic sigma weight residual -180.00 -154.92 -25.08 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ILE B1053 " pdb=" C ILE B1053 " pdb=" N LEU B1054 " pdb=" CA LEU B1054 " ideal model delta harmonic sigma weight residual -180.00 -154.93 -25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA ILE C1053 " pdb=" C ILE C1053 " pdb=" N LEU C1054 " pdb=" CA LEU C1054 " ideal model delta harmonic sigma weight residual -180.00 -154.94 -25.06 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 21113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4833 0.076 - 0.153: 890 0.153 - 0.229: 133 0.229 - 0.305: 56 0.305 - 0.382: 8 Chirality restraints: 5920 Sorted by residual: chirality pdb=" CA ASN C 607 " pdb=" N ASN C 607 " pdb=" C ASN C 607 " pdb=" CB ASN C 607 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" CA ASN A 607 " pdb=" N ASN A 607 " pdb=" C ASN A 607 " pdb=" CB ASN A 607 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA ASN D 607 " pdb=" N ASN D 607 " pdb=" C ASN D 607 " pdb=" CB ASN D 607 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 5917 not shown) Planarity restraints: 6344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 446 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C SER B 446 " -0.065 2.00e-02 2.50e+03 pdb=" O SER B 446 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU B 447 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 446 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C SER D 446 " -0.065 2.00e-02 2.50e+03 pdb=" O SER D 446 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU D 447 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 446 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C SER C 446 " -0.065 2.00e-02 2.50e+03 pdb=" O SER C 446 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU C 447 " 0.022 2.00e-02 2.50e+03 ... (remaining 6341 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 277 2.65 - 3.22: 31111 3.22 - 3.78: 51971 3.78 - 4.34: 63269 4.34 - 4.90: 107400 Nonbonded interactions: 254028 Sorted by model distance: nonbonded pdb=" OE1 GLN B 860 " pdb="CA CA B2002 " model vdw 2.093 2.510 nonbonded pdb=" OE1 GLN D 860 " pdb="CA CA D2002 " model vdw 2.093 2.510 nonbonded pdb=" OE1 GLN C 860 " pdb="CA CA C2002 " model vdw 2.093 2.510 nonbonded pdb=" OE1 GLN A 860 " pdb="CA CA A2002 " model vdw 2.093 2.510 nonbonded pdb=" O GLY A 970 " pdb=" NZ LYS B 912 " model vdw 2.252 3.120 ... (remaining 254023 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 36.680 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 : 0.007 0.085 36360 Z= 0.425 Angle : 1.135 9.755 49872 Z= 0.696 Chirality : 0.065 0.382 5920 Planarity : 0.009 0.127 6344 Dihedral : 10.899 87.515 11512 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.14 % Allowed : 4.37 % Favored : 95.49 % Cbeta Deviations : 0.17 % 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: -3.18 (0.10), residues: 5008 helix: -1.69 (0.08), residues: 2484 sheet: -1.87 (0.24), residues: 360 loop : -2.58 (0.11), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 120 TYR 0.036 0.003 TYR A1089 PHE 0.028 0.003 PHE B 395 TRP 0.038 0.003 TRP B 849 HIS 0.013 0.002 HIS D1104 Details of bonding type rmsd/Z covalent geometry : bond 0.00721 / 0.42 (36356) covalent geometry : angle 1.13481 / 0.70 (49864) SS BOND : bond 0.01227 / 0.62 ( 4) SS BOND : angle 0.26098 / 0.14 ( 8) hydrogen bonds : bond 0.15594 / 10.61 ( 1784) hydrogen bonds : angle 6.66273 / 4.74 ( 5364) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 803 time to evaluate : 1.180 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 118 TYR cc_start: 0.8534 (p90) cc_final: 0.8326 (p90) REVERT: A 284 LEU cc_start: 0.8410 (tp) cc_final: 0.8173 (tt) REVERT: A 404 ASP cc_start: 0.8485 (t70) cc_final: 0.8195 (t0) REVERT: A 481 GLU cc_start: 0.8402 (pp20) cc_final: 0.8194 (pp20) REVERT: A 825 TRP cc_start: 0.8116 (t60) cc_final: 0.7783 (t60) REVERT: A 945 ARG cc_start: 0.7984 (mtp-110) cc_final: 0.7727 (mtp85) REVERT: A 947 MET cc_start: 0.7342 (tmm) cc_final: 0.6831 (tmm) REVERT: A 949 ASP cc_start: 0.8100 (t70) cc_final: 0.7884 (m-30) REVERT: A 1043 MET cc_start: 0.8380 (ttm) cc_final: 0.8116 (ttp) REVERT: A 1054 LEU cc_start: 0.8728 (mp) cc_final: 0.8497 (mp) REVERT: A 1153 GLN cc_start: 0.7737 (pp30) cc_final: 0.7406 (pp30) REVERT: B 481 GLU cc_start: 0.8473 (pp20) cc_final: 0.7819 (pp20) REVERT: B 671 TRP cc_start: 0.8702 (t-100) cc_final: 0.8479 (t-100) REVERT: B 719 CYS cc_start: 0.8429 (t) cc_final: 0.8199 (m) REVERT: B 825 TRP cc_start: 0.7730 (t60) cc_final: 0.7498 (t60) REVERT: B 947 MET cc_start: 0.7505 (tmm) cc_final: 0.6807 (tmm) REVERT: B 949 ASP cc_start: 0.8231 (t70) cc_final: 0.7858 (m-30) REVERT: B 998 PHE cc_start: 0.8570 (t80) cc_final: 0.8326 (t80) REVERT: B 1153 GLN cc_start: 0.7840 (pp30) cc_final: 0.7396 (pp30) REVERT: C 106 ILE cc_start: 0.9075 (pt) cc_final: 0.8856 (mt) REVERT: C 284 LEU cc_start: 0.8571 (tp) cc_final: 0.8361 (tt) REVERT: C 404 ASP cc_start: 0.8424 (t70) cc_final: 0.8054 (t0) REVERT: C 481 GLU cc_start: 0.8499 (pp20) cc_final: 0.8032 (pp20) REVERT: C 719 CYS cc_start: 0.8513 (t) cc_final: 0.8240 (m) REVERT: C 825 TRP cc_start: 0.7952 (t60) cc_final: 0.7480 (t60) REVERT: C 856 GLU cc_start: 0.8234 (tp30) cc_final: 0.7694 (tm-30) REVERT: C 886 ASP cc_start: 0.3609 (m-30) cc_final: 0.3329 (m-30) REVERT: C 926 LEU cc_start: 0.8443 (tm) cc_final: 0.8177 (tp) REVERT: C 947 MET cc_start: 0.7405 (tmm) cc_final: 0.6702 (tmm) REVERT: C 949 ASP cc_start: 0.8267 (t70) cc_final: 0.7829 (m-30) REVERT: C 1140 GLU cc_start: 0.8314 (pp20) cc_final: 0.7628 (pp20) REVERT: C 1146 ASN cc_start: 0.8906 (t0) cc_final: 0.8685 (t0) REVERT: C 1153 GLN cc_start: 0.7860 (pp30) cc_final: 0.7463 (pp30) REVERT: D 284 LEU cc_start: 0.8697 (tp) cc_final: 0.8463 (tt) REVERT: D 352 MET cc_start: 0.8154 (mtp) cc_final: 0.7899 (ttm) REVERT: D 404 ASP cc_start: 0.8341 (t70) cc_final: 0.7989 (t0) REVERT: D 464 MET cc_start: 0.8999 (tpt) cc_final: 0.8708 (tpt) REVERT: D 481 GLU cc_start: 0.8426 (pp20) cc_final: 0.7931 (pp20) REVERT: D 825 TRP cc_start: 0.8003 (t60) cc_final: 0.7491 (t60) REVERT: D 856 GLU cc_start: 0.8082 (tp30) cc_final: 0.7743 (tm-30) REVERT: D 886 ASP cc_start: 0.3605 (m-30) cc_final: 0.3319 (m-30) REVERT: D 926 LEU cc_start: 0.8508 (tm) cc_final: 0.8146 (tp) REVERT: D 947 MET cc_start: 0.7400 (tmm) cc_final: 0.6711 (tmm) REVERT: D 949 ASP cc_start: 0.8297 (t70) cc_final: 0.7813 (m-30) REVERT: D 1140 GLU cc_start: 0.8369 (pp20) cc_final: 0.7758 (pp20) outliers start: 4 outliers final: 4 residues processed: 807 average time/residue: 0.2100 time to fit residues: 275.6705 Evaluate side-chains 451 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 447 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain D residue 991 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 0.