Starting phenix.real_space_refine on Sun Feb 8 02:38:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srb_40725/02_2026/8srb_40725.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srb_40725/02_2026/8srb_40725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8srb_40725/02_2026/8srb_40725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srb_40725/02_2026/8srb_40725.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8srb_40725/02_2026/8srb_40725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srb_40725/02_2026/8srb_40725.map" } resolution = 2.82 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= 0.137 sd= 1.465 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 204 5.16 5 C 25384 2.51 5 N 6840 2.21 5 O 6948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39384 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1349, 9726 Classifications: {'peptide': 1349} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 287} Link IDs: {'PTRANS': 55, 'TRANS': 1293} Chain breaks: 4 Unresolved non-hydrogen bonds: 1027 Unresolved non-hydrogen angles: 1293 Unresolved non-hydrogen dihedrals: 848 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'ARG:plan': 19, 'GLN:plan1': 16, 'GLU:plan': 37, 'ASP:plan': 46, 'ASN:plan1': 16, 'HIS:plan': 5, 'TYR:plan': 7, 'PHE:plan': 7, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 663 Chain: "D" Number of atoms: 9726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1349, 9726 Classifications: {'peptide': 1349} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 287} Link IDs: {'PTRANS': 55, 'TRANS': 1293} Chain breaks: 4 Unresolved non-hydrogen bonds: 1027 Unresolved non-hydrogen angles: 1293 Unresolved non-hydrogen dihedrals: 848 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'ARG:plan': 19, 'GLN:plan1': 16, 'GLU:plan': 37, 'ASP:plan': 46, 'ASN:plan1': 16, 'HIS:plan': 5, 'TYR:plan': 7, 'PHE:plan': 7, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 663 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 120 Unusual residues: {'APR': 1, 'CLR': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 120 Unusual residues: {'APR': 1, 'CLR': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B, C Time building chain proxies: 14.87, per 1000 atoms: 0.38 Number of scatterers: 39384 At special positions: 0 Unit cell: (152.81, 152.81, 184.198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 204 16.00 P 8 15.00 O 6948 8.00 N 6840 7.00 C 25384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 997 " - pdb=" SG CYS A1006 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 376 " distance=0.00 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 399 " distance=0.00 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 446 " distance=0.00 Simple disulfide: pdb=" SG CYS B 609 " - pdb=" SG CYS B 609 " distance=0.00 Simple disulfide: pdb=" SG CYS B 676 " - pdb=" SG CYS B 676 " distance=0.00 Simple disulfide: pdb=" SG CYS B 817 " - pdb=" SG CYS B 817 " distance=0.00 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.03 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B 997 " distance=0.00 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.03 Simple disulfide: pdb=" SG CYS B1006 " - pdb=" SG CYS B 997 " distance=2.03 Simple disulfide: pdb=" SG CYS B1006 " - pdb=" SG CYS B1006 " distance=0.00 Simple disulfide: pdb=" SG CYS B1060 " - pdb=" SG CYS B1060 " distance=0.00 Simple disulfide: pdb=" SG CYS B1439 " - pdb=" SG CYS B1439 " distance=0.00 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.03 Simple disulfide: pdb=" SG CYS C 997 " - pdb=" SG CYS C1006 " distance=2.03 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: 3.51 Conformation dependent library (CDL) restraints added in 1.5 seconds 10712 Ramachandran restraints generated. 5356 Oldfield, 0 Emsley, 5356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10160 Finding SS restraints... Secondary structure from input PDB file: 232 helices and 40 sheets defined 60.0% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 118 through 135 removed outlier: 3.800A pdb=" N ALA A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 187 through 203 removed outlier: 4.193A pdb=" N ALA A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 323 through 337 removed outlier: 3.554A pdb=" N ASN A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.560A pdb=" N PHE A 342 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 362 through 377 removed outlier: 3.604A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'A' and resid 410 through 421 removed outlier: 3.765A pdb=" N LYS A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.501A pdb=" N ALA A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 457 removed outlier: 3.555A pdb=" N ILE A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASN A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 469 Processing helix chain 'A' and resid 472 through 476 removed outlier: 3.682A pdb=" N LEU A 476 " --> pdb=" O ILE A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 494 through 509 Processing helix chain 'A' and resid 513 through 522 removed outlier: 3.619A pdb=" N ARG A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 553 Processing helix chain 'A' and resid 556 through 569 Processing helix chain 'A' and resid 577 through 586 removed outlier: 3.946A pdb=" N ILE A 580 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N SER A 583 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS A 584 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 585 " --> pdb=" O ASP A 582 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 586 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 removed outlier: 3.572A pdb=" N THR A 596 " --> pdb=" O GLN A 592 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 599 " --> pdb=" O ARG A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 623 Processing helix chain 'A' and resid 625 through 642 removed outlier: 3.657A pdb=" N THR A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 647 removed outlier: 3.696A pdb=" N GLN A 647 " --> pdb=" O ARG A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 651 through 680 Processing helix chain 'A' and resid 680 through 689 Processing helix chain 'A' and resid 699 through 707 Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 715 through 727 Processing helix chain 'A' and resid 735 through 745 Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.688A pdb=" N VAL A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 745 through 750' Processing helix chain 'A' and resid 792 through 799 removed outlier: 3.512A pdb=" N TYR A 799 " --> pdb=" O PHE A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 826 Processing helix chain 'A' and resid 833 through 856 Processing helix chain 'A' and resid 859 through 866 removed outlier: 3.903A pdb=" N ASP A 866 " --> pdb=" O GLU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 889 removed outlier: 3.630A pdb=" N ARG A 870 " --> pdb=" O ASP A 866 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 917 removed outlier: 3.999A pdb=" N PHE A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 908 " --> pdb=" O ALA A 904 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 909 " --> pdb=" O PHE A 905 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 914 " --> pdb=" O LEU A 910 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET A 915 " --> pdb=" O TRP A 911 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 916 " --> pdb=" O LEU A 912 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR A 917 " --> pdb=" O ARG A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 961 removed outlier: 3.838A pdb=" N LYS A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LYS A 936 " --> pdb=" O MET A 932 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASP A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 981 removed outlier: 3.716A pdb=" N PHE A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 982 through 984 No H-bonds generated for 'chain 'A' and resid 982 through 984' Processing helix chain 'A' and resid 987 through 995 Processing helix chain 'A' and resid 1010 through 1012 No H-bonds generated for 'chain 'A' and resid 1010 through 1012' Processing helix chain 'A' and resid 1013 through 1026 Processing helix chain 'A' and resid 1028 through 1066 removed outlier: 5.680A pdb=" N GLU A1046 " --> pdb=" O MET A1042 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ALA A1047 " --> pdb=" O LYS A1043 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR A1057 " --> pdb=" O ARG A1053 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP A1065 " --> pdb=" O ALA A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1072 No H-bonds generated for 'chain 'A' and resid 1070 through 1072' Processing helix chain 'A' and resid 1073 through 1090 removed outlier: 3.924A pdb=" N ALA A1077 " --> pdb=" O PHE A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1130 Processing helix chain 'A' and resid 1131 through 1165 Processing helix chain 'A' and resid 1166 through 1168 No H-bonds generated for 'chain 'A' and resid 1166 through 1168' Processing helix chain 'A' and resid 1255 through 1260 Processing helix chain 'A' and resid 1378 through 1391 Processing helix chain 'A' and resid 1403 through 1414 Processing helix chain 'A' and resid 1447 through 1452 removed outlier: 3.708A pdb=" N ARG A1452 " --> pdb=" O ARG A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1491 removed outlier: 3.567A pdb=" N LEU A1482 " --> pdb=" O SER A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 77 Processing helix chain 'B' and resid 118 through 135 removed outlier: 3.800A pdb=" N ALA B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 176 Processing helix chain 'B' and resid 187 through 203 removed outlier: 4.193A pdb=" N ALA B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 271 through 286 Processing helix chain 'B' and resid 298 through 311 Processing helix chain 'B' and resid 323 through 337 removed outlier: 3.554A pdb=" N ASN B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.560A pdb=" N PHE B 342 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 359 Processing helix chain 'B' and resid 362 through 377 removed outlier: 3.604A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 408 Processing helix chain 'B' and resid 410 through 421 removed outlier: 3.765A pdb=" N LYS B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.502A pdb=" N ALA B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 457 removed outlier: 3.555A pdb=" N ILE B 443 " --> pdb=" O GLN B 439 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASN B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 469 Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.682A pdb=" N LEU B 476 " --> pdb=" O ILE B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 494 through 509 Processing helix chain 'B' and resid 513 through 522 removed outlier: 3.619A pdb=" N ARG B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 553 Processing helix chain 'B' and resid 556 through 569 Processing helix chain 'B' and resid 577 through 586 removed outlier: 3.946A pdb=" N ILE B 580 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N SER B 583 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS B 584 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR B 585 " --> pdb=" O ASP B 582 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP B 586 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 610 removed outlier: 3.572A pdb=" N THR B 596 " --> pdb=" O GLN B 592 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA B 599 " --> pdb=" O ARG B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 623 Processing helix chain 'B' and resid 625 through 642 removed outlier: 3.657A pdb=" N THR B 642 " --> pdb=" O GLU B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 647 removed outlier: 3.696A pdb=" N GLN B 647 " --> pdb=" O ARG B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 650 No H-bonds generated for 'chain 'B' and resid 648 through 650' Processing helix chain 'B' and resid 651 through 680 Processing helix chain 'B' and resid 680 through 689 Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 709 through 714 Processing helix chain 'B' and resid 715 through 727 Processing helix chain 'B' and resid 735 through 745 Processing helix chain 'B' and resid 745 through 750 removed outlier: 3.688A pdb=" N VAL B 749 " --> pdb=" O PHE B 745 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 750 " --> pdb=" O PRO B 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 745 through 750' Processing helix chain 'B' and resid 792 through 799 removed outlier: 3.512A pdb=" N TYR B 799 " --> pdb=" O PHE B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 826 Processing helix chain 'B' and resid 833 through 856 Processing helix chain 'B' and resid 859 through 866 removed outlier: 3.902A pdb=" N ASP B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 889 removed outlier: 3.629A pdb=" N ARG B 870 " --> pdb=" O ASP B 866 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP B 889 " --> pdb=" O THR B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 917 removed outlier: 3.999A pdb=" N PHE B 905 " --> pdb=" O GLY B 901 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 908 " --> pdb=" O ALA B 904 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 909 " --> pdb=" O PHE B 905 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE B 914 " --> pdb=" O LEU B 910 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET B 915 " --> pdb=" O TRP B 911 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 916 " --> pdb=" O LEU B 912 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR B 917 " --> pdb=" O ARG B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 961 removed outlier: 3.838A pdb=" N LYS B 927 " --> pdb=" O ASN B 923 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LYS B 936 " --> pdb=" O MET B 932 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASP B 937 " --> pdb=" O GLU B 933 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE B 947 " --> pdb=" O PHE B 943 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 981 removed outlier: 3.716A pdb=" N PHE B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 982 through 984 No H-bonds generated for 'chain 'B' and resid 982 through 984' Processing helix chain 'B' and resid 987 through 995 Processing helix chain 'B' and resid 1010 through 1012 No H-bonds generated for 'chain 'B' and resid 1010 through 1012' Processing helix chain 'B' and resid 1013 through 1026 Processing helix chain 'B' and resid 1028 through 1066 removed outlier: 5.679A pdb=" N GLU B1046 " --> pdb=" O MET B1042 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ALA B1047 " --> pdb=" O LYS B1043 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR B1057 " --> pdb=" O ARG B1053 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP B1065 " --> pdb=" O ALA B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1072 No H-bonds generated for 'chain 'B' and resid 1070 through 1072' Processing helix chain 'B' and resid 1073 through 1090 removed outlier: 3.924A pdb=" N ALA B1077 " --> pdb=" O PHE B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1102 through 1130 Processing helix chain 'B' and resid 1131 through 1165 Processing helix chain 'B' and resid 1166 through 1168 No H-bonds generated for 'chain 'B' and resid 1166 through 1168' Processing helix chain 'B' and resid 1255 through 1260 Processing helix chain 'B' and resid 1378 through 1391 Processing helix chain 'B' and resid 1403 through 1414 Processing helix chain 'B' and resid 1447 through 1452 removed outlier: 3.708A pdb=" N ARG B1452 " --> pdb=" O ARG B1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 1478 through 1491 removed outlier: 3.567A pdb=" N LEU B1482 " --> pdb=" O SER B1478 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 77 Processing helix chain 'C' and resid 118 through 135 removed outlier: 3.800A pdb=" N ALA C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 176 Processing helix chain 'C' and resid 187 through 203 removed outlier: 4.193A pdb=" N ALA C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 227 Processing helix chain 'C' and resid 271 through 286 Processing helix chain 'C' and resid 298 through 311 Processing helix chain 'C' and resid 323 through 337 removed outlier: 3.554A pdb=" N ASN C 337 " --> pdb=" O ASN C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 343 removed outlier: 3.560A pdb=" N PHE C 342 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 359 Processing helix chain 'C' and resid 362 through 377 removed outlier: 3.604A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 408 Processing helix chain 'C' and resid 410 through 421 removed outlier: 3.765A pdb=" N LYS C 414 " --> pdb=" O LYS C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.502A pdb=" N ALA C 427 " --> pdb=" O GLN C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 457 removed outlier: 3.555A pdb=" N ILE C 443 " --> pdb=" O GLN C 439 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASP C 449 " --> pdb=" O