Starting phenix.real_space_refine on Fri Jun 27 05:31:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eu1_31306/06_2025/7eu1_31306.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eu1_31306/06_2025/7eu1_31306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eu1_31306/06_2025/7eu1_31306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eu1_31306/06_2025/7eu1_31306.map" model { file = "/net/cci-nas-00/data/ceres_data/7eu1_31306/06_2025/7eu1_31306.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eu1_31306/06_2025/7eu1_31306.cif" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 Mg 2 5.21 5 S 202 5.16 5 C 20197 2.51 5 N 5508 2.21 5 O 5843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.50s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31760 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 7701 Classifications: {'peptide': 1065} Incomplete info: {'truncation_to_alanine': 172} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 1017} Chain breaks: 8 Unresolved non-hydrogen bonds: 622 Unresolved non-hydrogen angles: 767 Unresolved non-hydrogen dihedrals: 497 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 10, 'ASP:plan': 29, 'PHE:plan': 2, 'GLU:plan': 26, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 392 Chain: "B" Number of atoms: 8170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8170 Classifications: {'peptide': 1073} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 1032} Chain breaks: 8 Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 308 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 15, 'PHE:plan': 1, 'GLU:plan': 26, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 244 Chain: "C" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2194 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 12, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 57 Chain: "E" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1526 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 6, 'TRANS': 192} Chain breaks: 1 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 85 Chain: "F" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 72} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1036 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 7, 'TRANS': 134} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "I" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 808 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 4, 'TRANS': 108} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 77 Chain: "J" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 503 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 60} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "K" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 737 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "L" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 333 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 44} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "M" Number of atoms: 8126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1055, 8126 Classifications: {'peptide': 1055} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 1014} Chain breaks: 4 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 415 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 204 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 320 SG CYS A 56 38.107 71.608 128.613 1.00 93.06 S ATOM 344 SG CYS A 59 38.236 74.321 131.221 1.00 90.75 S ATOM 391 SG CYS A 67 40.975 74.070 128.602 1.00 81.98 S ATOM 6121 SG CYS A1031 131.123 61.724 91.619 1.00 37.75 S ATOM 6190 SG CYS A1044 129.547 65.246 93.146 1.00 15.67 S ATOM 15506 SG CYS B1111 50.382 85.285 142.271 1.00 71.21 S ATOM 15600 SG CYS B1136 48.756 86.757 145.445 1.00 95.12 S ATOM 16556 SG CYS C 90 10.628 89.588 71.214 1.00 26.57 S ATOM 16608 SG CYS C 99 11.141 84.864 68.476 1.00 26.42 S ATOM 21765 SG CYS I 76 105.294 100.557 72.861 1.00 16.21 S ATOM 21786 SG CYS I 79 102.340 99.420 70.567 1.00 21.45 S ATOM 21957 SG CYS I 103 104.673 97.097 72.982 1.00 8.23 S ATOM 21992 SG CYS I 108 104.948 97.186 69.872 1.00 13.08 S ATOM 21286 SG CYS I 7 122.693 33.487 94.309 1.00 57.94 S ATOM 21302 SG CYS I 10 119.979 32.064 96.008 1.00 55.23 S ATOM 21440 SG CYS I 29 122.507 34.241 97.698 1.00 70.18 S ATOM 21465 SG CYS I 32 122.128 29.515 96.910 1.00 69.27 S ATOM 22106 SG CYS J 7 41.507 80.377 58.360 1.00 4.39 S ATOM 22130 SG CYS J 10 42.109 84.163 56.118 1.00 1.89 S ATOM 22400 SG CYS J 44 44.122 82.553 57.802 1.00 5.39 S ATOM 22406 SG CYS J 45 41.062 80.931 54.344 1.00 3.58 S ATOM 23335 SG CYS L 12 29.508 43.422 81.602 1.00 28.06 S ATOM 23353 SG CYS L 15 28.146 40.250 79.821 1.00 42.14 S ATOM 23441 SG CYS L 29 27.837 41.158 83.350 1.00 69.64 S ATOM 23467 SG CYS L 32 30.582 39.531 81.868 1.00 62.61 S Time building chain proxies: 17.96, per 1000 atoms: 0.57 Number of scatterers: 31760 At special positions: 0 Unit cell: (182.97, 167.99, 161.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 202 16.00 Mg 2 11.99 O 5843 8.00 N 5508 7.00 C 20197 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.64 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1601 " pdb="ZN ZN A1601 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1601 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1601 " - pdb=" ND1 HIS A 70 " pdb="ZN ZN A1601 " - pdb=" SG CYS A 56 " pdb=" ZN A1603 " pdb="ZN ZN A1603 " - pdb=" SG CYS A1031 " pdb="ZN ZN A1603 " - pdb=" SG CYS A1044 " pdb="ZN ZN A1603 " - pdb=" ND1 HIS A 983 " pdb="ZN ZN A1603 " - pdb=" NE2 HIS A 985 " pdb=" ZN B2001 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1111 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1136 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 99 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 90 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 79 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 108 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 76 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 29 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 32 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 15 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 12 " Number of angles added : 29 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7960 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 47 sheets defined 