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 494 optimal weight: 30.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 2.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 HIS A 231 HIS A 257 HIS A 259 HIS A 975 ASN B 137 GLN B 161 HIS B 224 HIS B 231 HIS B 256 ASN B 259 HIS B 816 ASN B 975 ASN C 137 GLN C 161 HIS C 224 HIS C 231 HIS C 256 ASN C 257 HIS C 259 HIS C 975 ASN D 137 GLN D 161 HIS D 224 HIS D 231 HIS D 256 ASN D 257 HIS D 259 HIS D 975 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.157765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.122853 restraints weight = 67408.561| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 3.22 r_work: 0.3500 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 36360 Z= 0.119 Angle : 0.575 7.709 49872 Z= 0.300 Chirality : 0.040 0.181 5920 Planarity : 0.005 0.052 6344 Dihedral : 5.186 51.124 5380 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.14 % Allowed : 12.13 % Favored : 84.73 % 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: -1.50 (0.11), residues: 5008 helix: 0.16 (0.10), residues: 2520 sheet: -1.58 (0.24), residues: 408 loop : -2.33 (0.12), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 440 TYR 0.015 0.001 TYR A1089 PHE 0.020 0.002 PHE D 449 TRP 0.025 0.001 TRP D 43 HIS 0.007 0.001 HIS D 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (36356) covalent geometry : angle 0.57461 / 0.30 (49864) SS BOND : bond 0.00294 / 0.15 ( 4) SS BOND : angle 0.51931 / 0.28 ( 8) hydrogen bonds : bond 0.05184 / 3.61 ( 1784) hydrogen bonds : angle 4.47736 / 3.19 ( 5364) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 521 time to evaluate : 1.185 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 118 TYR cc_start: 0.8998 (p90) cc_final: 0.8670 (p90) REVERT: A 239 TYR cc_start: 0.7906 (m-10) cc_final: 0.7649 (m-10) REVERT: A 404 ASP cc_start: 0.8693 (t70) cc_final: 0.8433 (t0) REVERT: A 657 TYR cc_start: 0.8889 (m-80) cc_final: 0.8622 (m-80) REVERT: A 658 GLU cc_start: 0.8353 (tt0) cc_final: 0.7794 (tt0) REVERT: A 719 CYS cc_start: 0.9165 (t) cc_final: 0.8743 (m) REVERT: A 825 TRP cc_start: 0.8207 (t60) cc_final: 0.7789 (t60) REVERT: A 862 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.6674 (t80) REVERT: A 945 ARG cc_start: 0.8020 (mtp-110) cc_final: 0.7715 (mtp85) REVERT: A 947 MET cc_start: 0.7165 (tmm) cc_final: 0.6880 (tmm) REVERT: A 1140 GLU cc_start: 0.8441 (pp20) cc_final: 0.8191 (pp20) REVERT: B 307 ASP cc_start: 0.8336 (p0) cc_final: 0.8126 (p0) REVERT: B 404 ASP cc_start: 0.8502 (t70) cc_final: 0.8276 (t0) REVERT: B 481 GLU cc_start: 0.8856 (pp20) cc_final: 0.8448 (pp20) REVERT: B 719 CYS cc_start: 0.9052 (t) cc_final: 0.8792 (m) REVERT: B 727 PRO cc_start: 0.8084 (Cg_exo) cc_final: 0.7748 (Cg_endo) REVERT: B 825 TRP cc_start: 0.7945 (t60) cc_final: 0.7609 (t60) REVERT: B 862 TYR cc_start: 0.6627 (OUTLIER) cc_final: 0.6198 (t80) REVERT: B 886 ASP cc_start: 0.7649 (m-30) cc_final: 0.7274 (m-30) REVERT: B 947 MET cc_start: 0.7346 (tmm) cc_final: 0.6786 (tmm) REVERT: B 949 ASP cc_start: 0.8180 (t70) cc_final: 0.7973 (m-30) REVERT: B 1026 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7224 (ppp) REVERT: B 1140 GLU cc_start: 0.8594 (pp20) cc_final: 0.8314 (pp20) REVERT: C 404 ASP cc_start: 0.8638 (t70) cc_final: 0.8368 (t0) REVERT: C 481 GLU cc_start: 0.8884 (pp20) cc_final: 0.8590 (pp20) REVERT: C 719 CYS cc_start: 0.9093 (t) cc_final: 0.8831 (m) REVERT: C 825 TRP cc_start: 0.8100 (t60) cc_final: 0.7564 (t60) REVERT: C 856 GLU cc_start: 0.8083 (tp30) cc_final: 0.7614 (tm-30) REVERT: C 862 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.6382 (t80) REVERT: C 886 ASP cc_start: 0.7720 (m-30) cc_final: 0.7434 (m-30) REVERT: C 888 LEU cc_start: 0.8827 (tt) cc_final: 0.8562 (tp) REVERT: C 947 MET cc_start: 0.7282 (tmm) cc_final: 0.6716 (tmm) REVERT: C 1026 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7157 (ppp) REVERT: C 1140 GLU cc_start: 0.8551 (pp20) cc_final: 0.8159 (pp20) REVERT: D 388 MET cc_start: 0.8808 (ptp) cc_final: 0.8508 (ptp) REVERT: D 404 ASP cc_start: 0.8586 (t70) cc_final: 0.8313 (t0) REVERT: D 481 GLU cc_start: 0.8808 (pp20) cc_final: 0.8515 (pp20) REVERT: D 825 TRP cc_start: 0.8091 (t60) cc_final: 0.7582 (t60) REVERT: D 856 GLU cc_start: 0.7875 (tp30) cc_final: 0.7570 (tm-30) REVERT: D 862 TYR cc_start: 0.7164 (OUTLIER) cc_final: 0.6368 (t80) REVERT: D 886 ASP cc_start: 0.7869 (m-30) cc_final: 0.7539 (m-30) REVERT: D 947 MET cc_start: 0.7324 (tmm) cc_final: 0.6660 (tmm) REVERT: D 949 ASP cc_start: 0.8291 (t70) cc_final: 0.7994 (m-30) REVERT: D 1052 ASN cc_start: 0.7783 (t0) cc_final: 0.7257 (p0) REVERT: D 1140 GLU cc_start: 0.8525 (pp20) cc_final: 0.8199 (pp20) outliers start: 89 outliers final: 53 residues processed: 580 average time/residue: 0.1980 time to fit residues: 196.1987 Evaluate side-chains 460 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 401 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 816 ASN Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 926 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 703 SER Chi-restraints excluded: chain C residue 862 TYR Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1099 PHE Chi-restraints excluded: chain D residue 224 HIS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 703 SER Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 991 TYR Chi-restraints excluded: chain D residue 1099 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 293 optimal weight: 0.6980 chunk 345 optimal weight: 0.0030 chunk 132 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 407 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 447 optimal weight: 0.0050 chunk 107 optimal weight: 4.9990 overall best weight: 0.4806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.158190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.123424 restraints weight = 67876.669| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 3.21 r_work: 0.3510 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 36360 Z= 0.102 Angle : 0.525 8.102 49872 Z= 0.271 Chirality : 0.039 0.165 5920 Planarity : 0.004 0.048 6344 Dihedral : 4.711 51.754 5380 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.93 % Allowed : 14.00 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.11), residues: 5008 helix: 0.93 (0.10), residues: 2524 sheet: -1.10 (0.25), residues: 404 loop : -2.20 (0.12), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 167 TYR 0.014 0.001 TYR B1089 PHE 0.020 0.001 PHE C 550 TRP 0.022 0.001 TRP D 43 HIS 0.010 0.001 HIS D 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (36356) covalent geometry : angle 0.52465 / 0.27 (49864) SS BOND : bond 0.00188 / 0.09 ( 4) SS BOND : angle 0.46063 / 0.25 ( 8) hydrogen bonds : bond 0.04221 / 2.94 ( 1784) hydrogen bonds : angle 4.07872 / 2.91 ( 5364) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 