ALA C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 469 Processing helix chain 'C' and resid 472 through 476 removed outlier: 3.683A pdb=" N LEU C 476 " --> pdb=" O ILE C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 494 through 509 Processing helix chain 'C' and resid 513 through 522 removed outlier: 3.619A pdb=" N ARG C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 553 Processing helix chain 'C' and resid 556 through 569 Processing helix chain 'C' and resid 577 through 586 removed outlier: 3.946A pdb=" N ILE C 580 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N SER C 583 " --> pdb=" O ILE C 580 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LYS C 584 " --> pdb=" O TYR C 581 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR C 585 " --> pdb=" O ASP C 582 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP C 586 " --> pdb=" O SER C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 610 removed outlier: 3.573A pdb=" N THR C 596 " --> pdb=" O GLN C 592 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA C 599 " --> pdb=" O ARG C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 623 Processing helix chain 'C' and resid 625 through 642 removed outlier: 3.658A pdb=" N THR C 642 " --> pdb=" O GLU C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 647 removed outlier: 3.697A pdb=" N GLN C 647 " --> pdb=" O ARG C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 651 through 680 Processing helix chain 'C' and resid 680 through 689 Processing helix chain 'C' and resid 699 through 707 Processing helix chain 'C' and resid 709 through 714 Processing helix chain 'C' and resid 715 through 727 Processing helix chain 'C' and resid 735 through 745 Processing helix chain 'C' and resid 745 through 750 removed outlier: 3.688A pdb=" N VAL C 749 " --> pdb=" O PHE C 745 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 750 " --> pdb=" O PRO C 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 745 through 750' Processing helix chain 'C' and resid 792 through 799 removed outlier: 3.512A pdb=" N TYR C 799 " --> pdb=" O PHE C 795 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 826 Processing helix chain 'C' and resid 833 through 856 Processing helix chain 'C' and resid 859 through 866 removed outlier: 3.904A pdb=" N ASP C 866 " --> pdb=" O GLU C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 889 removed outlier: 3.630A pdb=" N ARG C 870 " --> pdb=" O ASP C 866 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP C 889 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 917 removed outlier: 3.999A pdb=" N PHE C 905 " --> pdb=" O GLY C 901 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 908 " --> pdb=" O ALA C 904 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 909 " --> pdb=" O PHE C 905 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE C 914 " --> pdb=" O LEU C 910 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET C 915 " --> pdb=" O TRP C 911 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 916 " --> pdb=" O LEU C 912 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR C 917 " --> pdb=" O ARG C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 961 removed outlier: 3.837A pdb=" N LYS C 927 " --> pdb=" O ASN C 923 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LYS C 936 " --> pdb=" O MET C 932 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASP C 937 " --> pdb=" O GLU C 933 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 981 removed outlier: 3.716A pdb=" N PHE C 971 " --> pdb=" O SER C 967 " (cutoff:3.500A) Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 982 through 984 No H-bonds generated for 'chain 'C' and resid 982 through 984' Processing helix chain 'C' and resid 987 through 995 Processing helix chain 'C' and resid 1010 through 1012 No H-bonds generated for 'chain 'C' and resid 1010 through 1012' Processing helix chain 'C' and resid 1013 through 1026 Processing helix chain 'C' and resid 1028 through 1066 removed outlier: 5.681A pdb=" N GLU C1046 " --> pdb=" O MET C1042 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ALA C1047 " --> pdb=" O LYS C1043 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR C1057 " --> pdb=" O ARG C1053 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP C1065 " --> pdb=" O ALA C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1072 No H-bonds generated for 'chain 'C' and resid 1070 through 1072' Processing helix chain 'C' and resid 1073 through 1090 removed outlier: 3.924A pdb=" N ALA C1077 " --> pdb=" O PHE C1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1130 Processing helix chain 'C' and resid 1131 through 1165 Processing helix chain 'C' and resid 1166 through 1168 No H-bonds generated for 'chain 'C' and resid 1166 through 1168' Processing helix chain 'C' and resid 1255 through 1260 Processing helix chain 'C' and resid 1378 through 1391 Processing helix chain 'C' and resid 1403 through 1414 Processing helix chain 'C' and resid 1447 through 1452 removed outlier: 3.708A pdb=" N ARG C1452 " --> pdb=" O ARG C1448 " (cutoff:3.500A) Processing helix chain 'C' and resid 1478 through 1491 removed outlier: 3.567A pdb=" N LEU C1482 " --> pdb=" O SER C1478 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 77 Processing helix chain 'D' and resid 118 through 135 removed outlier: 3.800A pdb=" N ALA D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 176 Processing helix chain 'D' and resid 187 through 203 removed outlier: 4.194A pdb=" N ALA D 198 " --> pdb=" O GLN D 194 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU D 199 " --> pdb=" O ILE D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 227 Processing helix chain 'D' and resid 271 through 286 Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 323 through 337 removed outlier: 3.553A pdb=" N ASN D 337 " --> pdb=" O ASN D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 343 removed outlier: 3.560A pdb=" N PHE D 342 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 359 Processing helix chain 'D' and resid 362 through 377 removed outlier: 3.604A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'D' and resid 410 through 421 removed outlier: 3.765A pdb=" N LYS D 414 " --> pdb=" O LYS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.501A pdb=" N ALA D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 457 removed outlier: 3.555A pdb=" N ILE D 443 " --> pdb=" O GLN D 439 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASN D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 Processing helix chain 'D' and resid 472 through 476 removed outlier: 3.683A pdb=" N LEU D 476 " --> pdb=" O ILE D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'D' and resid 494 through 509 Processing helix chain 'D' and resid 513 through 522 removed outlier: 3.619A pdb=" N ARG D 517 " --> pdb=" O SER D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 553 Processing helix chain 'D' and resid 556 through 569 Processing helix chain 'D' and resid 577 through 586 removed outlier: 3.946A pdb=" N ILE D 580 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N SER D 583 " --> pdb=" O ILE D 580 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS D 584 " --> pdb=" O TYR D 581 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR D 585 " --> pdb=" O ASP D 582 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP D 586 " --> pdb=" O SER D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 610 removed outlier: 3.572A pdb=" N THR D 596 " --> pdb=" O GLN D 592 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA D 599 " --> pdb=" O ARG D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 623 Processing helix chain 'D' and resid 625 through 642 removed outlier: 3.657A pdb=" N THR D 642 " --> pdb=" O GLU D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 647 removed outlier: 3.696A pdb=" N GLN D 647 " --> pdb=" O ARG D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 650 No H-bonds generated for 'chain 'D' and resid 648 through 650' Processing helix chain 'D' and resid 651 through 680 Processing helix chain 'D' and resid 680 through 689 Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 709 through 714 Processing helix chain 'D' and resid 715 through 727 Processing helix chain 'D' and resid 735 through 745 Processing helix chain 'D' and resid 745 through 750 removed outlier: 3.688A pdb=" N VAL D 749 " --> pdb=" O PHE D 745 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU D 750 " --> pdb=" O PRO D 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 745 through 750' Processing helix chain 'D' and resid 792 through 799 removed outlier: 3.513A pdb=" N TYR D 799 " --> pdb=" O PHE D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 801 through 826 Processing helix chain 'D' and resid 833 through 856 Processing helix chain 'D' and resid 859 through 866 removed outlier: 3.903A pdb=" N ASP D 866 " --> pdb=" O GLU D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 889 removed outlier: 3.630A pdb=" N ARG D 870 " --> pdb=" O ASP D 866 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP D 889 " --> pdb=" O THR D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 917 removed outlier: 4.000A pdb=" N PHE D 905 " --> pdb=" O GLY D 901 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D 908 " --> pdb=" O ALA D 904 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 909 " --> pdb=" O PHE D 905 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 914 " --> pdb=" O LEU D 910 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET D 915 " --> pdb=" O TRP D 911 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG D 916 " --> pdb=" O LEU D 912 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR D 917 " --> pdb=" O ARG D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 961 removed outlier: 3.838A pdb=" N LYS D 927 " --> pdb=" O ASN D 923 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LYS D 936 " --> pdb=" O MET D 932 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASP D 937 " --> pdb=" O GLU D 933 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE D 948 " --> pdb=" O LEU D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 981 removed outlier: 3.716A pdb=" N PHE D 971 " --> pdb=" O SER D 967 " (cutoff:3.500A) Proline residue: D 978 - end of helix Processing helix chain 'D' and resid 982 through 984 No H-bonds generated for 'chain 'D' and resid 982 through 984' Processing helix chain 'D' and resid 987 through 995 Processing helix chain 'D' and resid 1010 through 1012 No H-bonds generated for 'chain 'D' and resid 1010 through 1012' Processing helix chain 'D' and resid 1013 through 1026 Processing helix chain 'D' and resid 1028 through 1066 removed outlier: 5.681A pdb=" N GLU D1046 " --> pdb=" O MET D1042 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ALA D1047 " --> pdb=" O LYS D1043 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR D1057 " --> pdb=" O ARG D1053 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP D1065 " --> pdb=" O ALA D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1070 through 1072 No H-bonds generated for 'chain 'D' and resid 1070 through 1072' Processing helix chain 'D' and resid 1073 through 1090 removed outlier: 3.924A pdb=" N ALA D1077 " --> pdb=" O PHE D1073 " (cutoff:3.500A) Processing helix chain 'D' and resid 1102 through 1130 Processing helix chain 'D' and resid 1131 through 1165 Processing helix chain 'D' and resid 1166 through 1168 No H-bonds generated for 'chain 'D' and resid 1166 through 1168' Processing helix chain 'D' and resid 1255 through 1260 Processing helix chain 'D' and resid 1378 through 1391 Processing helix chain 'D' and resid 1403 through 1414 Processing helix chain 'D' and resid 1447 through 1452 removed outlier: 3.708A pdb=" N ARG D1452 " --> pdb=" O ARG D1448 " (cutoff:3.500A) Processing helix chain 'D' and resid 1478 through 1491 removed outlier: 3.567A pdb=" N LEU D1482 " --> pdb=" O SER D1478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 60 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 181 removed outlier: 6.253A pdb=" N VAL A 179 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE A 213 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR A 181 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N THR A 215 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR A 210 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N LEU A 258 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY A 212 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL A 260 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA A 214 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU A 259 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 111 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ASP A 261 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 113 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE A 233 " --> pdb=" O TRP A 96 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR A 98 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 235 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 149 Processing sheet with id=AA5, first strand: chain 'A' and resid 1251 through 1254 removed outlier: 6.283A pdb=" N VAL A1251 " --> pdb=" O THR A1315 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ARG A1317 " --> pdb=" O VAL A1251 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N TYR A1253 " --> pdb=" O ARG A1317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1279 through 1281 Processing sheet with id=AA7, first strand: chain 'A' and resid 1297 through 1298 removed outlier: 3.991A pdb=" N SER A1297 " --> pdb=" O ILE A1306 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1366 through 1367 removed outlier: 5.351A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 11.329A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 13.952A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 17.823A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLY A1324 " --> pdb=" O TRP A1434 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU A1436 " --> pdb=" O GLY A1324 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ASN A1326 " --> pdb=" O GLU A1436 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR A1438 " --> pdb=" O ASN A1326 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA A1328 " --> pdb=" O THR A1438 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N VAL A1440 " --> pdb=" O ALA A1328 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP A1330 " --> pdb=" O VAL A1440 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N PHE A1442 " --> pdb=" O ASP A1330 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A1332 " --> pdb=" O PHE A1442 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP A1444 " --> pdb=" O VAL A1332 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR A1334 " --> pdb=" O ASP A1444 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A1420 " --> pdb=" O CYS A1439 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN A1441 " --> pdb=" O ILE A1418 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE A1418 " --> pdb=" O ASN A1441 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1370 through 1372 removed outlier: 17.823A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 13.952A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 11.329A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS A1463 " --> pdb=" O GLN A1359 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1346 through 1347 Processing sheet with id=AB2, first strand: chain 'B' and resid 56 through 60 Processing sheet with id=AB3, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AB4, first strand: chain 'B' and resid 179 through 181 removed outlier: 6.253A pdb=" N VAL B 179 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE B 213 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR B 181 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N THR B 215 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR B 210 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N LEU B 258 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLY B 212 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL B 260 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA B 214 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU B 259 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 111 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ASP B 261 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU B 113 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE B 233 " --> pdb=" O TRP B 96 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR B 98 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 235 " --> pdb=" O THR B 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 147 through 149 Processing sheet with id=AB6, first strand: chain 'B' and resid 1251 through 1254 removed outlier: 6.282A pdb=" N VAL B1251 " --> pdb=" O THR B1315 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ARG B1317 " --> pdb=" O VAL B1251 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N TYR B1253 " --> pdb=" O ARG B1317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 