28.0% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.48 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 removed outlier: 3.624A pdb=" N ARG A 28 " --> pdb=" O ASN A 24 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 30 " --> pdb=" O ASN A 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 24 through 30' Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.990A pdb=" N VAL A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.550A pdb=" N ASP A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 357 through 362 removed outlier: 4.131A pdb=" N VAL A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 420 removed outlier: 3.621A pdb=" N SER A 419 " --> pdb=" O HIS A 416 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 420 " --> pdb=" O GLN A 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 420' Processing helix chain 'A' and resid 438 through 442 removed outlier: 3.723A pdb=" N CYS A 441 " --> pdb=" O PRO A 438 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 442 " --> pdb=" O ILE A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 442' Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 491 through 504 removed outlier: 3.545A pdb=" N THR A 495 " --> pdb=" O GLN A 491 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LYS A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 547 removed outlier: 3.709A pdb=" N PHE A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 550 No H-bonds generated for 'chain 'A' and resid 548 through 550' Processing helix chain 'A' and resid 587 through 594 Processing helix chain 'A' and resid 605 through 610 removed outlier: 3.515A pdb=" N MET A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 617 removed outlier: 3.589A pdb=" N MET A 617 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 629 removed outlier: 3.749A pdb=" N LEU A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 658 removed outlier: 3.606A pdb=" N TYR A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 650 " --> pdb=" O GLY A 646 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 652 " --> pdb=" O ARG A 648 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 658 " --> pdb=" O CYS A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 660 No H-bonds generated for 'chain 'A' and resid 659 through 660' Processing helix chain 'A' and resid 661 through 665 removed outlier: 3.683A pdb=" N ARG A 665 " --> pdb=" O GLU A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 682 removed outlier: 3.967A pdb=" N ASP A 682 " --> pdb=" O ASP A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 692 removed outlier: 3.572A pdb=" N ARG A 690 " --> pdb=" O PHE A 686 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A 691 " --> pdb=" O CYS A 687 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A 692 " --> pdb=" O TYR A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 708 Processing helix chain 'A' and resid 711 through 716 removed outlier: 3.730A pdb=" N ALA A 715 " --> pdb=" O GLN A 712 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 716 " --> pdb=" O ALA A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 731 removed outlier: 3.706A pdb=" N MET A 728 " --> pdb=" O SER A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 745 removed outlier: 3.629A pdb=" N VAL A 741 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN A 742 " --> pdb=" O GLY A 738 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N HIS A 743 " --> pdb=" O LYS A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 816 removed outlier: 3.611A pdb=" N SER A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 816 " --> pdb=" O HIS A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 835 removed outlier: 3.683A pdb=" N LEU A 831 " --> pdb=" O LEU A 827 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER A 832 " --> pdb=" O PRO A 828 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG A 833 " --> pdb=" O GLY A 829 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 834 " --> pdb=" O THR A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 891 removed outlier: 4.000A pdb=" N CYS A 883 " --> pdb=" O SER A 879 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 884 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 888 " --> pdb=" O ALA A 884 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 913 Processing helix chain 'A' and resid 931 through 936 removed outlier: 4.212A pdb=" N SER A 934 " --> pdb=" O GLU A 931 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 935 " --> pdb=" O TYR A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 944 Processing helix chain 'A' and resid 946 through 951 Processing helix chain 'A' and resid 988 through 993 Processing helix chain 'A' and resid 1002 through 1010 Processing helix chain 'A' and resid 1059 through 1064 Processing helix chain 'A' and resid 1067 through 1072 Processing helix chain 'A' and resid 1146 through 1175 removed outlier: 3.779A pdb=" N SER A1152 " --> pdb=" O ARG A1148 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE A1156 " --> pdb=" O SER A1152 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N ASP A1157 " --> pdb=" O VAL A1153 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA A1158 " --> pdb=" O TYR A1154 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A1165 " --> pdb=" O SER A1161 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER A1169 " --> pdb=" O ALA A1165 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A1170 " --> pdb=" O ASN A1166 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A1172 " --> pdb=" O GLU A1168 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A1175 " --> pdb=" O VAL A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1190 removed outlier: 3.527A pdb=" N ALA A1187 " --> pdb=" O LEU A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1209 removed outlier: 3.613A pdb=" N LYS A1206 " --> pdb=" O LYS A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1221 Processing helix chain 'A' and resid 1225 through 1234 removed outlier: 3.901A pdb=" N PHE A1229 " --> pdb=" O PRO A1225 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A1230 " --> pdb=" O SER A1226 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS A1231 " --> pdb=" O GLN A1227 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A1232 " --> pdb=" O CYS A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1249 