448 time to evaluate : 1.443 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 118 TYR cc_start: 0.8981 (p90) cc_final: 0.8622 (p90) REVERT: A 384 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7874 (t0) REVERT: A 657 TYR cc_start: 0.8856 (m-80) cc_final: 0.8621 (m-80) REVERT: A 719 CYS cc_start: 0.9157 (t) cc_final: 0.8729 (m) REVERT: A 825 TRP cc_start: 0.8150 (t60) cc_final: 0.7742 (t60) REVERT: A 862 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6654 (t80) REVERT: A 947 MET cc_start: 0.7131 (tmm) cc_final: 0.6808 (tmm) REVERT: A 1026 MET cc_start: 0.8055 (ppp) cc_final: 0.7787 (ppp) REVERT: A 1052 ASN cc_start: 0.7999 (OUTLIER) cc_final: 0.7471 (p0) REVERT: A 1140 GLU cc_start: 0.8401 (pp20) cc_final: 0.8119 (pp20) REVERT: A 1157 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8274 (mt0) REVERT: B 404 ASP cc_start: 0.8476 (t70) cc_final: 0.8218 (t0) REVERT: B 481 GLU cc_start: 0.8818 (pp20) cc_final: 0.8556 (pp20) REVERT: B 719 CYS cc_start: 0.9035 (t) cc_final: 0.8743 (m) REVERT: B 727 PRO cc_start: 0.8082 (Cg_exo) cc_final: 0.7795 (Cg_endo) REVERT: B 825 TRP cc_start: 0.7944 (t60) cc_final: 0.7594 (t60) REVERT: B 862 TYR cc_start: 0.6559 (OUTLIER) cc_final: 0.6173 (t80) REVERT: B 886 ASP cc_start: 0.7660 (m-30) cc_final: 0.7253 (m-30) REVERT: B 947 MET cc_start: 0.7394 (tmm) cc_final: 0.6791 (tmm) REVERT: B 1026 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7285 (ppp) REVERT: B 1052 ASN cc_start: 0.7721 (t0) cc_final: 0.7250 (p0) REVERT: B 1140 GLU cc_start: 0.8567 (pp20) cc_final: 0.8285 (pp20) REVERT: C 384 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.8000 (t0) REVERT: C 404 ASP cc_start: 0.8645 (t70) cc_final: 0.8346 (t0) REVERT: C 481 GLU cc_start: 0.8816 (pp20) cc_final: 0.8585 (pp20) REVERT: C 719 CYS cc_start: 0.9086 (t) cc_final: 0.8790 (m) REVERT: C 825 TRP cc_start: 0.8118 (t60) cc_final: 0.7546 (t60) REVERT: C 856 GLU cc_start: 0.7956 (tp30) cc_final: 0.7538 (tm-30) REVERT: C 862 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.6429 (t80) REVERT: C 886 ASP cc_start: 0.7893 (m-30) cc_final: 0.7545 (m-30) REVERT: C 947 MET cc_start: 0.7259 (tmm) cc_final: 0.6729 (tmm) REVERT: C 1052 ASN cc_start: 0.7763 (OUTLIER) cc_final: 0.7286 (p0) REVERT: C 1140 GLU cc_start: 0.8512 (pp20) cc_final: 0.8104 (pp20) REVERT: D 261 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8556 (mp) REVERT: D 388 MET cc_start: 0.8607 (ptp) cc_final: 0.8213 (ptp) REVERT: D 404 ASP cc_start: 0.8581 (t70) cc_final: 0.8320 (t0) REVERT: D 464 MET cc_start: 0.9336 (tpp) cc_final: 0.8949 (tpt) REVERT: D 481 GLU cc_start: 0.8786 (pp20) cc_final: 0.8509 (pp20) REVERT: D 825 TRP cc_start: 0.8019 (t60) cc_final: 0.7442 (t60) REVERT: D 862 TYR cc_start: 0.7040 (OUTLIER) cc_final: 0.6425 (t80) REVERT: D 886 ASP cc_start: 0.7807 (m-30) cc_final: 0.7433 (m-30) REVERT: D 947 MET cc_start: 0.7174 (tmm) cc_final: 0.6719 (tmm) REVERT: D 949 ASP cc_start: 0.8262 (t70) cc_final: 0.8043 (m-30) REVERT: D 1052 ASN cc_start: 0.7760 (t0) cc_final: 0.7389 (p0) REVERT: D 1140 GLU cc_start: 0.8516 (pp20) cc_final: 0.8152 (pp20) outliers start: 83 outliers final: 39 residues processed: 500 average time/residue: 0.1879 time to fit residues: 161.9712 Evaluate side-chains 445 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 396 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 926 LEU Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 862 TYR Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1052 ASN Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 485 CYS Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 991 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 228 optimal weight: 4.9990 chunk 230 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 476 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 240 optimal weight: 7.9990 chunk 316 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 306 optimal weight: 5.9990 chunk 437 optimal weight: 0.0670 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 ASN B 224 HIS ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 ASN ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 816 ASN D 482 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.150229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.115060 restraints weight = 67546.720| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.45 r_work: 0.3355 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 36360 Z= 0.221 Angle : 0.610 7.665 49872 Z= 0.316 Chirality : 0.043 0.174 5920 Planarity : 0.004 0.046 6344 Dihedral : 4.742 50.838 5380 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.84 % Allowed : 15.06 % 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: -0.51 (0.12), residues: 5008 helix: 1.13 (0.10), residues: 2504 sheet: -0.88 (0.26), residues: 392 loop : -2.13 (0.12), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 226 TYR 0.016 0.002 TYR D1089 PHE 0.019 0.002 PHE A 550 TRP 0.023 0.002 TRP B 43 HIS 0.035 0.002 HIS A 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 (36356) covalent geometry : angle 0.60976 / 0.32 (49864) SS BOND : bond 0.00332 / 0.17 ( 4) SS BOND : angle 0.19118 / 0.11 ( 8) hydrogen bonds : bond 0.05523 / 3.84 ( 1784) hydrogen bonds : angle 4.19389 / 2.98 ( 5364) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 397 time to evaluate : 1.469 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 118 TYR cc_start: 0.9090 (p90) cc_final: 0.8633 (p90) REVERT: A 352 MET cc_start: 0.7637 (mtp) cc_final: 0.7322 (ttm) REVERT: A 719 CYS cc_start: 0.9204 (t) cc_final: 0.8801 (m) REVERT: A 1052 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7665 (p0) REVERT: A 1140 GLU cc_start: 0.8661 (pp20) cc_final: 0.8118 (pp20) REVERT: B 481 GLU cc_start: 0.9007 (pp20) cc_final: 0.8596 (pp20) REVERT: B 719 CYS cc_start: 0.9160 (t) cc_final: 0.8838 (m) REVERT: B 727 PRO cc_start: 0.8334 (Cg_exo) cc_final: 0.8054 (Cg_endo) REVERT: B 825 TRP cc_start: 0.8169 (t60) cc_final: 0.7519 (t60) REVERT: B 886 ASP cc_start: 0.7916 (m-30) cc_final: 0.7543 (m-30) REVERT: B 892 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8233 (mm) REVERT: B 947 MET cc_start: 0.7369 (tmm) cc_final: 0.7042 (tmm) REVERT: B 1026 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7397 (ppp) REVERT: B 1052 ASN cc_start: 0.7965 (t0) cc_final: 0.7544 (p0) REVERT: B 1140 GLU cc_start: 0.8699 (pp20) cc_final: 0.8411 (pp20) REVERT: C 404 ASP cc_start: 0.8789 (t70) cc_final: 0.8520 (t0) REVERT: C 481 GLU cc_start: 0.8994 (pp20) cc_final: 0.8606 (pp20) REVERT: C 719 CYS cc_start: 0.9156 (t) cc_final: 0.8821 (m) REVERT: C 825 TRP cc_start: 0.8216 (t60) cc_final: 0.7637 (t60) REVERT: C 886 ASP cc_start: 0.8040 (m-30) cc_final: 0.7669 (m-30) REVERT: C 947 MET cc_start: 0.7255 (tmm) cc_final: 0.6695 (tmm) REVERT: C 1026 