1279 through 1281 Processing sheet with id=AB8, first strand: chain 'B' and resid 1297 through 1298 removed outlier: 3.991A pdb=" N SER B1297 " --> pdb=" O ILE B1306 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1366 through 1367 removed outlier: 5.350A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 13.952A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 17.823A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLY B1324 " --> pdb=" O TRP B1434 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU B1436 " --> pdb=" O GLY B1324 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ASN B1326 " --> pdb=" O GLU B1436 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR B1438 " --> pdb=" O ASN B1326 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA B1328 " --> pdb=" O THR B1438 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N VAL B1440 " --> pdb=" O ALA B1328 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP B1330 " --> pdb=" O VAL B1440 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N PHE B1442 " --> pdb=" O ASP B1330 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL B1332 " --> pdb=" O PHE B1442 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP B1444 " --> pdb=" O VAL B1332 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR B1334 " --> pdb=" O ASP B1444 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA B1420 " --> pdb=" O CYS B1439 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN B1441 " --> pdb=" O ILE B1418 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE B1418 " --> pdb=" O ASN B1441 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1370 through 1372 removed outlier: 17.823A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) removed outlier: 13.952A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS B1463 " --> pdb=" O GLN B1359 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1346 through 1347 Processing sheet with id=AC3, first strand: chain 'C' and resid 56 through 60 Processing sheet with id=AC4, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AC5, first strand: chain 'C' and resid 179 through 181 removed outlier: 6.253A pdb=" N VAL C 179 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE C 213 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR C 181 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N THR C 215 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR C 210 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N LEU C 258 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY C 212 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL C 260 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA C 214 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU C 259 " --> pdb=" O PRO C 109 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU C 111 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ASP C 261 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU C 113 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE C 233 " --> pdb=" O TRP C 96 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR C 98 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU C 235 " --> pdb=" O THR C 98 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 147 through 149 Processing sheet with id=AC7, first strand: chain 'C' and resid 1251 through 1254 removed outlier: 6.283A pdb=" N VAL C1251 " --> pdb=" O THR C1315 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ARG C1317 " --> pdb=" O VAL C1251 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N TYR C1253 " --> pdb=" O ARG C1317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 1279 through 1281 Processing sheet with id=AC9, first strand: chain 'C' and resid 1297 through 1298 removed outlier: 3.992A pdb=" N SER C1297 " --> pdb=" O ILE C1306 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1366 through 1367 removed outlier: 5.351A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 13.951A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 17.823A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLY C1324 " --> pdb=" O TRP C1434 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU C1436 " --> pdb=" O GLY C1324 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ASN C1326 " --> pdb=" O GLU C1436 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR C1438 " --> pdb=" O ASN C1326 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA C1328 " --> pdb=" O THR C1438 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N VAL C1440 " --> pdb=" O ALA C1328 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP C1330 " --> pdb=" O VAL C1440 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE C1442 " --> pdb=" O ASP C1330 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL C1332 " --> pdb=" O PHE C1442 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP C1444 " --> pdb=" O VAL C1332 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR C1334 " --> pdb=" O ASP C1444 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA C1420 " --> pdb=" O CYS C1439 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN C1441 " --> pdb=" O ILE C1418 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE C1418 " --> pdb=" O ASN C1441 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1370 through 1372 removed outlier: 17.823A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) removed outlier: 13.951A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS C1463 " --> pdb=" O GLN C1359 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1346 through 1347 Processing sheet with id=AD4, first strand: chain 'D' and resid 56 through 60 Processing sheet with id=AD5, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AD6, first strand: chain 'D' and resid 179 through 181 removed outlier: 6.253A pdb=" N VAL D 179 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE D 213 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR D 181 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N THR D 215 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR D 210 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N LEU D 258 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY D 212 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL D 260 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA D 214 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU D 259 " --> pdb=" O PRO D 109 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU D 111 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ASP D 261 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU D 113 " --> pdb=" O ASP D 261 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE D 233 " --> pdb=" O TRP D 96 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR D 98 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 235 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 147 through 149 Processing sheet with id=AD8, first strand: chain 'D' and resid 1251 through 1254 removed outlier: 6.282A pdb=" N VAL D1251 " --> pdb=" O THR D1315 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ARG D1317 " --> pdb=" O VAL D1251 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N TYR D1253 " --> pdb=" O ARG D1317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 1279 through 1281 Processing sheet with id=AE1, first strand: chain 'D' and resid 1297 through 1298 removed outlier: 3.991A pdb=" N SER D1297 " --> pdb=" O ILE D1306 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1366 through 1367 removed outlier: 5.350A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 11.329A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 13.952A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 17.824A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLY D1324 " --> pdb=" O TRP D1434 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU D1436 " --> pdb=" O GLY D1324 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ASN D1326 " --> pdb=" O GLU D1436 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR D1438 " --> pdb=" O ASN D1326 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA D1328 " --> pdb=" O THR D1438 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N VAL D1440 " --> pdb=" O ALA D1328 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP D1330 " --> pdb=" O VAL D1440 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE D1442 " --> pdb=" O ASP D1330 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL D1332 " --> pdb=" O PHE D1442 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASP D1444 " --> pdb=" O VAL D1332 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR D1334 " --> pdb=" O ASP D1444 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA D1420 " --> pdb=" O CYS D1439 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN D1441 " --> pdb=" O ILE D1418 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE D1418 " --> pdb=" O ASN D1441 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1370 through 1372 removed outlier: 17.824A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 13.952A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 11.329A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS D1463 " --> pdb=" O GLN D1359 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1346 through 1347 2316 hydrogen bonds defined for protein. 6828 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: 10.76 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6328 1.31 - 1.44: 10676 1.44 - 1.57: 22896 1.57 - 1.69: 24 1.69 - 1.82: 368 Bond restraints: 40292 Sorted by residual: bond pdb=" C LEU D 910 " pdb=" O LEU D 910 " ideal model delta sigma weight residual 1.237 1.296 -0.060 1.17e-02 7.31e+03 2.61e+01 bond pdb=" C LEU C 910 " pdb=" O LEU C 910 " ideal model delta sigma weight residual 1.237 1.296 -0.060 1.17e-02 7.31e+03 2.61e+01 bond pdb=" C LEU A 910 " pdb=" O LEU A 910 " ideal model delta sigma weight residual 1.237 1.296 -0.060 1.17e-02 7.31e+03 2.61e+01 bond pdb=" C LEU B 910 " pdb=" O LEU B 910 " ideal model delta sigma weight residual 1.237 1.296 -0.060 1.17e-02 7.31e+03 2.61e+01 bond pdb=" CA SER C 961 " pdb=" CB SER C 961 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.07e-02 8.73e+03 2.45e+01 ... (remaining 40287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 49943 2.79 - 5.58: 4563 5.58 - 8.37: 457 8.37 - 11.17: 49 11.17 - 13.96: 8 Bond angle restraints: 55020 Sorted by residual: angle pdb=" N PRO A 244 " pdb=" CA PRO A 244 " pdb=" C PRO A 244 " ideal model delta sigma weight residual 110.70 124.66 -13.96 1.22e+00 6.72e-01 1.31e+02 angle pdb=" N PRO D 244 " pdb=" CA PRO D 244 " pdb=" C PRO D 244 " ideal model delta sigma weight residual 110.70 124.66 -13.96 1.22e+00 6.72e-01 1.31e+02 angle pdb=" N PRO B 244 " pdb=" CA PRO B 244 " pdb=" C PRO B 244 " ideal model delta sigma weight residual 110.70 124.66 -13.96 1.22e+00 6.72e-01 1.31e+02 angle pdb=" N PRO C 244 " pdb=" CA PRO C 244 " pdb=" C PRO C 244 " ideal model delta sigma weight residual 110.70 124.66 -13.96 1.22e+00 6.72e-01 1.31e+02 angle pdb=" N ALA C 83 " pdb=" CA ALA C 83 " pdb=" C ALA C 83 " ideal model delta sigma weight residual 113.12 103.67 9.45 1.25e+00 6.40e-01 5.72e+01 ... (remaining 55015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 22279 16.81 - 33.61: 1734 33.61 - 50.42: 380 50.42 - 67.22: 56 67.22 - 84.03: 44 Dihedral angle restraints: 24493 sinusoidal: 8829 harmonic: 15664 Sorted by residual: dihedral pdb=" N ASP D1141 " pdb=" C ASP D1141 " pdb=" CA ASP D1141 " pdb=" CB ASP D1141 " ideal model delta harmonic sigma weight residual 122.80 135.48 -12.68 0 2.50e+00 1.60e-01 2.57e+01 dihedral pdb=" N ASP A1141 " pdb=" C ASP A1141 " pdb=" CA ASP A1141 " pdb=" CB ASP A1141 " ideal model delta harmonic sigma weight residual 122.80 135.46 -12.66 0 2.50e+00 1.60e-01 2.56e+01 dihedral pdb=" N ASP B1141 " pdb=" C ASP B1141 " pdb=" CA ASP B1141 " pdb=" CB ASP B1141 " ideal model delta harmonic sigma weight residual 122.80 135.46 -12.66 0 2.50e+00 1.60e-01 2.56e+01 ... (remaining 24490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 4415 0.086 - 0.171: 1554 0.171 - 0.257: 322 0.257 - 0.342: 125 0.342 - 0.428: 36 Chirality restraints: 6452 Sorted by residual: chirality pdb=" CB VAL B1011 " pdb=" CA VAL B1011 " pdb=" CG1 VAL B1011 " pdb=" CG2 VAL B1011 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CB VAL A1011 " pdb=" CA VAL A1011 " pdb=" CG1 VAL A1011 " pdb=" CG2 VAL A1011 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" CB VAL D1011 " pdb=" CA VAL D1011 " pdb=" CG1 VAL D1011 " pdb=" CG2 VAL D1011 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.56e+00 ... (remaining 6449 not shown) Planarity restraints: 7020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS D 82 " -0.026 2.00e-02 2.50e+03 5.26e-02 2.76e+01 pdb=" C HIS D 82 " 0.091 2.00e-02 2.50e+03 pdb=" O HIS D 82 " -0.034 2.00e-02 2.50e+03 pdb=" N ALA D 83 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 82 " -0.026 2.00e-02 2.50e+03 5.24e-02 2.74e+01 pdb=" C HIS C 82 " 0.091 2.00e-02 2.50e+03 pdb=" O HIS C 82 " -0.034 2.00e-02 2.50e+03 pdb=" N ALA C 83 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 82 " -0.026 2.00e-02 2.50e+03 5.24e-02 2.74e+01 pdb=" C HIS B 82 " 0.091 2.00e-02 2.50e+03 pdb=" O HIS B 82 " -0.034 2.00e-02 2.50e+03 pdb=" N ALA B 83 " -0.030 2.00e-02 2.50e+03 ... (remaining 7017 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 241 2.60 - 3.18: 31093 3.18 - 3.75: 60353 3.75 - 4.33: 79954 4.33 - 4.90: 135040 Nonbonded interactions: 306681 Sorted by model distance: nonbonded pdb=" SG CYS D 997 " pdb=" SG CYS D1006 " model vdw 2.028 3.760 nonbonded pdb=" O ALA B1410 " pdb=" OG SER B1414 " model vdw 2.383 3.040 nonbonded pdb=" O ALA A1410 " pdb=" OG SER A1414 " model vdw 2.383 3.040 nonbonded pdb=" O ALA C1410 " pdb=" OG SER C1414 " model vdw 2.383 3.040 nonbonded pdb=" O ALA D1410 " pdb=" OG SER D1414 " model vdw 2.383 3.040 ... (remaining 306676 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: 0.12 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 48 through 1494 or resid 1702 or resid 1704)) selection = (chain 'B' and (resid 48 through 1494 or resid 1702 or resid 1704)) selection = (chain 'C' and (resid 48 through 1494 or resid 1702 or resid 1704)) selection = (chain 'D' and (resid 48 through 1494 or resid 6002 or resid 6004)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.800 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 44.330 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.090 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:10.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 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 : 0.011 0.084 40295 Z= 0.684 Angle : 1.654 13.957 55036 Z= 1.116 Chirality : 0.096 0.428 6452 Planarity : 0.011 0.053 7020 Dihedral : 13.150 84.026 14304 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.81 % Allowed : 2.88 % Favored : 96.32 % Cbeta Deviations : 0.55 % 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: -0.38 (0.11), residues: 5356 helix: 0.26 (0.09), residues: 2976 sheet: -1.20 (0.21), residues: 452 loop : -0.63 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 553 TYR 0.035 0.005 TYR D 504 PHE 0.050 0.005 PHE D 334 TRP 0.041 0.004 TRP B1052 HIS 0.022 0.004 HIS B 618 Details of bonding type rmsd covalent geometry : bond 0.01118 (40292) covalent geometry : angle 1.65416 (55020) SS BOND : bond 0.00254 ( 3) SS BOND : angle 1.04512 ( 16) hydrogen bonds : bond 0.17072 ( 2304) hydrogen bonds : angle 7.39675 ( 6828) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10712 Ramachandran restraints generated. 5356 Oldfield, 0 Emsley, 5356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10712 Ramachandran restraints generated. 