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7282 (ppp) REVERT: C 1052 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7536 (p0) REVERT: C 1140 GLU cc_start: 0.8706 (pp20) cc_final: 0.8270 (pp20) REVERT: D 388 MET cc_start: 0.8599 (ptp) cc_final: 0.8219 (ptp) REVERT: D 404 ASP cc_start: 0.8795 (t70) cc_final: 0.8510 (t0) REVERT: D 481 GLU cc_start: 0.8973 (pp20) cc_final: 0.8564 (pp20) REVERT: D 886 ASP cc_start: 0.8103 (m-30) cc_final: 0.7722 (m-30) REVERT: D 947 MET cc_start: 0.7223 (tmm) cc_final: 0.6695 (tmm) REVERT: D 1026 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7169 (ppp) REVERT: D 1052 ASN cc_start: 0.7868 (t0) cc_final: 0.7534 (p0) REVERT: D 1140 GLU cc_start: 0.8737 (pp20) cc_final: 0.8305 (pp20) outliers start: 109 outliers final: 75 residues processed: 465 average time/residue: 0.1932 time to fit residues: 157.2636 Evaluate side-chains 454 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 373 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 832 MET Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1065 TYR Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 816 ASN Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 942 ILE Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1065 TYR Chi-restraints excluded: chain B residue 1090 HIS Chi-restraints excluded: chain B residue 1257 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 703 SER Chi-restraints excluded: chain C residue 816 ASN Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 832 MET Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 862 TYR Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 942 ILE Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1052 ASN Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1099 PHE Chi-restraints excluded: chain C residue 1257 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 485 CYS Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 830 VAL Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 942 ILE Chi-restraints excluded: chain D residue 991 TYR Chi-restraints excluded: chain D residue 1026 MET Chi-restraints excluded: chain D residue 1065 TYR Chi-restraints excluded: chain D residue 1099 PHE Chi-restraints excluded: chain D residue 1257 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 12 optimal weight: 6.9990 chunk 355 optimal weight: 3.9990 chunk 497 optimal weight: 7.9990 chunk 382 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 291 optimal weight: 0.6980 chunk 191 optimal weight: 30.0000 chunk 360 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 HIS A 256 ASN A 411 GLN A1157 GLN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 ASN C 224 HIS C 341 HIS D 224 HIS D 341 HIS D 411 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.153787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.117261 restraints weight = 66973.949| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 3.75 r_work: 0.3383 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36360 Z= 0.127 Angle : 0.526 7.221 49872 Z= 0.273 Chirality : 0.040 0.141 5920 Planarity : 0.004 0.046 6344 Dihedral : 4.492 50.063 5380 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.63 % Allowed : 16.22 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.12), residues: 5008 helix: 1.40 (0.10), residues: 2512 sheet: -0.53 (0.27), residues: 388 loop : -2.04 (0.12), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 945 TYR 0.015 0.001 TYR B1089 PHE 0.024 0.001 PHE A 550 TRP 0.014 0.001 TRP B 43 HIS 0.011 0.001 HIS A 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (36356) covalent geometry : angle 0.52650 / 0.27 (49864) SS BOND : bond 0.00203 / 0.10 ( 4) SS BOND : angle 0.33088 / 0.18 ( 8) hydrogen bonds : bond 0.04461 / 3.11 ( 1784) hydrogen bonds : angle 3.95024 / 2.81 ( 5364) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 396 time to evaluate : 1.435 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 118 TYR cc_start: 0.9112 (p90) cc_final: 0.8667 (p90) REVERT: A 163 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8495 (ttmm) REVERT: A 719 CYS cc_start: 0.9257 (t) cc_final: 0.8790 (m) REVERT: A 826 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8087 (tt) REVERT: A 862 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.6710 (t80) REVERT: A 947 MET cc_start: 0.7206 (tmm) cc_final: 0.6905 (ttt) REVERT: A 1026 MET cc_start: 0.7908 (ppp) cc_final: 0.7526 (ppp) REVERT: A 1052 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7727 (p0) REVERT: A 1140 GLU cc_start: 0.8590 (pp20) cc_final: 0.8155 (pp20) REVERT: A 1153 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8449 (tm-30) REVERT: B 481 GLU cc_start: 0.8971 (pp20) cc_final: 0.8634 (pp20) REVERT: B 719 CYS cc_start: 0.9200 (t) cc_final: 0.8789 (m) REVERT: B 727 PRO cc_start: 0.8356 (Cg_exo) cc_final: 0.8050 (Cg_endo) REVERT: B 825 TRP cc_start: 0.8198 (t60) cc_final: 0.7548 (t60) REVERT: B 862 TYR cc_start: 0.6860 (OUTLIER) cc_final: 0.6242 (t80) REVERT: B 886 ASP cc_start: 0.7955 (m-30) cc_final: 0.7544 (m-30) REVERT: B 892 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8189 (mm) REVERT: B 1026 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7362 (ppp) REVERT: B 1052 ASN cc_start: 0.7857 (t0) cc_final: 0.7457 (p0) REVERT: B 1140 GLU cc_start: 0.8586 (pp20) cc_final: 0.8339 (pp20) REVERT: C 481 GLU cc_start: 0.8961 (pp20) cc_final: 0.8680 (pp20) REVERT: C 719 CYS cc_start: 0.9209 (t) cc_final: 0.8794 (m) REVERT: C 816 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8330 (m-40) REVERT: C 826 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7927 (tt) REVERT: C 862 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.6341 (t80) REVERT: C 886 ASP cc_start: 0.8066 (m-30) cc_final: 0.7667 (m-30) REVERT: C 1052 ASN cc_start: 0.7945 (OUTLIER) cc_final: 0.7466 (p0) REVERT: C 1140 GLU cc_start: 0.8629 (pp20) cc_final: 0.8173 (pp20) REVERT: D 352 MET cc_start: 0.7655 (mtm) cc_final: 0.7265 (ttm) REVERT: D 388 MET cc_start: 0.8482 (ptp) cc_final: 0.8165 (ptp) REVERT: D 481 GLU cc_start: 0.8906 (pp20) cc_final: 0.8625 (pp20) REVERT: D 862 TYR cc_start: 0.6986 (OUTLIER) cc_final: 0.6216 (t80) REVERT: D 886 ASP cc_start: 0.7990 (m-30) cc_final: 0.7583 (m-30) REVERT: D 949 ASP cc_start: 0.8245 (t70) cc_final: 0.8041 (m-30) REVERT: D 1026 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7181 (ppp) REVERT: D 1140 GLU cc_start: 0.8662 (pp20) cc_final: 0.8193 (pp20) outliers start: 103 outliers final: 68 residues processed: 460 average time/residue: 0.1874 time to fit residues: 152.2958 Evaluate side-chains 454 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 373 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 832 MET Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1057 ASN Chi-restraints excluded: chain A residue 1065 TYR Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 816 ASN Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 971 ILE Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1057 ASN Chi-restraints excluded: chain B residue 1065 TYR Chi-restraints excluded: chain B residue 1090 HIS Chi-restraints excluded: chain B residue 1257 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 703 SER Chi-restraints excluded: chain C residue 816 ASN Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 862 TYR Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1052 ASN Chi-restraints excluded: chain C residue 1057 ASN Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1257 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 482 ASN Chi-restraints excluded: chain D residue 485 CYS Chi-restraints excluded: chain D residue 703 SER Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 950 LEU Chi-restraints excluded: chain D residue 991 TYR Chi-restraints excluded: chain D residue 1026 MET Chi-restraints excluded: chain D residue 1065 TYR Chi-restraints excluded: chain D residue 1257 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 409 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 497 optimal weight: 8.9990 chunk 427 optimal weight: 6.9990 chunk 399 optimal weight: 20.0000 chunk 348 optimal weight: 20.0000 chunk 428 optimal weight: 5.9990 chunk 315 optimal weight: 10.0000 chunk 501 optimal weight: 50.0000 chunk 131 optimal weight: 6.9990 chunk 474 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 GLN B 411 GLN B 816 ASN C 137 GLN C 411 GLN C 816 ASN D 137 GLN D 256 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.145760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.109583 restraints weight = 67827.239| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.14 r_work: 0.3287 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 36360 Z= 0.344 Angle : 0.729 10.310 49872 Z= 0.376 Chirality : 0.047 0.189 5920 Planarity : 0.005 0.088 6344 Dihedral : 5.006 46.724 5380 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.87 % Allowed : 16.40 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.11), residues: 5008 helix: 0.89 (0.10), residues: 2512 sheet: -0.53 (0.28), residues: 368 loop : -2.10 (0.12), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 418 TYR 0.020 0.002 TYR B1089 PHE 0.023 0.002 PHE A 363 TRP 0.023 0.002 TRP C 438 HIS 0.009 0.002 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00815 / 0.34 (36356) covalent geometry : angle 0.72861 / 0.38 (49864) SS BOND : bond 0.00302 / 0.15 ( 4) SS BOND : angle 0.05119 / 0.03 ( 8) hydrogen bonds : bond 0.06673 / 4.63 ( 1784) hydrogen bonds : angle 4.54460 / 3.22 ( 5364) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 346 time to evaluate : 1.406 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 118 TYR cc_start: 0.9121 (p90) cc_final: 0.8639 (p90) REVERT: A 719 CYS cc_start: 0.9243 (t) cc_final: 0.8809 (m) REVERT: A 1052 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.7888 (p0) REVERT: A 1140 GLU cc_start: 0.8725 (pp20) cc_final: 0.8222 (pp20) REVERT: B 404 ASP cc_start: 0.8831 (t70) cc_final: 0.8576 (t0) REVERT: B 481 GLU cc_start: 0.9050 (pp20) cc_final: 0.8544 (pp20) REVERT: B 658 GLU cc_start: 0.8660 (tt0) cc_final: 0.8450 (tt0) REVERT: B 719 CYS cc_start: 0.9239 (t) cc_final: 0.8823 (m) REVERT: B 886 ASP cc_start: 0.8272 (m-30) cc_final: 0.7898 (m-30) REVERT: B 892 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8205 (mm) REVERT: B 1026 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7409 (ppp) REVERT: B 1140 GLU cc_start: 0.8758 (pp20) cc_final: 0.8385 (pp20) REVERT: C 481 GLU cc_start: 0.9065 (pp20) cc_final: 0.8561 (pp20) REVERT: C 719 CYS cc_start: 0.9209 (t) cc_final: 0.8799 (m) REVERT: C 817 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8168 (tp) REVERT: C 886 ASP cc_start: 0.8206 (m-30) cc_final: 0.7820 (m-30) REVERT: C 1026 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7295 (ppp) REVERT: C 1052 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.7937 (p0) REVERT: C 1140 GLU cc_start: 0.8757 (pp20) cc_final: 0.8267 (pp20) REVERT: D 134 MET cc_start: 0.8834 (tpt) cc_final: 0.8393 (tpt) REVERT: D 388 MET cc_start: 0.8692 (ptp) cc_final: 0.8398 (ptp) REVERT: D 481 GLU cc_start: 0.9070 (pp20) cc_final: 0.8587 (pp20) REVERT: D 886 ASP cc_start: 0.8215 (m-30) cc_final: 0.7811 (m-30) REVERT: D 1026 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7288 (ppp) REVERT: D 1140 GLU cc_start: 0.8814 (pp20) cc_final: 0.8313 (pp20) outliers start: 138 outliers final: 98 residues processed: 455 average time/residue: 0.1827 time to fit residues: 145.1628 Evaluate side-chains 441 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 336 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 621 CYS Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1065 TYR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 816 ASN Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 942 ILE Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1057 ASN Chi-restraints excluded: chain B residue 1065 TYR Chi-restraints excluded: chain B residue 1090 HIS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 703 SER Chi-restraints excluded: chain C residue 816 ASN Chi-restraints excluded: chain C residue 817 ILE Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 862 TYR Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 942 ILE Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1052 ASN Chi-restraints excluded: chain C residue 1057 ASN Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1099 PHE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 224 HIS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 485 CYS Chi-restraints excluded: chain D residue 703 SER Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 830 VAL Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 942 ILE Chi-restraints excluded: chain D residue 950 LEU Chi-restraints excluded: chain D residue 991 TYR Chi-restraints excluded: chain D residue 1026 MET Chi-restraints excluded: chain D residue 1057 ASN Chi-restraints excluded: chain D residue 1065 TYR Chi-restraints excluded: chain D residue 1099 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 59 optimal weight: 0.7980 chunk 27 optimal weight: 0.0980 chunk 464 optimal weight: 0.0870 chunk 98 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 402 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 483 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 overall best weight: 0.