5356 Oldfield, 0 Emsley, 5356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 983 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8154 (t0) cc_final: 0.7828 (m-30) REVERT: A 118 ASP cc_start: 0.7661 (t0) cc_final: 0.7444 (t0) REVERT: A 133 LYS cc_start: 0.7419 (tttt) cc_final: 0.7181 (ttmt) REVERT: A 134 TYR cc_start: 0.8245 (m-80) cc_final: 0.8014 (m-10) REVERT: A 216 TYR cc_start: 0.6152 (t80) cc_final: 0.5902 (t80) REVERT: A 218 VAL cc_start: 0.8054 (m) cc_final: 0.7846 (p) REVERT: A 220 ILE cc_start: 0.8255 (mm) cc_final: 0.8033 (mp) REVERT: A 313 THR cc_start: 0.8282 (m) cc_final: 0.8063 (m) REVERT: A 342 PHE cc_start: 0.7950 (m-80) cc_final: 0.7486 (m-80) REVERT: A 406 SER cc_start: 0.8182 (m) cc_final: 0.7822 (t) REVERT: A 429 ARG cc_start: 0.6262 (mtm-85) cc_final: 0.6062 (mtp180) REVERT: A 477 LYS cc_start: 0.7646 (mttp) cc_final: 0.7343 (mmtm) REVERT: A 502 GLU cc_start: 0.6219 (mt-10) cc_final: 0.5987 (mt-10) REVERT: A 516 GLN cc_start: 0.6710 (OUTLIER) cc_final: 0.6148 (tm130) REVERT: A 520 SER cc_start: 0.7509 (m) cc_final: 0.7273 (p) REVERT: A 552 THR cc_start: 0.8079 (m) cc_final: 0.7805 (p) REVERT: A 614 ARG cc_start: 0.6549 (ttt90) cc_final: 0.6229 (mpp-170) REVERT: A 659 GLN cc_start: 0.6813 (mt0) cc_final: 0.6508 (mm-40) REVERT: A 663 LYS cc_start: 0.7134 (mttp) cc_final: 0.5968 (mmmt) REVERT: A 666 GLU cc_start: 0.7494 (tp30) cc_final: 0.6195 (tm-30) REVERT: A 697 LYS cc_start: 0.7749 (mttt) cc_final: 0.7485 (mptp) REVERT: A 725 ASP cc_start: 0.7586 (t0) cc_final: 0.6875 (m-30) REVERT: A 745 PHE cc_start: 0.7369 (m-80) cc_final: 0.7035 (m-80) REVERT: A 931 MET cc_start: 0.7608 (mtp) cc_final: 0.7298 (mtp) REVERT: A 932 MET cc_start: 0.7019 (mmp) cc_final: 0.6733 (mmm) REVERT: A 933 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6846 (mm-30) REVERT: A 963 ASP cc_start: 0.7023 (m-30) cc_final: 0.6694 (t70) REVERT: A 1042 MET cc_start: 0.7851 (mtm) cc_final: 0.7193 (mmt) REVERT: A 1046 GLU cc_start: 0.7069 (mm-30) cc_final: 0.5765 (mp0) REVERT: A 1336 TRP cc_start: 0.7857 (m100) cc_final: 0.7271 (m100) REVERT: A 1346 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6679 (tp30) REVERT: A 1444 ASP cc_start: 0.7280 (t0) cc_final: 0.7062 (t0) REVERT: B 117 ASP cc_start: 0.8150 (t0) cc_final: 0.7821 (m-30) REVERT: B 118 ASP cc_start: 0.7649 (t0) cc_final: 0.7431 (t0) REVERT: B 133 LYS cc_start: 0.7419 (tttt) cc_final: 0.7185 (ttmt) REVERT: B 134 TYR cc_start: 0.8244 (m-80) cc_final: 0.8015 (m-10) REVERT: B 216 TYR cc_start: 0.6153 (t80) cc_final: 0.5902 (t80) REVERT: B 218 VAL cc_start: 0.8051 (m) cc_final: 0.7845 (p) REVERT: B 220 ILE cc_start: 0.8255 (mm) cc_final: 0.8033 (mp) REVERT: B 313 THR cc_start: 0.8283 (m) cc_final: 0.8064 (m) REVERT: B 342 PHE cc_start: 0.7956 (m-80) cc_final: 0.7494 (m-80) REVERT: B 406 SER cc_start: 0.8184 (m) cc_final: 0.7822 (t) REVERT: B 429 ARG cc_start: 0.6266 (mtm-85) cc_final: 0.6054 (mtp180) REVERT: B 477 LYS cc_start: 0.7651 (mttp) cc_final: 0.7333 (mmtm) REVERT: B 502 GLU cc_start: 0.6189 (mt-10) cc_final: 0.5961 (mt-10) REVERT: B 516 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.6153 (tm130) REVERT: B 520 SER cc_start: 0.7509 (m) cc_final: 0.7272 (p) REVERT: B 552 THR cc_start: 0.8077 (m) cc_final: 0.7803 (p) REVERT: B 614 ARG cc_start: 0.6582 (ttt90) cc_final: 0.6263 (mpp-170) REVERT: B 659 GLN cc_start: 0.6814 (mt0) cc_final: 0.6509 (mm-40) REVERT: B 663 LYS cc_start: 0.7134 (mttp) cc_final: 0.5961 (mmmt) REVERT: B 666 GLU cc_start: 0.7496 (tp30) cc_final: 0.6198 (tm-30) REVERT: B 697 LYS cc_start: 0.7756 (mttt) cc_final: 0.7495 (mptp) REVERT: B 725 ASP cc_start: 0.7587 (t0) cc_final: 0.6881 (m-30) REVERT: B 745 PHE cc_start: 0.7372 (m-80) cc_final: 0.7037 (m-80) REVERT: B 931 MET cc_start: 0.7590 (mtp) cc_final: 0.7276 (mtp) REVERT: B 932 MET cc_start: 0.7018 (mmp) cc_final: 0.6732 (mmm) REVERT: B 933 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6847 (mm-30) REVERT: B 963 ASP cc_start: 0.7023 (m-30) cc_final: 0.6693 (t70) REVERT: B 1042 MET cc_start: 0.7851 (mtm) cc_final: 0.7211 (mmt) REVERT: B 1046 GLU cc_start: 0.7070 (mm-30) cc_final: 0.5764 (mp0) REVERT: B 1332 VAL cc_start: 0.7028 (t) cc_final: 0.6767 (t) REVERT: B 1336 TRP cc_start: 0.7852 (m100) cc_final: 0.7268 (m100) REVERT: B 1346 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6677 (tp30) REVERT: B 1444 ASP cc_start: 0.7281 (t0) cc_final: 0.7064 (t0) REVERT: C 117 ASP cc_start: 0.8153 (t0) cc_final: 0.7831 (m-30) REVERT: C 118 ASP cc_start: 0.7654 (t0) cc_final: 0.7439 (t0) REVERT: C 133 LYS cc_start: 0.7417 (tttt) cc_final: 0.7183 (ttmt) REVERT: C 134 TYR cc_start: 0.8245 (m-80) cc_final: 0.8020 (m-10) REVERT: C 218 VAL cc_start: 0.8059 (m) cc_final: 0.7850 (p) REVERT: C 220 ILE cc_start: 0.8261 (mm) cc_final: 0.8037 (mp) REVERT: C 313 THR cc_start: 0.8286 (m) cc_final: 0.8067 (m) REVERT: C 342 PHE cc_start: 0.7950 (m-80) cc_final: 0.7512 (m-80) REVERT: C 406 SER cc_start: 0.8190 (m) cc_final: 0.7831 (t) REVERT: C 429 ARG cc_start: 0.6258 (mtm-85) cc_final: 0.6055 (mtp180) REVERT: C 477 LYS cc_start: 0.7652 (mttp) cc_final: 0.7343 (mmtm) REVERT: C 502 GLU cc_start: 0.6193 (mt-10) cc_final: 0.5976 (mt-10) REVERT: C 516 GLN cc_start: 0.6709 (OUTLIER) cc_final: 0.6146 (tm130) REVERT: C 520 SER cc_start: 0.7508 (m) cc_final: 0.7270 (p) REVERT: C 552 THR cc_start: 0.8076 (m) cc_final: 0.7802 (p) REVERT: C 614 ARG cc_start: 0.6551 (ttt90) cc_final: 0.6226 (mpp-170) REVERT: C 659 GLN cc_start: 0.6807 (mt0) cc_final: 0.6498 (mm-40) REVERT: C 663 LYS cc_start: 0.7133 (mttp) cc_final: 0.5963 (mmmt) REVERT: C 666 GLU cc_start: 0.7478 (tp30) cc_final: 0.6195 (tm-30) REVERT: C 697 LYS cc_start: 0.7744 (mttt) cc_final: 0.7480 (mptp) REVERT: C 725 ASP cc_start: 0.7555 (t0) cc_final: 0.6863 (m-30) REVERT: C 745 PHE cc_start: 0.7368 (m-80) cc_final: 0.7035 (m-80) REVERT: C 931 MET cc_start: 0.7622 (mtp) cc_final: 0.7311 (mtp) REVERT: C 932 MET cc_start: 0.7020 (mmp) cc_final: 0.6710 (mmm) REVERT: C 933 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6785 (mm-30) REVERT: C 963 ASP cc_start: 0.7022 (m-30) cc_final: 0.6691 (t70) REVERT: C 1042 MET cc_start: 0.7856 (mtm) cc_final: 0.7214 (mmt) REVERT: C 1046 GLU cc_start: 0.7073 (mm-30) cc_final: 0.5763 (mp0) REVERT: C 1332 VAL cc_start: 0.7025 (t) cc_final: 0.6765 (t) REVERT: C 1336 TRP cc_start: 0.7843 (m100) cc_final: 0.7259 (m100) REVERT: C 1346 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6655 (tp30) REVERT: C 1444 ASP cc_start: 0.7284 (t0) cc_final: 0.7063 (t0) REVERT: D 117 ASP cc_start: 0.8157 (t0) cc_final: 0.7831 (m-30) REVERT: D 118 ASP cc_start: 0.7676 (t0) cc_final: 0.7460 (t0) REVERT: D 133 LYS cc_start: 0.7422 (tttt) cc_final: 0.7186 (ttmt) REVERT: D 134 TYR cc_start: 0.8245 (m-80) cc_final: 0.8021 (m-10) REVERT: D 216 TYR cc_start: 0.6166 (t80) cc_final: 0.5911 (t80) REVERT: D 218 VAL cc_start: 0.8052 (m) cc_final: 0.7841 (p) REVERT: D 220 ILE cc_start: 0.8263 (mm) cc_final: 0.8038 (mp) REVERT: D 313 THR cc_start: 0.8258 (m) cc_final: 0.8043 (m) REVERT: D 342 PHE cc_start: 0.7942 (m-80) cc_final: 0.7502 (m-80) REVERT: D 406 SER cc_start: 0.8177 (m) cc_final: 0.7821 (t) REVERT: D 477 LYS cc_start: 0.7645 (mttp) cc_final: 0.7338 (mmtm) REVERT: D 502 GLU cc_start: 0.6222 (mt-10) cc_final: 0.5990 (mt-10) REVERT: D 516 GLN cc_start: 0.6715 (OUTLIER) cc_final: 0.6152 (tm130) REVERT: D 520 SER cc_start: 0.7507 (m) cc_final: 0.7270 (p) REVERT: D 552 THR cc_start: 0.8074 (m) cc_final: 0.7801 (p) REVERT: D 614 ARG cc_start: 0.6553 (ttt90) cc_final: 0.6226 (mpp-170) REVERT: D 659 GLN cc_start: 0.6811 (mt0) cc_final: 0.6505 (mm-40) REVERT: D 663 LYS cc_start: 0.7132 (mttp) cc_final: 0.5963 (mmmt) REVERT: D 666 GLU cc_start: 0.7464 (tp30) cc_final: 0.6173 (tm-30) REVERT: D 697 LYS cc_start: 0.7753 (mttt) cc_final: 0.7494 (mptp) REVERT: D 725 ASP cc_start: 0.7584 (t0) cc_final: 0.6878 (m-30) REVERT: D 745 PHE cc_start: 0.7370 (m-80) cc_final: 0.7039 (m-80) REVERT: D 931 MET cc_start: 0.7628 (mtp) cc_final: 0.7312 (mtp) REVERT: D 932 MET cc_start: 0.7020 (mmp) cc_final: 0.6709 (mmm) REVERT: D 933 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6831 (mm-30) REVERT: D 963 ASP cc_start: 0.7006 (m-30) cc_final: 0.6671 (t70) REVERT: D 1042 MET cc_start: 0.7856 (mtm) cc_final: 0.7104 (mmt) REVERT: D 1046 GLU cc_start: 0.7070 (mm-30) cc_final: 0.5763 (mp0) REVERT: D 1336 TRP cc_start: 0.7853 (m100) cc_final: 0.7271 (m100) REVERT: D 1346 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6685 (tp30) REVERT: D 1444 ASP cc_start: 0.7281 (t0) cc_final: 0.7060 (t0) outliers start: 28 outliers final: 4 residues processed: 995 average time/residue: 0.6909 time to fit residues: 836.1751 Evaluate side-chains 630 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 622 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 516 GLN Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 516 GLN Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 516 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 394 optimal weight: 7.9990 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 265 optimal weight: 0.9990 chunk 523 optimal weight: 0.9980 chunk 497 optimal weight: 0.9990 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 0.9990 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 0.9980 chunk 223 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN A 280 ASN A 356 GLN A 530 HIS A 562 GLN A 682 HIS A 702 ASN A1129 GLN A1140 ASN A1156 HIS A1456 GLN ** A1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1491 ASN B 253 ASN B 280 ASN B 356 GLN B 530 HIS B 562 GLN B 682 HIS B 702 ASN B1129 GLN B1140 ASN B1156 HIS B1456 GLN ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1491 ASN C 253 ASN C 280 ASN C 356 GLN C 530 HIS C 562 GLN C 682 HIS C 702 ASN C1129 GLN C1140 ASN C1156 HIS C1456 GLN ** C1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1491 ASN D 253 ASN D 280 ASN D 356 GLN D 530 HIS D 562 GLN D 682 HIS D 702 ASN D1129 GLN D1140 ASN D1156 HIS D1456 GLN ** D1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1491 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.181542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.122351 restraints weight = 50737.761| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.05 r_work: 0.3238 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40295 Z= 0.139 Angle : 0.566 6.274 55036 Z= 0.302 Chirality : 0.041 0.168 6452 Planarity : 0.005 0.045 7020 Dihedral : 6.761 68.355 6720 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.62 % Allowed : 11.57 % Favored : 84.81 % 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: 1.03 (0.11), residues: 5356 helix: 1.61 (0.09), residues: 3056 sheet: -0.78 (0.21), residues: 460 loop : -0.41 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1123 TYR 0.017 0.002 TYR D 979 PHE 0.012 0.002 PHE A 879 TRP 0.020 0.002 TRP A1052 HIS 0.010 0.001 HIS D 682 Details of bonding type rmsd covalent geometry : bond 0.00305 (40292) covalent geometry : angle 0.56568 (55020) SS BOND : bond 0.00041 ( 3) SS BOND : angle 0.18267 ( 16) hydrogen bonds : bond 0.04899 ( 2304) hydrogen bonds : angle 4.15364 ( 6828) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10712 Ramachandran restraints generated. 5356 Oldfield, 0 Emsley, 5356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10712 Ramachandran restraints generated. 5356 Oldfield, 0 Emsley, 5356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 594 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.7928 (t0) cc_final: 0.7698 (m-30) REVERT: A 280 ASN cc_start: 0.7642 (m110) cc_final: 0.7380 (t0) REVERT: A 335 MET cc_start: 0.8791 (mtp) cc_final: 0.8570 (mtt) REVERT: A 406 SER cc_start: 0.8438 (m) cc_final: 0.8173 (m) REVERT: A 419 MET cc_start: 0.8729 (tmm) cc_final: 0.8451 (tmm) REVERT: A 429 ARG cc_start: 0.6564 (mtm-85) cc_final: 0.6309 (mtt-85) REVERT: A 449 ASP cc_start: 0.7884 (t0) cc_final: 0.7646 (t70) REVERT: A 477 LYS cc_start: 0.8234 (mttp) cc_final: 0.7936 (mmtm) REVERT: A 516 GLN cc_start: 0.7832 (tp40) cc_final: 0.7331 (tm130) REVERT: A 614 ARG cc_start: 0.7784 (ttt90) cc_final: 0.7413 (mpp-170) REVERT: A 659 GLN cc_start: 0.7648 (mt0) cc_final: 0.7369 (mm-40) REVERT: A 663 LYS cc_start: 0.8292 (mttp) cc_final: 0.7589 (mmmt) REVERT: A 725 ASP cc_start: 0.8350 (t0) cc_final: 0.8002 (m-30) REVERT: A 745 PHE cc_start: 0.7736 (m-80) cc_final: 0.7477 (m-80) REVERT: A 932 MET cc_start: 0.8041 (mmp) cc_final: 0.7836 (mmm) REVERT: A 933 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7768 (mm-30) REVERT: A 963 ASP cc_start: 0.7291 (m-30) cc_final: 0.7088 (t70) REVERT: A 1046 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7276 (mp0) REVERT: A 1336 TRP cc_start: 0.7703 (m100) cc_final: 0.7236 (m100) REVERT: A 1346 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7402 (tt0) REVERT: A 1354 GLU cc_start: 0.7401 (tt0) cc_final: 0.6994 (tt0) REVERT: A 1469 VAL cc_start: 0.8122 (OUTLIER) cc_final: 0.7915 (t) REVERT: A 1474 ASN cc_start: 0.7278 (OUTLIER) cc_final: 0.6558 (t0) REVERT: A 1487 THR cc_start: 0.7909 (OUTLIER) cc_final: 0.7661 (t) REVERT: B 58 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7123 (mt) REVERT: B 117 ASP cc_start: 0.7945 (t0) cc_final: 0.7706 (m-30) REVERT: B 280 ASN cc_start: 0.7633 (m110) cc_final: 0.7374 (t0) REVERT: B 335 MET cc_start: 0.8794 (mtp) cc_final: 0.8572 (mtt) REVERT: B 406 SER cc_start: 0.8439 (m) cc_final: 0.8173 (m) REVERT: B 419 MET cc_start: 0.8745 (tmm) cc_final: 0.8473 (tmm) REVERT: B 429 ARG cc_start: 0.6600 (mtm-85) cc_final: 0.6342 (mtt-85) REVERT: B 449 ASP cc_start: 0.7911 (t0) cc_final: 0.7676 (t70) REVERT: B 477 LYS cc_start: 0.8217 (mttp) cc_final: 0.7917 (mmtm) REVERT: B 502 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7421 (mt-10) REVERT: B 516 GLN cc_start: 0.7833 (tp40) cc_final: 0.7331 (tm130) REVERT: B 614 ARG cc_start: 0.7784 (ttt90) cc_final: 0.7422 (mpp-170) REVERT: B 659 GLN cc_start: 0.7650 (mt0) cc_final: 0.7368 (mm-40) REVERT: B 663 LYS cc_start: 0.8300 (mttp) cc_final: 0.7589 (mmmt) REVERT: B 725 ASP cc_start: 0.8361 (t0) cc_final: 0.8014 (m-30) REVERT: B 933 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7753 (mm-30) REVERT: B 963 ASP cc_start: 0.7273 (m-30) cc_final: 0.7071 (t70) REVERT: B 1046 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7236 (mp0) REVERT: B 1336 TRP cc_start: 0.7728 (m100) cc_final: 0.7256 (m100) REVERT: B 1346 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7399 (tt0) REVERT: B 1354 GLU cc_start: 0.7386 (tt0) cc_final: 0.7004 (tt0) REVERT: B 1469 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7935 (t) REVERT: B 1474 ASN cc_start: 0.7275 (OUTLIER) cc_final: 0.6554 (t0) REVERT: B 1487 THR cc_start: 0.7913 (OUTLIER) cc_final: 0.7666 (t) REVERT: C 58 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7103 (mt) REVERT: C 117 ASP cc_start: 0.7914 (t0) cc_final: 0.7684 (m-30) REVERT: C 280 ASN cc_start: 0.7630 (m110) cc_final: 0.7376 (t0) REVERT: C 335 MET cc_start: 0.8787 (mtp) cc_final: 0.8574 (mtt) REVERT: C 406 SER cc_start: 0.8434 (m) cc_final: 0.8167 (m) REVERT: C 419 MET cc_start: 0.8720 (tmm) cc_final: 0.8448 (tmm) REVERT: C 429 ARG cc_start: 0.6553 (mtm-85) cc_final: 0.6294 (mtt-85) REVERT: C 449 ASP cc_start: 0.7895 (t0) cc_final: 0.7659 (t70) REVERT: C 477 LYS cc_start: 0.8235 (mttp) cc_final: 0.7933 (mmtm) REVERT: C 502 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7444 (mt-10) REVERT: C 516 GLN cc_start: 0.7823 (tp40) cc_final: 0.7323 (tm130) REVERT: C 614 ARG cc_start: 0.7776 (ttt90) cc_final: 0.7395 (mpp-170) REVERT: C 659 GLN cc_start: 0.7642 (mt0) cc_final: 0.7355 (mm-40) REVERT: C 663 LYS cc_start: 0.8290 (mttp) cc_final: 0.7580 (mmmt) REVERT: C 725 ASP cc_start: 0.8351 (t0) cc_final: 0.8004 (m-30) REVERT: C 745 PHE cc_start: 0.7752 (m-80) cc_final: 0.7496 (m-80) REVERT: C 932 MET cc_start: 0.8060 (mmp) cc_final: 0.7848 (mmm) REVERT: C 933 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7764 (mm-30) REVERT: C 963 ASP cc_start: 0.7275 (m-30) cc_final: 0.7072 (t70) REVERT: C 1046 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7194 (mp0) REVERT: C 1152 GLN cc_start: 0.7712 (tm-30) cc_final: 0.7500 (tm-30) REVERT: C 1336 TRP cc_start: 0.7676 (m100) cc_final: 0.7201 (m100) REVERT: C 1354 GLU cc_start: 0.7394 (tt0) cc_final: 0.7014 (tt0) REVERT: C 1474 ASN cc_start: 0.7248 (OUTLIER) cc_final: 0.6548 (t0) REVERT: C 1487 THR cc_start: 0.7903 (OUTLIER) cc_final: 0.7657 (t) REVERT: D 58 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7116 (mt) REVERT: D 117 ASP cc_start: 0.7912 (t0) cc_final: 0.7685 (m-30) REVERT: D 220 ILE cc_start: 0.8190 (mm) cc_final: 0.7979 (mp) REVERT: D 280 ASN cc_start: 0.7652 (m110) cc_final: 0.7401 (t0) REVERT: D 335 MET cc_start: 0.8789 (mtp) cc_final: 0.8568 (mtt) REVERT: D 406 SER cc_start: 0.8435 (m) cc_final: 0.8168 (m) REVERT: D 419 MET cc_start: 0.8720 (tmm) cc_final: 0.8443 (tmm) REVERT: D 449 ASP cc_start: 0.7892 (t0) cc_final: 0.7658 (t70) REVERT: D 477 LYS cc_start: 0.8237 (mttp) cc_final: 0.7936 (mmtm) REVERT: D 516 GLN cc_start: 0.7840 (tp40) cc_final: 0.7337 (tm130) REVERT: D 614 ARG cc_start: 0.7773 (ttt90) cc_final: 0.7409 (mpp-170) REVERT: D 659 GLN cc_start: 0.7638 (mt0) cc_final: 0.7352 (mm-40) REVERT: D 663 LYS cc_start: 0.8290 (mttp) cc_final: 0.7582 (mmmt) REVERT: D 725 ASP cc_start: 0.8351 (t0) cc_final: 0.8000 (m-30) REVERT: D 745 PHE cc_start: 0.7736 (m-80) cc_final: 0.7479 (m-80) REVERT: D 932 MET cc_start: 0.8053 (mmp) cc_final: 0.7839 (mmm) REVERT: D 933 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7756 (mm-30) REVERT: D 963 ASP cc_start: 0.7277 (m-30) cc_final: 0.7071 (t70) REVERT: D 1046 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7231 (mp0) REVERT: D 1336 TRP cc_start: 0.7699 (m100) cc_final: 0.7234 (m100) REVERT: D 1346 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7379 (tt0) REVERT: D 1354 GLU cc_start: 0.7400 (tt0) cc_final: 0.6997 (tt0) REVERT: D 1469 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7898 (t) REVERT: D 1474 ASN cc_start: 0.7272 (OUTLIER) cc_final: 0.6555 (t0) REVERT: D 1487 THR cc_start: 0.7911 (OUTLIER) cc_final: 0.7662 (t) outliers start: 126 outliers final: 35 residues processed: 658 average time/residue: 0.6223 time to fit residues: 513.4178 Evaluate side-chains 568 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 519 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1473 LEU Chi-restraints excluded: chain A residue 1474 ASN Chi-restraints excluded: chain A residue 1487 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 530 HIS Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1469 VAL Chi-restraints excluded: chain B residue 1473 LEU Chi-restraints excluded: chain B residue 1474 ASN Chi-restraints excluded: chain B residue 1487 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 530 HIS Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 1333 VAL Chi-restraints excluded: chain C residue 1469 VAL Chi-restraints excluded: chain C residue 1473 LEU Chi-restraints excluded: chain C residue 1474 ASN Chi-restraints excluded: chain C residue 1487 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 530 HIS Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 844 VAL Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1469 VAL Chi-restraints excluded: chain D residue 1473 LEU Chi-restraints excluded: chain D residue 1474 ASN Chi-restraints excluded: chain D residue 1487 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 301 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 431 optimal weight: 5.9990 chunk 345 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 505 optimal weight: 5.9990 chunk 292 optimal weight: 3.9990 chunk 448 optimal weight: 0.0570 chunk 210 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 overall best weight: 2.