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 HIS A1157 GLN B 816 ASN C 816 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.153629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.117260 restraints weight = 67362.735| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.88 r_work: 0.3375 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 36360 Z= 0.105 Angle : 0.528 8.885 49872 Z= 0.272 Chirality : 0.039 0.154 5920 Planarity : 0.004 0.090 6344 Dihedral : 4.415 46.611 5380 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.93 % Allowed : 18.30 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.12), residues: 5008 helix: 1.41 (0.10), residues: 2536 sheet: -0.22 (0.29), residues: 364 loop : -2.13 (0.12), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 945 TYR 0.014 0.001 TYR A1089 PHE 0.029 0.001 PHE A 550 TRP 0.018 0.001 TRP A 43 HIS 0.004 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (36356) covalent geometry : angle 0.52850 / 0.27 (49864) SS BOND : bond 0.00222 / 0.11 ( 4) SS BOND : angle 0.42664 / 0.23 ( 8) hydrogen bonds : bond 0.04092 / 2.86 ( 1784) hydrogen bonds : angle 3.88992 / 2.76 ( 5364) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 389 time to evaluate : 1.410 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 118 TYR cc_start: 0.9028 (p90) cc_final: 0.8619 (p90) REVERT: A 196 MET cc_start: 0.8407 (mmp) cc_final: 0.8175 (mmp) REVERT: A 199 ARG cc_start: 0.8348 (ptm160) cc_final: 0.7703 (tmm-80) REVERT: A 719 CYS cc_start: 0.9304 (t) cc_final: 0.8797 (m) REVERT: A 862 TYR cc_start: 0.7450 (OUTLIER) cc_final: 0.6699 (t80) REVERT: A 947 MET cc_start: 0.7100 (tmm) cc_final: 0.6838 (ttt) REVERT: A 1026 MET cc_start: 0.8046 (ppp) cc_final: 0.7792 (ptp) REVERT: A 1052 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7768 (p0) REVERT: A 1140 GLU cc_start: 0.8571 (pp20) cc_final: 0.8129 (pp20) REVERT: A 1153 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8410 (tm-30) REVERT: B 404 ASP cc_start: 0.8709 (t70) cc_final: 0.8453 (t0) REVERT: B 481 GLU cc_start: 0.8941 (pp20) cc_final: 0.8678 (pp20) REVERT: B 719 CYS cc_start: 0.9317 (t) cc_final: 0.8819 (m) REVERT: B 816 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8288 (m-40) REVERT: B 862 TYR cc_start: 0.6782 (OUTLIER) cc_final: 0.6186 (t80) REVERT: B 886 ASP cc_start: 0.8110 (m-30) cc_final: 0.7674 (m-30) REVERT: B 892 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8227 (mm) REVERT: B 947 MET cc_start: 0.7389 (tmm) cc_final: 0.7075 (tmm) REVERT: B 1140 GLU cc_start: 0.8567 (pp20) cc_final: 0.8277 (pp20) REVERT: C 199 ARG cc_start: 0.8505 (ptm160) cc_final: 0.7917 (tmm-80) REVERT: C 481 GLU cc_start: 0.8941 (pp20) cc_final: 0.8685 (pp20) REVERT: C 719 CYS cc_start: 0.9281 (t) cc_final: 0.8785 (m) REVERT: C 862 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6538 (t80) REVERT: C 886 ASP cc_start: 0.8003 (m-30) cc_final: 0.7592 (m-30) REVERT: C 947 MET cc_start: 0.7320 (tmm) cc_final: 0.7021 (tmm) REVERT: C 1052 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7741 (p0) REVERT: C 1140 GLU cc_start: 0.8576 (pp20) cc_final: 0.8124 (pp20) REVERT: D 199 ARG cc_start: 0.8496 (ptm160) cc_final: 0.7905 (tmm-80) REVERT: D 388 MET cc_start: 0.8480 (ptp) cc_final: 0.8195 (ptp) REVERT: D 481 GLU cc_start: 0.8921 (pp20) cc_final: 0.8669 (pp20) REVERT: D 862 TYR cc_start: 0.7151 (OUTLIER) cc_final: 0.6380 (t80) REVERT: D 886 ASP cc_start: 0.7991 (m-30) cc_final: 0.7559 (m-30) REVERT: D 927 MET cc_start: 0.9135 (mtm) cc_final: 0.8911 (mtm) REVERT: D 1140 GLU cc_start: 0.8610 (pp20) cc_final: 0.8164 (pp20) outliers start: 83 outliers final: 49 residues processed: 444 average time/residue: 0.1822 time to fit residues: 141.8287 Evaluate side-chains 406 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 349 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1057 ASN Chi-restraints excluded: chain A residue 1065 TYR Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 816 ASN Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain B residue 1057 ASN Chi-restraints excluded: chain B residue 1065 TYR Chi-restraints excluded: chain B residue 1090 HIS Chi-restraints excluded: chain B residue 1121 HIS Chi-restraints excluded: chain B residue 1257 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 703 SER Chi-restraints excluded: chain C residue 862 TYR Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1052 ASN Chi-restraints excluded: chain C residue 1057 ASN Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1257 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 224 HIS Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 703 SER Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 1057 ASN Chi-restraints excluded: chain D residue 1065 TYR Chi-restraints excluded: chain D residue 1257 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 17 optimal weight: 9.9990 chunk 257 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 336 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 400 optimal weight: 0.0030 chunk 104 optimal weight: 3.9990 chunk 34 optimal weight: 0.0270 chunk 129 optimal weight: 9.9990 overall best weight: 1.6052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 969 GLN A1157 GLN B 816 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.152815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.116539 restraints weight = 66963.703| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.59 r_work: 0.3368 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36360 Z= 0.124 Angle : 0.533 9.368 49872 Z= 0.271 Chirality : 0.040 0.157 5920 Planarity : 0.004 0.095 6344 Dihedral : 4.165 46.221 5376 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.75 % Allowed : 18.79 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.12), residues: 5008 helix: 1.58 (0.10), residues: 2536 sheet: -0.11 (0.28), residues: 364 loop : -2.04 (0.12), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 945 TYR 0.014 0.001 TYR A1089 PHE 0.022 0.001 PHE A 550 TRP 0.016 0.001 TRP D 43 HIS 0.009 0.001 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (36356) covalent geometry : angle 0.53280 / 0.27 (49864) SS BOND : bond 0.00209 / 0.10 ( 4) SS BOND : angle 0.22759 / 0.12 ( 8) hydrogen bonds : bond 0.04164 / 2.90 ( 1784) hydrogen bonds : angle 3.80448 / 2.70 ( 5364) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 364 time to evaluate : 1.452 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 118 TYR cc_start: 0.9073 (p90) cc_final: 0.8640 (p90) REVERT: A 196 MET cc_start: 0.8410 (mmp) cc_final: 0.8139 (mmp) REVERT: A 199 ARG cc_start: 0.8399 (ptm160) cc_final: 0.7747 (tmm-80) REVERT: A 719 CYS cc_start: 0.9264 (t) cc_final: 0.8789 (m) REVERT: A 862 TYR cc_start: 0.7589 (OUTLIER) cc_final: 0.6798 (t80) REVERT: A 1026 MET cc_start: 0.8051 (ppp) cc_final: 0.7777 (ppp) REVERT: A 1052 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7840 (p0) REVERT: A 1140 GLU cc_start: 0.8646 (pp20) cc_final: 0.8175 (pp20) REVERT: B 404 ASP cc_start: 0.8710 (t70) cc_final: 0.8450 (t0) REVERT: B 481 GLU cc_start: 0.8949 (pp20) cc_final: 0.8662 (pp20) REVERT: B 719 CYS cc_start: 0.9274 (t) cc_final: 0.8797 (m) REVERT: B 816 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8333 (m-40) REVERT: B 862 TYR cc_start: 0.6820 (OUTLIER) cc_final: 0.6201 (t80) REVERT: B 886 ASP cc_start: 0.8160 (m-30) cc_final: 0.7719 (m-30) REVERT: B 892 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8221 (mm) REVERT: B 947 MET cc_start: 0.7336 (tmm) cc_final: 0.7019 (tmm) REVERT: B 1140 GLU cc_start: 0.8615 (pp20) cc_final: 0.8301 (pp20) REVERT: C 481 GLU cc_start: 0.8945 (pp20) cc_final: 0.8652 (pp20) REVERT: C 719 CYS cc_start: 0.9243 (t) cc_final: 0.8776 (m) REVERT: C 862 TYR cc_start: 0.7304 (OUTLIER) cc_final: 0.6549 (t80) REVERT: C 886 ASP cc_start: 0.8018 (m-30) cc_final: 0.7613 (m-30) REVERT: C 947 MET cc_start: 0.7301 (tmm) cc_final: 0.6984 (tmm) REVERT: C 1052 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7753 (p0) REVERT: C 1140 GLU cc_start: 0.8635 (pp20) cc_final: 0.8188 (pp20) REVERT: D 134 MET cc_start: 0.8623 (tpt) cc_final: 0.8201 (tpt) REVERT: D 388 MET cc_start: 0.8431 (ptp) cc_final: 0.8140 (ptp) REVERT: D 481 GLU cc_start: 0.8946 (pp20) cc_final: 0.8651 (pp20) REVERT: D 862 TYR cc_start: 0.7175 (OUTLIER) cc_final: 0.6465 (t80) REVERT: D 886 ASP cc_start: 0.8016 (m-30) cc_final: 0.7580 (m-30) REVERT: D 1140 GLU cc_start: 0.8658 (pp20) cc_final: 0.8194 (pp20) outliers start: 78 outliers final: 55 residues processed: 420 average time/residue: 0.1746 time to fit residues: 129.3142 Evaluate side-chains 416 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 353 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1057 ASN Chi-restraints excluded: chain A residue 1065 TYR Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 816 ASN Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain B residue 1057 ASN Chi-restraints excluded: chain B residue 1065 TYR Chi-restraints excluded: chain B residue 1090 HIS Chi-restraints excluded: chain B residue 1121 HIS Chi-restraints excluded: chain B residue 1257 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 703 SER Chi-restraints excluded: chain C residue 862 TYR Chi-restraints excluded: chain C residue 994 ILE Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1052 ASN Chi-restraints excluded: chain C residue 1057 ASN Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1257 LEU Chi-restraints excluded: chain D residue 224 HIS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 485 CYS Chi-restraints excluded: chain D residue 703 SER Chi-restraints excluded: chain D residue 830 VAL Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 991 TYR Chi-restraints excluded: chain D residue 1057 ASN Chi-restraints excluded: chain D residue 1065 TYR Chi-restraints excluded: chain D residue 1257 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 204 optimal weight: 6.9990 chunk 369 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 349 optimal weight: 20.0000 chunk 366 optimal weight: 0.0070 chunk 341 optimal weight: 0.5980 chunk 331 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 overall best weight: 2.1204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 816 ASN C 816 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.152293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.115982 restraints weight = 67061.217| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.58 r_work: 0.3360 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36360 Z= 0.143 Angle : 0.543 9.312 49872 Z= 0.276 Chirality : 0.040 0.170 5920 Planarity : 0.004 0.099 6344 Dihedral : 4.098 45.846 5374 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.64 % Allowed : 19.04 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.12), residues: 5008 helix: 1.60 (0.10), residues: 2536 sheet: -0.13 (0.28), residues: 364 loop : -2.03 (0.12), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1092 TYR 0.015 0.001 TYR A1089 PHE 0.024 0.001 PHE A 550 TRP 0.016 0.001 TRP D 43 HIS 0.007 0.001 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (36356) covalent geometry : angle 0.54302 / 0.28 (49864) SS BOND : bond 0.00215 / 0.11 ( 4) SS BOND : angle 0.25512 / 0.14 ( 8) hydrogen bonds : bond 0.04265 / 2.97 ( 1784) hydrogen bonds : angle 3.80651 / 2.70 ( 5364) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 357 time to evaluate : 1.421 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 118 TYR cc_start: 0.9055 (p90) cc_final: 0.8633 (p90) REVERT: A 199 ARG cc_start: 0.8403 (ptm160) cc_final: 0.7766 (tmm-80) REVERT: A 719 CYS cc_start: 0.9282 (t) cc_final: 0.8786 (m) REVERT: A 862 TYR cc_start: 0.7605 (OUTLIER) cc_final: 0.6771 (t80) REVERT: A 1026 MET cc_start: 0.8091 (ppp) cc_final: 0.7814 (ppp) REVERT: A 1052 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7857 (p0) REVERT: A 1140 GLU cc_start: 0.8662 (pp20) cc_final: 0.8190 (pp20) REVERT: B 404 ASP cc_start: 0.8720 (t70) cc_final: 0.8455 (t0) REVERT: B 481 GLU cc_start: 0.8974 (pp20) cc_final: 0.8661 (pp20) REVERT: B 719 CYS cc_start: 0.9295 (t) cc_final: 0.8816 (m) REVERT: B 862 TYR cc_start: 0.6894 (OUTLIER) cc_final: 0.6238 (t80) REVERT: B 886 ASP cc_start: 0.8172 (m-30) cc_final: 0.7732 (m-30) REVERT: B 892 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8232 (mm) REVERT: B 947 MET cc_start: 0.7314 (tmm) cc_final: 0.6989 (tmm) REVERT: B 1140 GLU cc_start: 0.8613 (pp20) cc_final: 0.8305 (pp20) REVERT: C 481 GLU cc_start: 0.8976 (pp20) cc_final: 0.8668 (pp20) REVERT: C 719 CYS cc_start: 0.9256 (t) cc_final: 0.8775 (m) REVERT: C 862 TYR cc_start: 0.7348 (OUTLIER) cc_final: 0.6611 (t80) REVERT: C 886 ASP cc_start: 0.8046 (m-30) cc_final: 0.7641 (m-30) REVERT: C 947 MET cc_start: 0.7225 (tmm) cc_final: 0.6997 (tmm) REVERT: C 1052 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7773 (p0) REVERT: C 1140 GLU cc_start: 0.8633 (pp20) cc_final: 0.8175 (pp20) REVERT: D 134 MET cc_start: 0.8639 (tpt) cc_final: 0.8218 (tpt) REVERT: D 388 MET cc_start: 0.8456 (ptp) cc_final: 0.8165 (ptp) REVERT: D 481 GLU cc_start: 0.8973 (pp20) cc_final: 0.8662 (pp20) REVERT: D 862 TYR cc_start: 0.7145 (OUTLIER) cc_final: 0.6393 (t80) REVERT: D 886 ASP cc_start: 0.8025 (m-30) cc_final: 0.7596 (m-30) REVERT: D 1140 GLU cc_start: 0.8662 (pp20) cc_final: 0.8193 (pp20) outliers start: 75 outliers final: 63 residues processed: 415 average time/residue: 0.1767 time to fit residues: 129.0868 Evaluate side-chains 417 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 347 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1057 ASN Chi-restraints excluded: chain A residue 1065 TYR Chi-restraints excluded: chain A residue 1090 HIS Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain B residue 1057 ASN Chi-restraints excluded: chain B residue 1065 TYR Chi-restraints excluded: chain B residue 1090 HIS Chi-restraints excluded: chain B residue 1121 HIS Chi-restraints excluded: chain B residue 1257 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 