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 255 ASN A 682 HIS A1156 HIS ** A1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 HIS B 255 ASN B 682 HIS B1156 HIS ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS C 255 ASN C 682 HIS C1156 HIS ** C1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN D 682 HIS D1156 HIS ** D1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.175849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.113349 restraints weight = 50666.914| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.98 r_work: 0.3147 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 40295 Z= 0.237 Angle : 0.623 6.642 55036 Z= 0.333 Chirality : 0.044 0.187 6452 Planarity : 0.005 0.050 7020 Dihedral : 6.623 65.714 6700 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.69 % Allowed : 13.41 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.11), residues: 5356 helix: 1.52 (0.09), residues: 3036 sheet: -0.92 (0.21), residues: 476 loop : -0.37 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1123 TYR 0.025 0.003 TYR D 727 PHE 0.020 0.002 PHE D 879 TRP 0.019 0.002 TRP D1052 HIS 0.031 0.002 HIS D 530 Details of bonding type rmsd covalent geometry : bond 0.00564 (40292) covalent geometry : angle 0.62291 (55020) SS BOND : bond 0.00063 ( 3) SS BOND : angle 0.47759 ( 16) hydrogen bonds : bond 0.05615 ( 2304) hydrogen bonds : angle 4.13583 ( 6828) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10712 Ramachandran restraints generated. 5356 Oldfield, 0 Emsley, 5356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10712 Ramachandran restraints generated. 5356 Oldfield, 0 Emsley, 5356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 543 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.7105 (p-90) cc_final: 0.6863 (p-90) REVERT: A 117 ASP cc_start: 0.7950 (t0) cc_final: 0.7685 (m-30) REVERT: A 332 TYR cc_start: 0.8409 (t80) cc_final: 0.8163 (t80) REVERT: A 357 THR cc_start: 0.7361 (t) cc_final: 0.7150 (t) REVERT: A 419 MET cc_start: 0.8774 (tmm) cc_final: 0.8453 (tmm) REVERT: A 429 ARG cc_start: 0.7079 (mtm-85) cc_final: 0.6670 (mtt-85) REVERT: A 516 GLN cc_start: 0.8005 (tp40) cc_final: 0.7357 (tm130) REVERT: A 592 GLN cc_start: 0.8159 (tt0) cc_final: 0.7955 (tm130) REVERT: A 614 ARG cc_start: 0.7943 (ttt90) cc_final: 0.7450 (mpp-170) REVERT: A 659 GLN cc_start: 0.7793 (mt0) cc_final: 0.7404 (mm-40) REVERT: A 725 ASP cc_start: 0.8375 (t0) cc_final: 0.7842 (m-30) REVERT: A 932 MET cc_start: 0.8043 (mmp) cc_final: 0.7824 (mmm) REVERT: A 933 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7886 (mm-30) REVERT: A 963 ASP cc_start: 0.7096 (m-30) cc_final: 0.6820 (t70) REVERT: A 1046 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7081 (mp0) REVERT: A 1336 TRP cc_start: 0.7652 (m100) cc_final: 0.7124 (m100) REVERT: A 1354 GLU cc_start: 0.7417 (tt0) cc_final: 0.7080 (tt0) REVERT: A 1469 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.8122 (t) REVERT: B 96 TRP cc_start: 0.7095 (p-90) cc_final: 0.6568 (p-90) REVERT: B 117 ASP cc_start: 0.7975 (t0) cc_final: 0.7690 (m-30) REVERT: B 332 TYR cc_start: 0.8418 (t80) cc_final: 0.8171 (t80) REVERT: B 357 THR cc_start: 0.7346 (t) cc_final: 0.7137 (t) REVERT: B 419 MET cc_start: 0.8776 (tmm) cc_final: 0.8452 (tmm) REVERT: B 429 ARG cc_start: 0.7079 (mtm-85) cc_final: 0.6669 (mtt-85) REVERT: B 516 GLN cc_start: 0.7995 (tp40) cc_final: 0.7342 (tm130) REVERT: B 592 GLN cc_start: 0.8160 (tt0) cc_final: 0.7953 (tm130) REVERT: B 614 ARG cc_start: 0.7939 (ttt90) cc_final: 0.7453 (mpp-170) REVERT: B 659 GLN cc_start: 0.7802 (mt0) cc_final: 0.7413 (mm-40) REVERT: B 725 ASP cc_start: 0.8376 (t0) cc_final: 0.7845 (m-30) REVERT: B 933 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7793 (mm-30) REVERT: B 963 ASP cc_start: 0.7090 (m-30) cc_final: 0.6815 (t70) REVERT: B 1046 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7073 (mp0) REVERT: B 1336 TRP cc_start: 0.7639 (m100) cc_final: 0.7102 (m100) REVERT: B 1354 GLU cc_start: 0.7423 (tt0) cc_final: 0.7083 (tt0) REVERT: B 1469 VAL cc_start: 0.8369 (OUTLIER) cc_final: 0.8142 (t) REVERT: C 96 TRP cc_start: 0.7102 (p-90) cc_final: 0.6864 (p-90) REVERT: C 117 ASP cc_start: 0.7957 (t0) cc_final: 0.7692 (m-30) REVERT: C 332 TYR cc_start: 0.8403 (t80) cc_final: 0.8156 (t80) REVERT: C 357 THR cc_start: 0.7364 (t) cc_final: 0.7155 (t) REVERT: C 419 MET cc_start: 0.8768 (tmm) cc_final: 0.8442 (tmm) REVERT: C 429 ARG cc_start: 0.7026 (mtm-85) cc_final: 0.6617 (mtt-85) REVERT: C 516 GLN cc_start: 0.7971 (tp40) cc_final: 0.7330 (tm130) REVERT: C 592 GLN cc_start: 0.8152 (tt0) cc_final: 0.7945 (tm130) REVERT: C 614 ARG cc_start: 0.7938 (ttt90) cc_final: 0.7437 (mpp-170) REVERT: C 659 GLN cc_start: 0.7797 (mt0) cc_final: 0.7408 (mm-40) REVERT: C 725 ASP cc_start: 0.8374 (t0) cc_final: 0.7836 (m-30) REVERT: C 932 MET cc_start: 0.8033 (mmp) cc_final: 0.7822 (mmm) REVERT: C 933 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7884 (mm-30) REVERT: C 963 ASP cc_start: 0.7099 (m-30) cc_final: 0.6819 (t70) REVERT: C 1042 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8219 (mmt) REVERT: C 1046 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7075 (mp0) REVERT: C 1336 TRP cc_start: 0.7621 (m100) cc_final: 0.7094 (m100) REVERT: C 1354 GLU cc_start: 0.7420 (tt0) cc_final: 0.7075 (tt0) REVERT: C 1469 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.8107 (t) REVERT: D 60 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: D 96 TRP cc_start: 0.7107 (p-90) cc_final: 0.6716 (p-90) REVERT: D 117 ASP cc_start: 0.7960 (t0) cc_final: 0.7688 (m-30) REVERT: D 332 TYR cc_start: 0.8422 (t80) cc_final: 0.8177 (t80) REVERT: D 357 THR cc_start: 0.7385 (t) cc_final: 0.7181 (t) REVERT: D 419 MET cc_start: 0.8775 (tmm) cc_final: 0.8453 (tmm) REVERT: D 516 GLN cc_start: 0.7981 (tp40) cc_final: 0.7337 (tm130) REVERT: D 592 GLN cc_start: 0.8126 (tt0) cc_final: 0.7922 (tm130) REVERT: D 614 ARG cc_start: 0.7944 (ttt90) cc_final: 0.7444 (mpp-170) REVERT: D 659 GLN cc_start: 0.7783 (mt0) cc_final: 0.7392 (mm-40) REVERT: D 725 ASP cc_start: 0.8368 (t0) cc_final: 0.7828 (m-30) REVERT: D 932 MET cc_start: 0.8024 (mmp) cc_final: 0.7815 (mmm) REVERT: D 933 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7895 (mm-30) REVERT: D 963 ASP cc_start: 0.7106 (m-30) cc_final: 0.6827 (t70) REVERT: D 1042 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8149 (mmt) REVERT: D 1046 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7076 (mp0) REVERT: D 1336 TRP cc_start: 0.7650 (m100) cc_final: 0.7122 (m100) REVERT: D 1354 GLU cc_start: 0.7409 (tt0) cc_final: 0.7074 (tt0) REVERT: D 1469 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.8083 (t) outliers start: 163 outliers final: 67 residues processed: 640 average time/residue: 0.6226 time to fit residues: 495.3632 Evaluate side-chains 563 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 489 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1473 LEU Chi-restraints excluded: chain A residue 1474 ASN Chi-restraints excluded: chain A residue 1487 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1469 VAL Chi-restraints excluded: chain B residue 1473 LEU Chi-restraints excluded: chain B residue 1474 ASN Chi-restraints excluded: chain B residue 1487 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 455 MET Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 681 SER Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1042 MET Chi-restraints excluded: chain C residue 1333 VAL Chi-restraints excluded: chain C residue 1469 VAL Chi-restraints excluded: chain C residue 1473 LEU Chi-restraints excluded: chain C residue 1474 ASN Chi-restraints excluded: chain C residue 1487 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 681 SER Chi-restraints excluded: chain D residue 844 VAL Chi-restraints excluded: chain D residue 1042 MET Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1469 VAL Chi-restraints excluded: chain D residue 1473 LEU Chi-restraints excluded: chain D residue 1474 ASN Chi-restraints excluded: chain D residue 1487 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 274 optimal weight: 6.9990 chunk 327 optimal weight: 0.9980 chunk 532 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 297 optimal weight: 9.9990 chunk 122 optimal weight: 30.0000 chunk 243 optimal weight: 30.0000 chunk 364 optimal weight: 0.5980 chunk 415 optimal weight: 8.9990 chunk 488 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 530 HIS ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 HIS ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 HIS ** C1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 530 HIS ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.178489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.119795 restraints weight = 50532.888| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.10 r_work: 0.3164 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 40295 Z= 0.120 Angle : 0.498 7.570 55036 Z= 0.261 Chirality : 0.039 0.161 6452 Planarity : 0.004 0.044 7020 Dihedral : 6.185 73.503 6700 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.22 % Allowed : 16.40 % Favored : 80.38 % 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: 1.28 (0.11), residues: 5356 helix: 1.85 (0.09), residues: 3056 sheet: -0.90 (0.22), residues: 476 loop : -0.30 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 517 TYR 0.014 0.002 TYR A 979 PHE 0.020 0.001 PHE C 752 TRP 0.015 0.001 TRP C1052 HIS 0.004 0.001 HIS C 601 Details of bonding type rmsd covalent geometry : bond 0.00270 (40292) covalent geometry : angle 0.49805 (55020) SS BOND : bond 0.00054 ( 3) SS BOND : angle 0.29572 ( 16) hydrogen bonds : bond 0.04070 ( 2304) hydrogen bonds : angle 3.80326 ( 6828) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10712 Ramachandran restraints generated. 5356 Oldfield, 0 Emsley, 5356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10712 Ramachandran restraints generated. 5356 Oldfield, 0 Emsley, 5356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 527 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7180 (mt) REVERT: A 96 TRP cc_start: 0.7340 (p-90) cc_final: 0.7072 (p-90) REVERT: A 117 ASP cc_start: 0.7883 (t0) cc_final: 0.7627 (m-30) REVERT: A 342 PHE cc_start: 0.8187 (m-80) cc_final: 0.7459 (m-80) REVERT: A 357 THR cc_start: 0.7371 (t) cc_final: 0.7152 (t) REVERT: A 428 LYS cc_start: 0.7915 (mtpp) cc_final: 0.7188 (mtmt) REVERT: A 429 ARG cc_start: 0.7114 (mtm-85) cc_final: 0.6694 (mtt-85) REVERT: A 516 GLN cc_start: 0.8042 (tp40) cc_final: 0.7791 (tm-30) REVERT: A 614 ARG cc_start: 0.7987 (ttt90) cc_final: 0.7514 (mpp-170) REVERT: A 638 GLU cc_start: 0.7800 (pt0) cc_final: 0.7358 (pt0) REVERT: A 659 GLN cc_start: 0.7852 (mt0) cc_final: 0.7521 (mm-40) REVERT: A 725 ASP cc_start: 0.8322 (t0) cc_final: 0.8029 (m-30) REVERT: A 933 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7933 (mm-30) REVERT: A 963 ASP cc_start: 0.6904 (m-30) cc_final: 0.6540 (t70) REVERT: A 1046 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7244 (mp0) REVERT: A 1156 HIS cc_start: 0.5738 (OUTLIER) cc_final: 0.5166 (m170) REVERT: A 1332 VAL cc_start: 0.7723 (t) cc_final: 0.7521 (t) REVERT: A 1336 TRP cc_start: 0.7621 (m100) cc_final: 0.7017 (m100) REVERT: A 1354 GLU cc_start: 0.7411 (tt0) cc_final: 0.7199 (tt0) REVERT: A 1485 HIS cc_start: 0.7602 (m170) cc_final: 0.7275 (m90) REVERT: A 1487 THR cc_start: 0.7981 (OUTLIER) cc_final: 0.7719 (t) REVERT: B 58 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7193 (mt) REVERT: B 96 TRP cc_start: 0.7343 (p-90) cc_final: 0.7073 (p-90) REVERT: B 117 ASP cc_start: 0.7909 (t0) cc_final: 0.7639 (m-30) REVERT: B 342 PHE cc_start: 0.8184 (m-80) cc_final: 0.7442 (m-80) REVERT: B 357 THR cc_start: 0.7376 (t) cc_final: 0.7154 (t) REVERT: B 428 LYS cc_start: 0.7907 (mtpp) cc_final: 0.7178 (mtmt) REVERT: B 429 ARG cc_start: 0.7131 (mtm-85) cc_final: 0.6715 (mtt-85) REVERT: B 516 GLN cc_start: 0.8047 (tp40) cc_final: 0.7797 (tm-30) REVERT: B 614 ARG cc_start: 0.7970 (ttt90) cc_final: 0.7511 (mpp-170) REVERT: B 638 GLU cc_start: 0.7804 (pt0) cc_final: 0.7367 (pt0) REVERT: B 659 GLN cc_start: 0.7863 (mt0) cc_final: 0.7533 (mm-40) REVERT: B 725 ASP cc_start: 0.8333 (t0) cc_final: 0.8041 (m-30) REVERT: B 933 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7886 (mm-30) REVERT: B 963 ASP cc_start: 0.6903 (m-30) cc_final: 0.6541 (t70) REVERT: B 1046 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7233 (mp0) REVERT: B 1332 VAL cc_start: 0.7726 (t) cc_final: 0.7501 (t) REVERT: B 1336 TRP cc_start: 0.7629 (m100) cc_final: 0.7019 (m100) REVERT: B 1354 GLU cc_start: 0.7421 (tt0) cc_final: 0.7203 (tt0) REVERT: B 1487 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7717 (t) REVERT: C 58 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7204 (mt) REVERT: C 96 TRP cc_start: 0.7363 (p-90) cc_final: 0.7074 (p-90) REVERT: C 117 ASP cc_start: 0.7926 (t0) cc_final: 0.7636 (m-30) REVERT: C 342 PHE cc_start: 0.8126 (m-80) cc_final: 0.7373 (m-80) REVERT: C 357 THR cc_start: 0.7345 (t) cc_final: 0.7127 (t) REVERT: C 428 LYS cc_start: 0.7896 (mtpp) cc_final: 0.7162 (mtmt) REVERT: C 429 ARG cc_start: 0.7088 (mtm-85) cc_final: 0.6669 (mtt-85) REVERT: C 516 GLN cc_start: 0.8027 (tp40) cc_final: 0.7775 (tm-30) REVERT: C 614 ARG cc_start: 0.7979 (ttt90) cc_final: 0.7502 (mpp-170) REVERT: C 638 GLU cc_start: 0.7794 (pt0) cc_final: 0.7357 (pt0) REVERT: C 659 GLN cc_start: 0.7863 (mt0) cc_final: 0.7530 (mm-40) REVERT: C 725 ASP cc_start: 0.8322 (t0) cc_final: 0.8027 (m-30) REVERT: C 933 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7915 (mm-30) REVERT: C 963 ASP cc_start: 0.6902 (m-30) cc_final: 0.6542 (t70) REVERT: C 1046 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7243 (mp0) REVERT: C 1336 TRP cc_start: 0.7604 (m100) cc_final: 0.7003 (m100) REVERT: C 1354 GLU cc_start: 0.7408 (tt0) cc_final: 0.7186 (tt0) REVERT: C 1443 HIS cc_start: 0.7018 (t70) cc_final: 0.6816 (t-90) REVERT: C 1487 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7727 (t) REVERT: D 58 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7202 (mt) REVERT: D 96 TRP cc_start: 0.7345 (p-90) cc_final: 0.7043 (p-90) REVERT: D 117 ASP cc_start: 0.7882 (t0) cc_final: 0.7631 (m-30) REVERT: D 342 PHE cc_start: 0.8184 (m-80) cc_final: 0.7420 (m-80) REVERT: D 357 THR cc_start: 0.7353 (t) cc_final: 0.7138 (t) REVERT: D 428 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7185 (mtmt) REVERT: D 429 ARG cc_start: 0.7255 (mtp180) cc_final: 0.6516 (mtt-85) REVERT: D 516 GLN cc_start: 0.8024 (tp40) cc_final: 0.7774 (tm-30) REVERT: D 614 ARG cc_start: 0.7977 (ttt90) cc_final: 0.7504 (mpp-170) REVERT: D 638 GLU cc_start: 0.7787 (pt0) cc_final: 0.7343 (pt0) REVERT: D 659 GLN cc_start: 0.7849 (mt0) cc_final: 0.7514 (mm-40) REVERT: D 725 ASP cc_start: 0.8321 (t0) cc_final: 0.8029 (m-30) REVERT: D 933 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7946 (mm-30) REVERT: D 963 ASP cc_start: 0.6915 (m-30) cc_final: 0.6553 (t70) REVERT: D 1046 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7228 (mp0) REVERT: D 1156 HIS cc_start: 0.5881 (OUTLIER) cc_final: 0.5190 (m170) REVERT: D 1336 TRP cc_start: 0.7621 (m100) cc_final: 0.7016 (m100) REVERT: D 1354 GLU cc_start: 0.7408 (tt0) cc_final: 0.7194 (tt0) REVERT: D 1485 HIS cc_start: 0.7603 (m170) cc_final: 0.7278 (m90) REVERT: D 1487 THR cc_start: 0.7984 (OUTLIER) cc_final: 0.7723 (t) outliers start: 112 outliers final: 51 residues processed: 592 average time/residue: 0.6414 time to fit residues: 473.0173 Evaluate side-chains 554 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 493 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1345 LEU Chi-restraints excluded: chain A residue 1444 ASP Chi-restraints excluded: chain A residue 1474 ASN Chi-restraints excluded: chain A residue 1487 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1345 LEU Chi-restraints excluded: chain B residue 1444 ASP Chi-restraints excluded: chain B residue 1474 ASN Chi-restraints excluded: chain B residue 1487 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 455 MET Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 1333 VAL Chi-restraints excluded: chain C residue 1345 LEU Chi-restraints excluded: chain C residue 1444 ASP Chi-restraints excluded: chain C residue 1474 ASN Chi-restraints excluded: chain C residue 1487 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 1156 HIS Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1345 LEU Chi-restraints excluded: chain D residue 1444 ASP Chi-restraints excluded: chain D residue 1474 ASN Chi-restraints excluded: chain D residue 1487 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 430 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 365 optimal weight: 0.3980 chunk 462 optimal weight: 0.6980 chunk 179 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 511 optimal weight: 30.0000 chunk 103 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 228 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 592 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 GLN ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 592 GLN C1156 HIS ** C1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.178457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120273 restraints weight = 50598.479| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.06 r_work: 0.3164 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 40295 Z= 0.116 Angle : 0.489 6.890 55036 Z= 0.255 Chirality : 0.038 0.166 6452 Planarity : 0.004 0.040 7020 Dihedral : 6.036 79.684 6700 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.34 % Allowed : 17.09 % Favored : 79.57 % 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: 1.41 (0.11), residues: 5356 helix: 1.96 (0.09), residues: 3064 sheet: -0.92 (0.22), residues: 476 loop : -0.25 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1480 TYR 0.013 0.002 TYR A 979 PHE 0.014 0.001 PHE D 879 TRP 0.012 0.001 TRP A1052 HIS 0.005 0.001 HIS C1443 Details of bonding type rmsd covalent geometry : bond 0.00262 (40292) covalent geometry : angle 0.48876 (55020) SS BOND : bond 0.00022 ( 3) SS BOND : angle 0.24761 ( 16) hydrogen bonds : bond 0.03972 ( 2304) hydrogen bonds : angle 3.72990 ( 6828) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10712 Ramachandran restraints generated. 5356 Oldfield, 0 Emsley, 5356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10712 Ramachandran restraints generated. 5356 Oldfield, 0 Emsley, 5356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 520 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7228 (mt) REVERT: A 96 TRP cc_start: 0.7262 (p-90) cc_final: 0.6754 (p-90) REVERT: A 117 ASP cc_start: 0.7897 (t0) cc_final: 0.7633 (m-30) REVERT: A 342 PHE cc_start: 0.8162 (m-80) cc_final: 0.7342 (m-80) REVERT: A 357 THR cc_start: 0.7413 (t) cc_final: 0.7191 (t) REVERT: A 429 ARG cc_start: 0.7157 (mtm-85) cc_final: 0.6724 (mtt-85) REVERT: A 516 GLN cc_start: 0.8084 (tp40) cc_final: 0.7824 (tm-30) REVERT: A 614 ARG cc_start: 0.8014 (ttt90) cc_final: 0.7536 (mpp-170) REVERT: A 638 GLU cc_start: 0.7819 (pt0) cc_final: 0.7553 (tm-30) REVERT: A 659 GLN cc_start: 0.7911 (mt0) cc_final: 0.7586 (mm-40) REVERT: A 694 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7374 (ttm) REVERT: A 725 ASP cc_start: 0.8329 (t0) cc_final: 0.8038 (m-30) REVERT: A 933 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7971 (mm-30) REVERT: A 1046 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7309 (mp0) REVERT: A 1332 VAL cc_start: 0.7704 (t) cc_final: 0.7464 (t) REVERT: A 1336 TRP cc_start: 0.7600 (m100) cc_final: 0.6969 (m100) REVERT: A 1485 HIS cc_start: 0.7589 (m170) cc_final: 0.7282 (m90) REVERT: A 1487 THR cc_start: 0.7985 (OUTLIER) cc_final: 0.7713 (t) REVERT: B 58 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7156 (mt) REVERT: B 96 TRP cc_start: 0.7248 (p-90) cc_final: 0.6739 (p-90) REVERT: B 117 ASP cc_start: 0.7913 (t0) cc_final: 0.7632 (m-30) REVERT: B 342 PHE cc_start: 0.8162 (m-80) cc_final: 0.7332 (m-80) REVERT: B 357 THR cc_start: 0.7429 (t) cc_final: 0.7207 (t) REVERT: B 429 ARG cc_start: 0.7145 (mtm-85) cc_final: 0.6712 (mtt-85) REVERT: B 475 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7721 (mp0) REVERT: B 516 GLN cc_start: 0.8097 (tp40) cc_final: 0.7837 (tm-30) REVERT: B 614 ARG cc_start: 0.8007 (ttt90) cc_final: 0.7536 (mpp-170) REVERT: B 638 GLU cc_start: 0.7822 (pt0) cc_final: 0.7557 (tm-30) REVERT: B 659 GLN cc_start: 0.7916 (mt0) cc_final: 0.7594 (mm-40) REVERT: B 694 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7336 (ttm) REVERT: B 725 ASP cc_start: 0.8331 (t0) cc_final: 0.8075 (m-30) REVERT: B 933 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7921 (mm-30) REVERT: B 1046 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7295 (mp0) REVERT: B 1332 VAL cc_start: 0.7687 (t) cc_final: 0.7473 (t) REVERT: B 1336 TRP cc_start: 0.7595 (m100) cc_final: 0.6949 (m100) REVERT: B 1485 HIS cc_start: 0.7477 (m170) cc_final: 0.7146 (m90) REVERT: B 1487 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7685 (t) REVERT: C 58 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7163 (mt) REVERT: C 96 TRP cc_start: 0.7259 (p-90) cc_final: 0.6722 (p-90) REVERT: C 117 ASP cc_start: 0.7916 (t0) cc_final: 0.7631 (m-30) REVERT: C 342 PHE cc_start: 0.8106 (m-80) cc_final: 0.7361 (m-80) REVERT: C 357 THR cc_start: 0.7399 (t) cc_final: 0.7174 (t) REVERT: C 429 ARG cc_start: 0.7128 (mtm-85) cc_final: 0.6703 (mtt-85) REVERT: C 475 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7741 (mp0) REVERT: C 516 GLN cc_start: 0.8079 (tp40) cc_final: 0.7817 (tm-30) REVERT: C 614 ARG cc_start: 0.8020 (ttt90) cc_final: 0.7534 (mpp-170) REVERT: C 638 GLU cc_start: 0.7807 (pt0) cc_final: 0.7542 (tm-30) REVERT: C 659 GLN cc_start: 0.7922 (mt0) cc_final: 0.7593 (mm-40) REVERT: C 694 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7351 (ttm) REVERT: C 725 ASP cc_start: 0.8312 (t0) cc_final: 0.8058 (m-30) REVERT: C 933 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7963 (mm-30) REVERT: C 1046 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7303 (mp0) REVERT: C 1336 TRP cc_start: 0.7581 (m100) cc_final: 0.6969 (m100) REVERT: C 1443 HIS cc_start: 0.6929 (t70) cc_final: 0.6721 (t-90) REVERT: D 58 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7185 (mt) REVERT: D 96 TRP cc_start: 0.7231 (p-90) cc_final: 0.6730 (p-90) REVERT: D 117 ASP cc_start: 0.7946 (t0) cc_final: 0.7704 (m-30) REVERT: D 342 PHE cc_start: 0.8118 (m-80) cc_final: 0.7299 (m-80) REVERT: D 357 THR cc_start: 0.7407 (t) cc_final: 0.7186 (t) REVERT: D 428 LYS cc_start: 0.7949 (mtpp) cc_final: 0.7234 (mtmt) REVERT: D 429 ARG cc_start: 0.7267 (mtp180) cc_final: 0.6566 (mtt-85) REVERT: D 516 GLN cc_start: 0.8072 (tp40) cc_final: 0.7813 (tm-30) REVERT: D 614 ARG cc_start: 0.8015 (ttt90) cc_final: 0.7525 (mpp-170) REVERT: D 638 GLU cc_start: 0.7809 (pt0) cc_final: 0.7548 (tm-30) REVERT: D 659 GLN cc_start: 0.7905 (mt0) cc_final: 0.7577 (mm-40) REVERT: D 725 ASP cc_start: 0.8312 (t0) cc_final: 0.8062 (m-30) REVERT: D 933 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7972 (mm-30) REVERT: D 1046 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7292 (mp0) REVERT: D 1332 VAL cc_start: 0.7702 (t) cc_final: 0.7461 (t) REVERT: D 1336 TRP cc_start: 0.7591 (m100) cc_final: 0.6982 (m100) REVERT: D 1487 THR cc_start: 0.7985 (OUTLIER) cc_final: 0.7715 (t) outliers start: 116 outliers final: 66 residues processed: 594 average time/residue: 0.5897 time to fit residues: 442.1863 Evaluate side-chains 568 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 492 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 1150 MET Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1345 LEU Chi-restraints excluded: chain A residue 1444 ASP Chi-restraints excluded: chain A residue 1473 LEU Chi-restraints excluded: chain A residue 1487 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 1150 MET Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1345 LEU Chi-restraints excluded: chain B residue 1444 ASP Chi-restraints excluded: chain B residue 1473 LEU Chi-restraints excluded: chain B residue 1487 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 455 MET Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 681 SER Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1150 MET Chi-restraints excluded: chain C residue 1333 VAL Chi-restraints excluded: chain C residue 1345 LEU Chi-restraints excluded: chain C residue 1444 ASP Chi-restraints excluded: chain C residue 1473 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 681 SER Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 844 VAL Chi-restraints excluded: chain D residue 1150 MET Chi-restraints excluded: chain D residue 1157 MET Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1345 LEU Chi-restraints excluded: chain D residue 1444 ASP Chi-restraints excluded: chain D residue 1473 LEU Chi-restraints excluded: chain D residue 1487 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 424 optimal weight: 0.6980 chunk 255 optimal weight: 10.0000 chunk 494 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 413 optimal weight: 0.9990 chunk 182 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 358 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1485 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.177584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116695 restraints weight = 50660.595| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.99 r_work: 0.3180 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 40295 Z= 0.125 Angle : 0.495 7.082 55036 Z= 0.259 Chirality : 0.039 0.150 6452 Planarity : 0.004 0.042 7020 Dihedral : 5.988 85.062 6700 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.68 % Allowed : 16.63 % Favored : 79.69 % 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: 1.45 (0.11), residues: 5356 helix: 2.00 (0.09), residues: 3064 sheet: -0.95 (0.22), residues: 476 loop : -0.23 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 112 TYR 0.038 0.002 TYR C 216 PHE 0.022 0.001 PHE A 752 TRP 0.012 0.001 TRP A1052 HIS 0.004 0.001 HIS B1443 Details of bonding type rmsd covalent geometry : bond 0.00287 (40292) covalent geometry : angle 0.49483 (55020) SS BOND : bond 0.00023 ( 3) SS BOND : angle 0.28152 ( 16) hydrogen bonds : bond 0.04064 ( 2304) hydrogen bonds : angle 3.72805 ( 6828) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10712 Ramachandran restraints generated. 5356 Oldfield, 0 Emsley, 5356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10712 Ramachandran restraints generated. 5356 Oldfield, 0 Emsley, 5356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 518 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7192 (mt) REVERT: A 117 ASP cc_start: 0.7914 (t0) cc_final: 0.7625 (m-30) REVERT: A 256 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7920 (tt) REVERT: A 357 THR cc_start: 0.7398 (t) cc_final: 0.7170 (t) REVERT: A 428 LYS cc_start: 0.7893 (mtpp) cc_final: 0.7141 (mtmt) REVERT: A 429 ARG cc_start: 0.7133 (mtm-85) cc_final: 0.6600 (mtt-85) REVERT: A 516 GLN cc_start: 0.8031 (tp40) cc_final: 0.7781 (tm-30) REVERT: A 614 ARG cc_start: 0.7938 (ttt90) cc_final: 0.7430 (mpp-170) REVERT: A 625 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7594 (mp10) REVERT: A 638 GLU cc_start: 0.7710 (pt0) cc_final: 0.7394 (tm-30) REVERT: A 659 GLN cc_start: 0.7817 (mt0) cc_final: 0.7422 (mm-40) REVERT: A 725 ASP cc_start: 0.8348 (t0) cc_final: 0.8040 (m-30) REVERT: A 933 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7862 (mm-30) REVERT: A 1046 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7159 (mp0) REVERT: A 1156 HIS cc_start: 0.5617 (OUTLIER) cc_final: 0.5235 (m170) REVERT: A 1332 VAL cc_start: 0.7627 (t) cc_final: 0.7410 (t) REVERT: A 1336 TRP cc_start: 0.7552 (m100) cc_final: 0.6891 (m100) REVERT: A 1487 THR cc_start: 0.7996 (OUTLIER) cc_final: 0.7723 (t) REVERT: B 58 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7208 (mt) REVERT: B 117 ASP cc_start: 0.7929 (t0) cc_final: 0.7640 (m-30) REVERT: B 256 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7922 (tt) REVERT: B 357 THR cc_start: 0.7398 (t) cc_final: 0.7169 (t) REVERT: B 428 LYS cc_start: 0.7888 (mtpp) cc_final: 0.7137 (mtmt) REVERT: B 429 ARG cc_start: 0.7122 (mtm-85) cc_final: 0.6591 (mtt-85) REVERT: B 475 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7643 (mp0) REVERT: B 516 GLN cc_start: 0.8041 (tp40) cc_final: 0.7789 (tm-30) REVERT: B 614 ARG cc_start: 0.7913 (ttt90) cc_final: 0.7418 (mpp-170) REVERT: B 625 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7593 (mp10) REVERT: B 638 GLU cc_start: 0.7705 (pt0) cc_final: 0.7388 (tm-30) REVERT: B 659 GLN cc_start: 0.7826 (mt0) cc_final: 0.7431 (mm-40) REVERT: B 725 ASP cc_start: 0.8346 (t0) cc_final: 0.8045 (m-30) REVERT: B 933 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7833 (mm-30) REVERT: B 1046 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7150 (mp0) REVERT: B 1332 VAL cc_start: 0.7648 (t) cc_final: 0.7430 (t) REVERT: B 1336 TRP cc_start: 0.7552 (m100) cc_final: 0.6938 (m100) REVERT: B 1487 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7721 (t) REVERT: C 58 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7210 (mt) REVERT: C 117 ASP cc_start: 0.7935 (t0) cc_final: 0.7639 (m-30) REVERT: C 256 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7918 (tt) REVERT: C 342 PHE cc_start: 0.8128 (m-80) cc_final: 0.7341 (m-80) REVERT: C 357 THR cc_start: 0.7407 (t) cc_final: 0.7178 (t) REVERT: C 428 LYS cc_start: 0.7874 (mtpp) cc_final: 0.7122 (mtmt) REVERT: C 429 ARG cc_start: 0.7129 (mtm-85) cc_final: 0.6606 (mtt-85) REVERT: C 475 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7663 (mp0) REVERT: C 516 GLN cc_start: 0.8029 (tp40) cc_final: 0.7777 (tm-30) REVERT: C 614 ARG cc_start: 0.7921 (ttt90) cc_final: 0.7403 (mpp-170) REVERT: C 625 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7584 (mp10) REVERT: C 638 GLU cc_start: 0.7693 (pt0) cc_final: 0.7376 (tm-30) REVERT: C 659 GLN cc_start: 0.7805 (mt0) cc_final: 0.7411 (mm-40) REVERT: C 725 ASP cc_start: 0.8336 (t0) cc_final: 0.8037 (m-30) REVERT: C 933 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7859 (mm-30) REVERT: C 1046 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7134 (mp0) REVERT: C 1332 VAL cc_start: 0.7802 (t) cc_final: 0.7587 (t) REVERT: C 1336 TRP cc_start: 0.7537 (m100) cc_final: 0.6890 (m100) REVERT: C 1443 HIS cc_start: 0.6932 (t70) cc_final: 0.6482 (t70) REVERT: D 58 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7169 (mt) REVERT: D 96 TRP cc_start: 0.7113 (p-90) cc_final: 0.6876 (p-90) REVERT: D 117 ASP cc_start: 0.7951 (t0) cc_final: 0.7681 (m-30) REVERT: D 256 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7897 (tt) REVERT: D 357 THR cc_start: 0.7413 (t) cc_final: 0.7185 (t) REVERT: D 429 ARG cc_start: 0.7246 (mtp180) cc_final: 0.6549 (mtt-85) REVERT: D 516 GLN cc_start: 0.8024 (tp40) cc_final: 0.7773 (tm-30) REVERT: D 614 ARG cc_start: 0.7918 (ttt90) cc_final: 0.7400 (mpp-170) REVERT: D 625 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7581 (mp10) REVERT: D 638 GLU cc_start: 0.7694 (pt0) cc_final: 0.7382 (tm-30) REVERT: D 659 GLN cc_start: 0.7790 (mt0) cc_final: 0.7397 (mm-40) REVERT: D 725 ASP cc_start: 0.8329 (t0) cc_final: 0.8029 (m-30) REVERT: D 933 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7883 (mm-30) REVERT: D 1046 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7155 (mp0) REVERT: D 1332 VAL cc_start: 0.7642 (t) cc_final: 0.7426 (t) REVERT: D 1336 TRP cc_start: 0.7552 (m100) cc_final: 0.6906 (m100) REVERT: D 1487 THR cc_start: 0.8000 (OUTLIER) cc_final: 0.7728 (t) outliers start: 128 outliers final: 82 residues processed: 602 average time/residue: 0.6138 time to fit residues: 466.1643 Evaluate side-chains 601 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 503 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 1150 MET Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1345 LEU Chi-restraints excluded: chain A residue 1444 ASP Chi-restraints excluded: chain A residue 1473 LEU Chi-restraints excluded: chain A residue 1474 ASN Chi-restraints excluded: chain A residue 1487 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 530 HIS Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 1150 MET Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1345 LEU Chi-restraints excluded: chain B residue 1444 ASP Chi-restraints excluded: chain B residue 1473 LEU Chi-restraints excluded: chain B residue 1474 ASN Chi-restraints excluded: chain B residue 1487 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 455 MET Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 530 HIS Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 625 GLN Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 681 SER Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1150 MET Chi-restraints excluded: chain C residue 1333 VAL Chi-restraints excluded: chain C residue 1345 LEU Chi-restraints excluded: chain C residue 1473 LEU Chi-restraints excluded: chain C residue 1474 ASN Chi-restraints excluded: chain C residue 1487 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 530 HIS Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 681 SER Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 844 VAL Chi-restraints excluded: chain D residue 1150 MET Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1345 LEU Chi-restraints excluded: chain D residue 1444 ASP Chi-restraints excluded: chain D residue 1473 LEU Chi-restraints excluded: chain D residue 1474 ASN Chi-restraints excluded: chain D residue 1487 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 343 optimal weight: 0.7980 chunk 287 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 333 optimal weight: 0.5980 chunk 429 optimal weight: 1.9990 chunk 375 optimal weight: 10.0000 chunk 415 optimal weight: 9.9990 chunk 348 optimal weight: 0.8980 chunk 201 optimal weight: 0.9990 chunk 361 optimal weight: 2.9990 chunk 310 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1156 HIS ** A1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1479 HIS ** D1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1485 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.178013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.119900 restraints weight = 50703.596| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.99 r_work: 0.3176 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 40295 Z= 0.114 Angle : 0.491 7.449 55036 Z= 0.256 Chirality : 0.038 0.148 6452 Planarity : 0.004 0.044 7020 Dihedral : 5.879 89.262 6700 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.83 % Allowed : 16.94 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.11), residues: 5356 helix: 2.07 (0.09), residues: 3064 sheet: -0.96 (0.23), residues: 436 loop : -0.17 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 517 TYR 0.024 0.002 TYR B1493 PHE 0.013 0.001 PHE D 879 TRP 0.011 0.001 TRP C1052 HIS 0.003 0.001 HIS A 601 Details of bonding type rmsd covalent geometry : bond 0.00256 (40292) covalent geometry : angle 0.49088 (55020) SS BOND : bond 0.00024 ( 3) SS BOND : angle 0.24131 ( 16) hydrogen bonds : bond 0.03881 ( 2304) hydrogen bonds : angle 3.68442 ( 6828) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10712 Ramachandran restraints generated. 