862 TYR Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 994 ILE Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1052 ASN Chi-restraints excluded: chain C residue 1057 ASN Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1257 LEU Chi-restraints excluded: chain D residue 224 HIS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 383 GLN Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 485 CYS Chi-restraints excluded: chain D residue 703 SER Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 991 TYR Chi-restraints excluded: chain D residue 1057 ASN Chi-restraints excluded: chain D residue 1065 TYR Chi-restraints excluded: chain D residue 1257 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 467 optimal weight: 0.5980 chunk 466 optimal weight: 1.9990 chunk 415 optimal weight: 0.0470 chunk 305 optimal weight: 3.9990 chunk 379 optimal weight: 9.9990 chunk 318 optimal weight: 10.0000 chunk 408 optimal weight: 2.9990 chunk 326 optimal weight: 0.9980 chunk 462 optimal weight: 0.0020 chunk 300 optimal weight: 0.7980 chunk 390 optimal weight: 5.9990 overall best weight: 0.4886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 GLN ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.156814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.118954 restraints weight = 66986.513| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 3.29 r_work: 0.3433 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 36360 Z= 0.093 Angle : 0.510 9.929 49872 Z= 0.255 Chirality : 0.039 0.148 5920 Planarity : 0.004 0.094 6344 Dihedral : 3.761 31.288 5372 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.83 % Allowed : 20.17 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.12), residues: 5008 helix: 1.85 (0.10), residues: 2544 sheet: 0.02 (0.28), residues: 364 loop : -2.06 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 675 TYR 0.012 0.001 TYR C1089 PHE 0.026 0.001 PHE A 550 TRP 0.019 0.001 TRP D 43 HIS 0.005 0.001 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 (36356) covalent geometry : angle 0.51002 / 0.25 (49864) SS BOND : bond 0.00175 / 0.09 ( 4) SS BOND : angle 0.50007 / 0.27 ( 8) hydrogen bonds : bond 0.03161 / 2.21 ( 1784) hydrogen bonds : angle 3.59489 / 2.56 ( 5364) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 402 time to evaluate : 1.269 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 118 TYR cc_start: 0.9021 (p90) cc_final: 0.8601 (p90) REVERT: A 199 ARG cc_start: 0.8320 (ptm160) cc_final: 0.7685 (tmm-80) REVERT: A 593 ASP cc_start: 0.8557 (t0) cc_final: 0.8292 (t70) REVERT: A 719 CYS cc_start: 0.9254 (t) cc_final: 0.8759 (m) REVERT: A 862 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.6634 (t80) REVERT: A 1026 MET cc_start: 0.8155 (ppp) cc_final: 0.7773 (ptp) REVERT: A 1140 GLU cc_start: 0.8505 (pp20) cc_final: 0.8078 (pp20) REVERT: B 404 ASP cc_start: 0.8629 (t70) cc_final: 0.8328 (t0) REVERT: B 481 GLU cc_start: 0.8863 (pp20) cc_final: 0.8633 (pp20) REVERT: B 719 CYS cc_start: 0.9241 (t) cc_final: 0.8737 (m) REVERT: B 727 PRO cc_start: 0.8239 (Cg_exo) cc_final: 0.7938 (Cg_endo) REVERT: B 862 TYR cc_start: 0.6751 (OUTLIER) cc_final: 0.6285 (t80) REVERT: B 886 ASP cc_start: 0.7990 (m-30) cc_final: 0.7541 (m-30) REVERT: B 1140 GLU cc_start: 0.8528 (pp20) cc_final: 0.8233 (pp20) REVERT: C 481 GLU cc_start: 0.8859 (pp20) cc_final: 0.8643 (pp20) REVERT: C 658 GLU cc_start: 0.8326 (tt0) cc_final: 0.8079 (tt0) REVERT: C 719 CYS cc_start: 0.9211 (t) cc_final: 0.8721 (m) REVERT: C 862 TYR cc_start: 0.7102 (OUTLIER) cc_final: 0.6502 (t80) REVERT: C 886 ASP cc_start: 0.7924 (m-30) cc_final: 0.7526 (m-30) REVERT: C 1140 GLU cc_start: 0.8464 (pp20) cc_final: 0.8125 (pp20) REVERT: D 134 MET cc_start: 0.8600 (tpt) cc_final: 0.8208 (tpt) REVERT: D 352 MET cc_start: 0.7748 (mtm) cc_final: 0.7184 (ttm) REVERT: D 388 MET cc_start: 0.8173 (ptp) cc_final: 0.7961 (ptp) REVERT: D 404 ASP cc_start: 0.8698 (t70) cc_final: 0.8399 (t0) REVERT: D 481 GLU cc_start: 0.8861 (pp20) cc_final: 0.8642 (pp20) REVERT: D 862 TYR cc_start: 0.7041 (OUTLIER) cc_final: 0.6416 (t80) REVERT: D 886 ASP cc_start: 0.7963 (m-30) cc_final: 0.7534 (m-30) REVERT: D 1140 GLU cc_start: 0.8519 (pp20) cc_final: 0.8159 (pp20) outliers start: 52 outliers final: 40 residues processed: 439 average time/residue: 0.1879 time to fit residues: 146.0102 Evaluate side-chains 418 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 374 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1057 ASN Chi-restraints excluded: chain A residue 1065 TYR Chi-restraints excluded: chain A residue 1090 HIS Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 1057 ASN Chi-restraints excluded: chain B residue 1065 TYR Chi-restraints excluded: chain B residue 1090 HIS Chi-restraints excluded: chain B residue 1257 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 862 TYR Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 1057 ASN Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1257 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 485 CYS Chi-restraints excluded: chain D residue 703 SER Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 991 TYR Chi-restraints excluded: chain D residue 1057 ASN Chi-restraints excluded: chain D residue 1065 TYR Chi-restraints excluded: chain D residue 1257 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 344 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 232 optimal weight: 0.1980 chunk 446 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 248 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 171 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 443 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.155930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.118815 restraints weight = 66795.445| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 3.72 r_work: 0.3424 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 36360 Z= 0.092 Angle : 0.511 10.163 49872 Z= 0.254 Chirality : 0.039 0.136 5920 Planarity : 0.004 0.077 6344 Dihedral : 3.657 31.366 5372 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.83 % Allowed : 20.87 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.12), residues: 5008 helix: 1.95 (0.10), residues: 2560 sheet: 0.10 (0.29), residues: 364 loop : -1.98 (0.12), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 945 TYR 0.013 0.001 TYR A1089 PHE 0.024 0.001 PHE A 550 TRP 0.033 0.001 TRP A 43 HIS 0.004 0.001 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (36356) covalent geometry : angle 0.51062 / 0.25 (49864) SS BOND : bond 0.00148 / 0.07 ( 4) SS BOND : angle 0.34596 / 0.19 ( 8) hydrogen bonds : bond 0.03208 / 2.24 ( 1784) hydrogen bonds : angle 3.52837 / 2.52 ( 5364) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8498.45 seconds wall clock time: 145 minutes 47.29 seconds (8747.29 seconds total)