5356 Oldfield, 0 Emsley, 5356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10712 Ramachandran restraints generated. 5356 Oldfield, 0 Emsley, 5356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 523 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7216 (mt) REVERT: A 117 ASP cc_start: 0.7917 (t0) cc_final: 0.7663 (m-30) REVERT: A 256 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7986 (tt) REVERT: A 357 THR cc_start: 0.7478 (t) cc_final: 0.7227 (t) REVERT: A 429 ARG cc_start: 0.7203 (mtm-85) cc_final: 0.6666 (mtt-85) REVERT: A 502 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7486 (tt0) REVERT: A 614 ARG cc_start: 0.7999 (ttt90) cc_final: 0.7511 (mpp-170) REVERT: A 625 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7647 (mp10) REVERT: A 638 GLU cc_start: 0.7785 (pt0) cc_final: 0.7478 (tm-30) REVERT: A 659 GLN cc_start: 0.7882 (mt0) cc_final: 0.7514 (mm-40) REVERT: A 725 ASP cc_start: 0.8399 (t0) cc_final: 0.8160 (m-30) REVERT: A 933 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7931 (mm-30) REVERT: A 1046 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7255 (mp0) REVERT: A 1336 TRP cc_start: 0.7589 (m100) cc_final: 0.6983 (m100) REVERT: A 1487 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7696 (t) REVERT: B 58 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7235 (mt) REVERT: B 96 TRP cc_start: 0.7027 (p-90) cc_final: 0.6788 (p-90) REVERT: B 117 ASP cc_start: 0.7935 (t0) cc_final: 0.7672 (m-30) REVERT: B 256 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7987 (tt) REVERT: B 357 THR cc_start: 0.7462 (t) cc_final: 0.7211 (t) REVERT: B 429 ARG cc_start: 0.7182 (mtm-85) cc_final: 0.6648 (mtt-85) REVERT: B 475 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7861 (mt-10) REVERT: B 502 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7551 (tt0) REVERT: B 614 ARG cc_start: 0.7985 (ttt90) cc_final: 0.7509 (mpp-170) REVERT: B 625 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7646 (mp10) REVERT: B 638 GLU cc_start: 0.7783 (pt0) cc_final: 0.7477 (tm-30) REVERT: B 659 GLN cc_start: 0.7889 (mt0) cc_final: 0.7521 (mm-40) REVERT: B 725 ASP cc_start: 0.8399 (t0) cc_final: 0.8168 (m-30) REVERT: B 933 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7922 (mm-30) REVERT: B 1046 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7245 (mp0) REVERT: B 1332 VAL cc_start: 0.7716 (t) cc_final: 0.7503 (t) REVERT: B 1336 TRP cc_start: 0.7586 (m100) cc_final: 0.6974 (m100) REVERT: B 1443 HIS cc_start: 0.6887 (t-90) cc_final: 0.6670 (t70) REVERT: B 1487 THR cc_start: 0.7960 (OUTLIER) cc_final: 0.7672 (t) REVERT: C 58 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7188 (mt) REVERT: C 117 ASP cc_start: 0.7917 (t0) cc_final: 0.7653 (m-30) REVERT: C 256 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7982 (tt) REVERT: C 357 THR cc_start: 0.7468 (t) cc_final: 0.7217 (t) REVERT: C 429 ARG cc_start: 0.7182 (mtm-85) cc_final: 0.6651 (mtt-85) REVERT: C 502 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7557 (tt0) REVERT: C 614 ARG cc_start: 0.7995 (ttt90) cc_final: 0.7505 (mpp-170) REVERT: C 625 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: C 638 GLU cc_start: 0.7769 (pt0) cc_final: 0.7461 (tm-30) REVERT: C 659 GLN cc_start: 0.7889 (mt0) cc_final: 0.7516 (mm-40) REVERT: C 725 ASP cc_start: 0.8384 (t0) cc_final: 0.8152 (m-30) REVERT: C 933 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7938 (mm-30) REVERT: C 1046 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7249 (mp0) REVERT: C 1332 VAL cc_start: 0.7887 (t) cc_final: 0.7666 (t) REVERT: C 1336 TRP cc_start: 0.7577 (m100) cc_final: 0.6987 (m100) REVERT: C 1443 HIS cc_start: 0.6942 (t70) cc_final: 0.6742 (t-90) REVERT: D 58 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7197 (mt) REVERT: D 96 TRP cc_start: 0.7064 (p-90) cc_final: 0.6796 (p-90) REVERT: D 117 ASP cc_start: 0.7916 (t0) cc_final: 0.7688 (m-30) REVERT: D 256 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7975 (tt) REVERT: D 357 THR cc_start: 0.7478 (t) cc_final: 0.7228 (t) REVERT: D 428 LYS cc_start: 0.7963 (mtpp) cc_final: 0.7241 (mtmt) REVERT: D 429 ARG cc_start: 0.7307 (mtp180) cc_final: 0.6607 (mtt-85) REVERT: D 502 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7485 (tt0) REVERT: D 614 ARG cc_start: 0.7989 (ttt90) cc_final: 0.7497 (mpp-170) REVERT: D 625 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7647 (mp10) REVERT: D 638 GLU cc_start: 0.7781 (pt0) cc_final: 0.7477 (tm-30) REVERT: D 659 GLN cc_start: 0.7874 (mt0) cc_final: 0.7501 (mm-40) REVERT: D 725 ASP cc_start: 0.8385 (t0) cc_final: 0.8155 (m-30) REVERT: D 933 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7975 (mm-30) REVERT: D 1046 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7255 (mp0) REVERT: D 1336 TRP cc_start: 0.7588 (m100) cc_final: 0.6991 (m100) REVERT: D 1487 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7704 (t) outliers start: 133 outliers final: 87 residues processed: 600 average time/residue: 0.6130 time to fit residues: 462.4353 Evaluate side-chains 597 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 495 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 1150 MET Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1345 LEU Chi-restraints excluded: chain A residue 1473 LEU Chi-restraints excluded: chain A residue 1474 ASN Chi-restraints excluded: chain A residue 1487 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 530 HIS Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 1150 MET Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1345 LEU Chi-restraints excluded: chain B residue 1473 LEU Chi-restraints excluded: chain B residue 1474 ASN Chi-restraints excluded: chain B residue 1487 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 530 HIS Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 625 GLN Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 681 SER Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1150 MET Chi-restraints excluded: chain C residue 1333 VAL Chi-restraints excluded: chain C residue 1345 LEU Chi-restraints excluded: chain C residue 1473 LEU Chi-restraints excluded: chain C residue 1474 ASN Chi-restraints excluded: chain C residue 1487 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 530 HIS Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 681 SER Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 844 VAL Chi-restraints excluded: chain D residue 1150 MET Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1345 LEU Chi-restraints excluded: chain D residue 1473 LEU Chi-restraints excluded: chain D residue 1474 ASN Chi-restraints excluded: chain D residue 1487 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 179 optimal weight: 4.9990 chunk 254 optimal weight: 10.0000 chunk 16 optimal weight: 0.4980 chunk 266 optimal weight: 1.9990 chunk 446 optimal weight: 6.9990 chunk 386 optimal weight: 20.0000 chunk 462 optimal weight: 1.9990 chunk 303 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 223 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1485 HIS B 556 ASN C 556 ASN C1479 HIS D 556 ASN D1485 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.176663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.117537 restraints weight = 50485.088| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.06 r_work: 0.3124 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 40295 Z= 0.170 Angle : 0.549 9.648 55036 Z= 0.288 Chirality : 0.040 0.167 6452 Planarity : 0.005 0.059 7020 Dihedral : 6.049 88.310 6700 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.71 % Allowed : 17.35 % Favored : 78.94 % 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: 1.31 (0.11), residues: 5356 helix: 1.86 (0.09), residues: 3068 sheet: -0.99 (0.23), residues: 440 loop : -0.28 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 112 TYR 0.044 0.002 TYR B 216 PHE 0.024 0.002 PHE B 752 TRP 0.011 0.001 TRP D1052 HIS 0.004 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00402 (40292) covalent geometry : angle 0.54878 (55020) SS BOND : bond 0.00032 ( 3) SS BOND : angle 0.39698 ( 16) hydrogen bonds : bond 0.04746 ( 2304) hydrogen bonds : angle 3.84635 ( 6828) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10712 Ramachandran restraints generated. 5356 Oldfield, 0 Emsley, 5356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10712 Ramachandran restraints generated. 5356 Oldfield, 0 Emsley, 5356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 496 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7171 (mt) REVERT: A 117 ASP cc_start: 0.7943 (t0) cc_final: 0.7625 (m-30) REVERT: A 256 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7995 (tt) REVERT: A 357 THR cc_start: 0.7480 (t) cc_final: 0.7218 (t) REVERT: A 428 LYS cc_start: 0.7898 (mtpp) cc_final: 0.7132 (mtmt) REVERT: A 429 ARG cc_start: 0.7186 (mtm-85) cc_final: 0.6724 (mtt-85) REVERT: A 614 ARG cc_start: 0.7990 (ttt90) cc_final: 0.7535 (mpp-170) REVERT: A 625 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7592 (mp10) REVERT: A 638 GLU cc_start: 0.7769 (pt0) cc_final: 0.7395 (tm-30) REVERT: A 659 GLN cc_start: 0.7872 (mt0) cc_final: 0.7502 (mm-40) REVERT: A 725 ASP cc_start: 0.8450 (t0) cc_final: 0.8039 (m-30) REVERT: A 933 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7937 (mm-30) REVERT: A 1046 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7222 (mp0) REVERT: A 1336 TRP cc_start: 0.7602 (m100) cc_final: 0.6847 (m100) REVERT: B 58 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7171 (mt) REVERT: B 117 ASP cc_start: 0.7944 (t0) cc_final: 0.7619 (m-30) REVERT: B 256 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7988 (tt) REVERT: B 357 THR cc_start: 0.7480 (t) cc_final: 0.7216 (t) REVERT: B 428 LYS cc_start: 0.7900 (mtpp) cc_final: 0.7137 (mtmt) REVERT: B 429 ARG cc_start: 0.7185 (mtm-85) cc_final: 0.6723 (mtt-85) REVERT: B 475 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7783 (mt-10) REVERT: B 614 ARG cc_start: 0.7975 (ttt90) cc_final: 0.7528 (mpp-170) REVERT: B 625 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.7590 (mp10) REVERT: B 638 GLU cc_start: 0.7762 (pt0) cc_final: 0.7390 (tm-30) REVERT: B 659 GLN cc_start: 0.7867 (mt0) cc_final: 0.7498 (mm-40) REVERT: B 725 ASP cc_start: 0.8452 (t0) cc_final: 0.8043 (m-30) REVERT: B 933 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7903 (mm-30) REVERT: B 1046 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7190 (mp0) REVERT: B 1332 VAL cc_start: 0.7696 (t) cc_final: 0.7490 (t) REVERT: B 1336 TRP cc_start: 0.7623 (m100) cc_final: 0.6855 (m100) REVERT: C 58 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7158 (mt) REVERT: C 117 ASP cc_start: 0.7973 (t0) cc_final: 0.7592 (m-30) REVERT: C 159 ARG cc_start: 0.7113 (mtp85) cc_final: 0.6741 (mtp85) REVERT: C 256 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7986 (tt) REVERT: C 357 THR cc_start: 0.7510 (t) cc_final: 0.7237 (t) REVERT: C 428 LYS cc_start: 0.7884 (mtpp) cc_final: 0.7121 (mtmt) REVERT: C 429 ARG cc_start: 0.7172 (mtm-85) cc_final: 0.6715 (mtt-85) REVERT: C 614 ARG cc_start: 0.7980 (ttt90) cc_final: 0.7522 (mpp-170) REVERT: C 625 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.7590 (mp10) REVERT: C 638 GLU cc_start: 0.7754 (pt0) cc_final: 0.7385 (tm-30) REVERT: C 659 GLN cc_start: 0.7870 (mt0) cc_final: 0.7496 (mm-40) REVERT: C 725 ASP cc_start: 0.8440 (t0) cc_final: 0.8034 (m-30) REVERT: C 933 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7946 (mm-30) REVERT: C 1046 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7180 (mp0) REVERT: C 1332 VAL cc_start: 0.7828 (t) cc_final: 0.7593 (t) REVERT: C 1336 TRP cc_start: 0.7624 (m100) cc_final: 0.6944 (m100) REVERT: D 58 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7142 (mt) REVERT: D 117 ASP cc_start: 0.7965 (t0) cc_final: 0.7606 (m-30) REVERT: D 159 ARG cc_start: 0.7116 (mtp85) cc_final: 0.6736 (mtp85) REVERT: D 216 TYR cc_start: 0.6562 (OUTLIER) cc_final: 0.6225 (t80) REVERT: D 256 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8013 (tt) REVERT: D 357 THR cc_start: 0.7492 (t) cc_final: 0.7221 (t) REVERT: D 429 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6665 (mtt-85) REVERT: D 614 ARG cc_start: 0.7986 (ttt90) cc_final: 0.7519 (mpp-170) REVERT: D 625 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.7587 (mp10) REVERT: D 638 GLU cc_start: 0.7758 (pt0) cc_final: 0.7393 (tm-30) REVERT: D 659 GLN cc_start: 0.7858 (mt0) cc_final: 0.7486 (mm-40) REVERT: D 725 ASP cc_start: 0.8445 (t0) cc_final: 0.8033 (m-30) REVERT: D 933 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7954 (mm-30) REVERT: D 1046 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7203 (mp0) REVERT: D 1336 TRP cc_start: 0.7616 (m100) cc_final: 0.6860 (m100) outliers start: 129 outliers final: 80 residues processed: 583 average time/residue: 0.5963 time to fit residues: 436.6775 Evaluate side-chains 564 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 470 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 1150 MET Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1345 LEU Chi-restraints excluded: chain A residue 1473 LEU Chi-restraints excluded: chain A residue 1474 ASN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1345 LEU Chi-restraints excluded: chain B residue 1473 LEU Chi-restraints excluded: chain B residue 1474 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 625 GLN Chi-restraints excluded: chain C residue 681 SER Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1333 VAL Chi-restraints excluded: chain C residue 1345 LEU Chi-restraints excluded: chain C residue 1444 ASP Chi-restraints excluded: chain C residue 1473 LEU Chi-restraints excluded: chain C residue 1474 ASN Chi-restraints excluded: chain C residue 1487 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 216 TYR Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 429 ARG Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain D residue 681 SER Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 844 VAL Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1345 LEU Chi-restraints excluded: chain D residue 1473 LEU Chi-restraints excluded: chain D residue 1474 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 318 optimal weight: 1.9990 chunk 451 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 466 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 524 optimal weight: 20.0000 chunk 479 optimal weight: 6.9990 chunk 384 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN A1156 HIS A1485 HIS B 692 ASN C 692 ASN C1140 ASN D1485 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.176052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.118518 restraints weight = 50707.644| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.11 r_work: 0.3114 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 40295 Z= 0.185 Angle : 0.561 7.853 55036 Z= 0.296 Chirality : 0.041 0.169 6452 Planarity : 0.005 0.051 7020 Dihedral : 6.159 88.650 6700 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.48 % Allowed : 17.64 % Favored : 78.88 % 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: 1.23 (0.11), residues: 5356 helix: 1.78 (0.09), residues: 3068 sheet: -0.59 (0.24), residues: 392 loop : -0.42 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1480 TYR 0.028 0.003 TYR C 110 PHE 0.017 0.002 PHE B 879 TRP 0.032 0.002 TRP B 96 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00439 (40292) covalent geometry : angle 0.56101 (55020) SS BOND : bond 0.00015 ( 3) SS BOND : angle 0.42064 ( 16) hydrogen bonds : bond 0.04847 ( 2304) hydrogen bonds : angle 3.92599 ( 6828) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10712 Ramachandran restraints generated. 5356 Oldfield, 0 Emsley, 5356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10712 Ramachandran restraints generated. 5356 Oldfield, 0 Emsley, 5356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 483 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7102 (mt) REVERT: A 117 ASP cc_start: 0.7943 (t0) cc_final: 0.7591 (m-30) REVERT: A 159 ARG cc_start: 0.7162 (mtp85) cc_final: 0.6798 (mtp85) REVERT: A 189 MET cc_start: 0.8427 (mpp) cc_final: 0.8128 (mtm) REVERT: A 256 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8064 (tt) REVERT: A 429 ARG cc_start: 0.7240 (mtm-85) cc_final: 0.6699 (mtt-85) REVERT: A 614 ARG cc_start: 0.8036 (ttt90) cc_final: 0.7594 (mpp-170) REVERT: A 625 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7648 (mp10) REVERT: A 638 GLU cc_start: 0.7829 (pt0) cc_final: 0.7445 (tm-30) REVERT: A 659 GLN cc_start: 0.7914 (mt0) cc_final: 0.7582 (mm-40) REVERT: A 666 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8096 (tp30) REVERT: A 725 ASP cc_start: 0.8506 (t0) cc_final: 0.8089 (m-30) REVERT: A 933 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7907 (mm-30) REVERT: A 1046 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7250 (mp0) REVERT: A 1336 TRP cc_start: 0.7649 (m100) cc_final: 0.6823 (m100) REVERT: A 1465 ARG cc_start: 0.4063 (pmt170) cc_final: 0.3571 (ptt-90) REVERT: B 58 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7131 (mt) REVERT: B 117 ASP cc_start: 0.7984 (t0) cc_final: 0.7622 (m-30) REVERT: B 159 ARG cc_start: 0.7150 (mtp85) cc_final: 0.6782 (mtp85) REVERT: B 189 MET cc_start: 0.8436 (mpp) cc_final: 0.8137 (mtm) REVERT: B 256 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8059 (tt) REVERT: B 429 ARG cc_start: 0.7238 (mtm-85) cc_final: 0.6697 (mtt-85) REVERT: B 614 ARG cc_start: 0.8023 (ttt90) cc_final: 0.7590 (mpp-170) REVERT: B 625 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.7653 (mp10) REVERT: B 638 GLU cc_start: 0.7836 (pt0) cc_final: 0.7453 (tm-30) REVERT: B 659 GLN cc_start: 0.7906 (mt0) cc_final: 0.7576 (mm-40) REVERT: B 666 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8081 (tp30) REVERT: B 725 ASP cc_start: 0.8508 (t0) cc_final: 0.8095 (m-30) REVERT: B 933 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7940 (mm-30) REVERT: B 1046 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7231 (mp0) REVERT: B 1336 TRP cc_start: 0.7676 (m100) cc_final: 0.6849 (m100) REVERT: B 1465 ARG cc_start: 0.4078 (pmt170) cc_final: 0.3581 (ptt-90) REVERT: B 1482 LEU cc_start: 0.8199 (mp) cc_final: 0.7946 (pp) REVERT: C 58 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7111 (mt) REVERT: C 117 ASP cc_start: 0.7954 (t0) cc_final: 0.7577 (m-30) REVERT: C 159 ARG cc_start: 0.7133 (mtp85) cc_final: 0.6771 (mtp85) REVERT: C 189 MET cc_start: 0.8420 (mpp) cc_final: 0.8118 (mtm) REVERT: C 256 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8056 (tt) REVERT: C 429 ARG cc_start: 0.7243 (mtm-85) cc_final: 0.6696 (mtt-85) REVERT: C 614 ARG cc_start: 0.8030 (ttt90) cc_final: 0.7581 (mpp-170) REVERT: C 625 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7654 (mp10) REVERT: C 638 GLU cc_start: 0.7815 (pt0) cc_final: 0.7435 (tm-30) REVERT: C 659 GLN cc_start: 0.7910 (mt0) cc_final: 0.7574 (mm-40) REVERT: C 666 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8085 (tp30) REVERT: C 725 ASP cc_start: 0.8504 (t0) cc_final: 0.8090 (m-30) REVERT: C 933 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7920 (mm-30) REVERT: C 1046 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7214 (mp0) REVERT: C 1332 VAL cc_start: 0.7826 (t) cc_final: 0.7594 (t) REVERT: C 1336 TRP cc_start: 0.7657 (m100) cc_final: 0.6894 (m100) REVERT: C 1443 HIS cc_start: 0.7039 (t70) cc_final: 0.6764 (t-90) REVERT: C 1465 ARG cc_start: 0.4113 (pmt170) cc_final: 0.3749 (ptt-90) REVERT: D 58 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7134 (mt) REVERT: D 81 MET cc_start: 0.5984 (tpp) cc_final: 0.4951 (tmm) REVERT: D 117 ASP cc_start: 0.7965 (t0) cc_final: 0.7602 (m-30) REVERT: D 159 ARG cc_start: 0.7142 (mtp85) cc_final: 0.6771 (mtp85) REVERT: D 189 MET cc_start: 0.8416 (mpp) cc_final: 0.7970 (mtm) REVERT: D 216 TYR cc_start: 0.6607 (OUTLIER) cc_final: 0.6214 (t80) REVERT: D 256 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8068 (tt) REVERT: D 429 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6703 (mtt-85) REVERT: D 614 ARG cc_start: 0.8036 (ttt90) cc_final: 0.7586 (mpp-170) REVERT: D 625 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.7666 (mp10) REVERT: D 638 GLU cc_start: 0.7831 (pt0) cc_final: 0.7442 (tm-30) REVERT: D 659 GLN cc_start: 0.7904 (mt0) cc_final: 0.7571 (mm-40) REVERT: D 666 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8100 (tp30) REVERT: D 725 ASP cc_start: 0.8504 (t0) cc_final: 0.8087 (m-30) REVERT: D 933 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7938 (mm-30) REVERT: D 1046 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7232 (mp0) REVERT: D 1336 TRP cc_start: 0.7660 (m100) cc_final: 0.6832 (m100) REVERT: D 1465 ARG cc_start: 0.4022 (pmt170) cc_final: 0.3520 (ptt-90) outliers start: 121 outliers final: 79 residues processed: 572 average time/residue: 0.5980 time to fit residues: 429.0547 Evaluate side-chains 564 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 467 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 1150 MET Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1345 LEU Chi-restraints excluded: chain A residue 1444 ASP Chi-restraints excluded: chain A residue 1473 LEU Chi-restraints excluded: chain A residue 1474 ASN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 1150 MET Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1345 LEU Chi-restraints excluded: chain B residue 1473 LEU Chi-restraints excluded: chain B residue 1474 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 455 MET Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 625 GLN Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 681 SER Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1333 VAL Chi-restraints excluded: chain C residue 1345 LEU Chi-restraints excluded: chain C residue 1473 LEU Chi-restraints excluded: chain C residue 1474 ASN Chi-restraints excluded: chain C residue 1487 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 216 TYR Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 429 ARG Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 681 SER Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 844 VAL Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1345 LEU Chi-restraints excluded: chain D residue 1444 ASP Chi-restraints excluded: chain D residue 1473 LEU Chi-restraints excluded: chain D residue 1474 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 357 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 364 optimal weight: 0.9980 chunk 348 optimal weight: 0.9990 chunk 523 optimal weight: 6.9990 chunk 455 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 433 optimal weight: 0.8980 chunk 48 optimal weight: 0.0770 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.178456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.119146 restraints weight = 50483.182| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.88 r_work: 0.3191 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 40295 Z= 0.115 Angle : 0.507 8.074 55036 Z= 0.262 Chirality : 0.038 0.156 6452 Planarity : 0.004 0.050 7020 Dihedral : 5.820 82.592 6700 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.76 % Allowed : 18.79 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.12), residues: 5356 helix: 2.04 (0.09), residues: 3068 sheet: -0.47 (0.25), residues: 392 loop : -0.27 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1161 TYR 0.024 0.002 TYR D 110 PHE 0.030 0.001 PHE C 752 TRP 0.023 0.001 TRP D 96 HIS 0.003 0.001 HIS A1156 Details of bonding type rmsd covalent geometry : bond 0.00260 (40292) covalent geometry : angle 0.50675 (55020) SS BOND : bond 0.00001 ( 3) SS BOND : angle 0.23526 ( 16) hydrogen bonds : bond 0.03857 ( 2304) hydrogen bonds : angle 3.77590 ( 6828) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10712 Ramachandran restraints generated. 5356 Oldfield, 0 Emsley, 5356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10712 Ramachandran restraints generated. 5356 Oldfield, 0 Emsley, 5356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 495 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7156 (mt) REVERT: A 76 MET cc_start: 0.7763 (ttm) cc_final: 0.7524 (mmm) REVERT: A 115 VAL cc_start: 0.8013 (OUTLIER) cc_final: 0.7736 (m) REVERT: A 117 ASP cc_start: 0.7858 (t0) cc_final: 0.7561 (m-30) REVERT: A 133 LYS cc_start: 0.7829 (tttt) cc_final: 0.6684 (mttt) REVERT: A 159 ARG cc_start: 0.7127 (mtp85) cc_final: 0.6797 (mtp85) REVERT: A 189 MET cc_start: 0.8343 (mpp) cc_final: 0.7914 (mtm) REVERT: A 256 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7928 (tt) REVERT: A 614 ARG cc_start: 0.7888 (ttt90) cc_final: 0.7412 (mpp-170) REVERT: A 625 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7498 (mp10) REVERT: A 638 GLU cc_start: 0.7750 (pt0) cc_final: 0.7362 (tm-30) REVERT: A 659 GLN cc_start: 0.7688 (mt0) cc_final: 0.7362 (mm-40) REVERT: A 725 ASP cc_start: 0.8306 (t0) cc_final: 0.7992 (m-30) REVERT: A 933 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7867 (mm-30) REVERT: A 1046 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7138 (mp0) REVERT: A 1081 MET cc_start: 0.6832 (mtm) cc_final: 0.6591 (mtt) REVERT: A 1336 TRP cc_start: 0.7600 (m100) cc_final: 0.6756 (m100) REVERT: A 1465 ARG cc_start: 0.3864 (pmt170) cc_final: 0.3508 (ptt-90) REVERT: B 58 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7171 (mt) REVERT: B 115 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7732 (m) REVERT: B 117 ASP cc_start: 0.7944 (t0) cc_final: 0.7602 (m-30) REVERT: B 133 LYS cc_start: 0.7844 (tttt) cc_final: 0.6694 (mttt) REVERT: B 159 ARG cc_start: 0.7128 (mtp85) cc_final: 0.6778 (mtp85) REVERT: B 256 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7886 (tt) REVERT: B 614 ARG cc_start: 0.7886 (ttt90) cc_final: 0.7412 (mpp-170) REVERT: B 625 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.7507 (mp10) REVERT: B 638 GLU cc_start: 0.7751 (pt0) cc_final: 0.7356 (tm-30) REVERT: B 659 GLN cc_start: 0.7701 (mt0) cc_final: 0.7374 (mm-40) REVERT: B 725 ASP cc_start: 0.8315 (t0) cc_final: 0.8005 (m-30) REVERT: B 933 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7838 (mm-30) REVERT: B 1046 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7113 (mp0) REVERT: B 1336 TRP cc_start: 0.7582 (m100) cc_final: 0.6790 (m100) REVERT: B 1465 ARG cc_start: 0.3858 (pmt170) cc_final: 0.3507 (ptt-90) REVERT: C 58 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7122 (mt) REVERT: C 76 MET cc_start: 0.7761 (ttm) cc_final: 0.7466 (tpp) REVERT: C 115 VAL cc_start: 0.7986 (OUTLIER) cc_final: 0.7712 (m) REVERT: C 117 ASP cc_start: 0.7894 (t0) cc_final: 0.7495 (m-30) REVERT: C 133 LYS cc_start: 0.7810 (tttt) cc_final: 0.6652 (mttt) REVERT: C 159 ARG cc_start: 0.7069 (mtp85) cc_final: 0.6803 (mtp85) REVERT: C 189 MET cc_start: 0.8350 (mpp) cc_final: 0.7914 (mtm) REVERT: C 256 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7926 (tt) REVERT: C 614 ARG cc_start: 0.7885 (ttt90) cc_final: 0.7412 (mpp-170) REVERT: C 625 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7489 (mp10) REVERT: C 638 GLU cc_start: 0.7749 (pt0) cc_final: 0.7356 (tm-30) REVERT: C 659 GLN cc_start: 0.7697 (mt0) cc_final: 0.7368 (mm-40) REVERT: C 725 ASP cc_start: 0.8302 (t0) cc_final: 0.7997 (m-30) REVERT: C 933 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7840 (mm-30) REVERT: C 1046 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7107 (mp0) REVERT: C 1081 MET cc_start: 0.6817 (mtm) cc_final: 0.6576 (mtt) REVERT: C 1332 VAL cc_start: 0.7769 (t) cc_final: 0.7561 (t) REVERT: C 1336 TRP cc_start: 0.7596 (m100) cc_final: 0.6797 (m100) REVERT: C 1465 ARG cc_start: 0.3858 (pmt170) cc_final: 0.3507 (ptt-90) REVERT: D 58 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7155 (mt) REVERT: D 81 MET cc_start: 0.5700 (tpp) cc_final: 0.4849 (tmm) REVERT: D 117 ASP cc_start: 0.7932 (t0) cc_final: 0.7602 (m-30) REVERT: D 133 LYS cc_start: 0.7834 (tttt) cc_final: 0.6690 (mttt) REVERT: D 159 ARG cc_start: 0.7077 (mtp85) cc_final: 0.6797 (mtp85) REVERT: D 189 MET cc_start: 0.8344 (mpp) cc_final: 0.7919 (mtm) REVERT: D 256 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7940 (tt) REVERT: D 429 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6618 (mtt-85) REVERT: D 614 ARG cc_start: 0.7893 (ttt90) cc_final: 0.7405 (mpp-170) REVERT: D 625 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7504 (mp10) REVERT: D 638 GLU cc_start: 0.7738 (pt0) cc_final: 0.7351 (tm-30) REVERT: D 659 GLN cc_start: 0.7691 (mt0) cc_final: 0.7396 (mm-40) REVERT: D 725 ASP cc_start: 0.8297 (t0) cc_final: 0.7990 (m-30) REVERT: D 933 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7890 (mm-30) REVERT: D 1046 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7125 (mp0) REVERT: D 1081 MET cc_start: 0.6815 (mtm) cc_final: 0.6575 (mtt) REVERT: D 1336 TRP cc_start: 0.7607 (m100) cc_final: 0.6773 (m100) REVERT: D 1465 ARG cc_start: 0.3880 (pmt170) cc_final: 0.3405 (ptt-90) outliers start: 96 outliers final: 58 residues processed: 561 average time/residue: 0.6339 time to fit residues: 446.0940 Evaluate side-chains 538 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 464 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 1150 MET Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1345 LEU Chi-restraints excluded: chain A residue 1444 ASP Chi-restraints excluded: chain A residue 1474 ASN Chi-restraints excluded: chain A residue 1487 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1345 LEU Chi-restraints excluded: chain B residue 1444 ASP Chi-restraints excluded: chain B residue 1474 ASN Chi-restraints excluded: chain B residue 1487 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 625 GLN Chi-restraints excluded: chain C residue 681 SER Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 1333 VAL Chi-restraints excluded: chain C residue 1345 LEU Chi-restraints excluded: chain C residue 1474 ASN Chi-restraints excluded: chain C residue 1487 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 429 ARG Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain D residue 681 SER Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1345 LEU Chi-restraints excluded: chain D residue 1444 ASP Chi-restraints excluded: chain D residue 1474 ASN Chi-restraints excluded: chain D residue 1487 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 451 optimal weight: 0.5980 chunk 218 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 403 optimal weight: 4.9990 chunk 471 optimal weight: 3.9990 chunk 399 optimal weight: 10.0000 chunk 462 optimal weight: 4.9990 chunk 442 optimal weight: 0.8980 chunk 239 optimal weight: 0.9980 chunk 318 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1485 HIS B 296 GLN B1156 HIS D1156 HIS D1485 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.178388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.117576 restraints weight = 50653.259| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.94 r_work: 0.3195 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 40295 Z= 0.117 Angle : 0.509 8.780 55036 Z= 0.264 Chirality : 0.038 0.150 6452 Planarity : 0.004 0.048 7020 Dihedral : 5.688 78.714 6700 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.45 % Allowed : 18.96 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.12), residues: 5356 helix: 2.06 (0.09), residues: 3080 sheet: -0.70 (0.24), residues: 416 loop : -0.21 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 112 TYR 0.027 0.002 TYR D 110 PHE 0.020 0.001 PHE B 154 TRP 0.032 0.001 TRP D 96 HIS 0.003 0.001 HIS D 601 Details of bonding type rmsd covalent geometry : bond 0.00264 (40292) covalent geometry : angle 0.50878 (55020) SS BOND : bond 0.00022 ( 3) SS BOND : angle 0.24077 ( 16) hydrogen bonds : bond 0.03877 ( 2304) hydrogen bonds : angle 3.75228 ( 6828) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18963.44 seconds wall clock time: 321 minutes 50.03 seconds (19310.03 seconds total)