Processing helix chain 'B' and resid 27 through 46 removed outlier: 3.537A pdb=" N LEU B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N CYS B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LYS B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 63 removed outlier: 3.571A pdb=" N GLU B 61 " --> pdb=" O ASN B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 removed outlier: 3.827A pdb=" N PHE B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 123 removed outlier: 3.670A pdb=" N LEU B 123 " --> pdb=" O TRP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 286 removed outlier: 4.026A pdb=" N LEU B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 295 removed outlier: 4.029A pdb=" N MET B 295 " --> pdb=" O LYS B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 320 removed outlier: 3.806A pdb=" N SER B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 removed outlier: 4.233A pdb=" N ALA B 331 " --> pdb=" O CYS B 327 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR B 334 " --> pdb=" O ASN B 330 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL B 335 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 357 removed outlier: 4.038A pdb=" N LEU B 354 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N HIS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 384 removed outlier: 4.095A pdb=" N PHE B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 372 " --> pdb=" O LYS B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 429 removed outlier: 4.250A pdb=" N GLU B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 416 " --> pdb=" O ARG B 412 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.739A pdb=" N SER B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG B 454 " --> pdb=" O ASN B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'B' and resid 504 through 508 removed outlier: 4.444A pdb=" N ARG B 507 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 599 removed outlier: 3.717A pdb=" N ALA B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 599 " --> pdb=" O LYS B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 656 removed outlier: 3.624A pdb=" N HIS B 656 " --> pdb=" O HIS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 669 removed outlier: 3.542A pdb=" N GLU B 668 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP B 669 " --> pdb=" O GLU B 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 665 through 669' Processing helix chain 'B' and resid 715 through 720 removed outlier: 4.274A pdb=" N GLN B 720 " --> pdb=" O LEU B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 759 removed outlier: 3.549A pdb=" N GLU B 759 " --> pdb=" O LEU B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 955 Processing helix chain 'B' and resid 958 through 969 removed outlier: 3.675A pdb=" N LYS B 967 " --> pdb=" O ALA B 963 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 968 " --> pdb=" O ALA B 964 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE B 969 " --> pdb=" O LEU B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1001 removed outlier: 3.508A pdb=" N ILE B1000 " --> pdb=" O GLY B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1008 removed outlier: 3.735A pdb=" N ALA B1007 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY B1008 " --> pdb=" O HIS B1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1004 through 1008' Processing helix chain 'B' and resid 1076 through 1086 removed outlier: 3.947A pdb=" N LEU B1083 " --> pdb=" O GLU B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1090 through 1097 removed outlier: 3.844A pdb=" N GLU B1094 " --> pdb=" O ALA B1090 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B1095 " --> pdb=" O ASN B1091 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B1096 " --> pdb=" O LEU B1092 " (cutoff:3.500A) Processing helix chain 'B' and resid 1148 through 1162 removed outlier: 3.893A pdb=" N LEU B1154 " --> pdb=" O GLY B1150 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 42 removed outlier: 4.023A pdb=" N ALA C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 37 " --> pdb=" O MET C 33 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 71 removed outlier: 3.788A pdb=" N HIS C 69 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 121 through 125 removed outlier: 3.738A pdb=" N LEU C 125 " --> pdb=" O SER C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 214 Processing helix chain 'C' and resid 244 through 250 Processing helix chain 'C' and resid 277 through 287 removed outlier: 4.045A pdb=" N VAL C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.709A pdb=" N LEU C 293 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 removed outlier: 3.888A pdb=" N MET E 18 " --> pdb=" O GLN E 14 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN E 19 " --> pdb=" O LYS E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 43 Processing helix chain 'E' and resid 83 through 92 removed outlier: 3.604A pdb=" N ARG E 88 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N MET E 89 " --> pdb=" O TYR E 85 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 111 Processing helix chain 'E' and resid 147 through 156 removed outlier: 4.608A pdb=" N THR E 153 " --> pdb=" O GLU E 149 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 154 " --> pdb=" O GLU E 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 83 removed outlier: 4.031A pdb=" N ARG F 72 " --> pdb=" O TYR F 68 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN F 80 " --> pdb=" O THR F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 107 removed outlier: 3.525A pdb=" N ALA F 101 " --> pdb=" O PRO F 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 35 through 39 removed outlier: 3.632A pdb=" N GLN J 39 " --> pdb=" O ASP J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 51 Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.882A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG K 47 " --> pdb=" O GLY K 43 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET K 48 " --> pdb=" O ASN K 44 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN K 49 " --> pdb=" O ILE K 45 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 112 removed outlier: 4.351A pdb=" N ASN K 88 " --> pdb=" O MET K 84 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN K 89 " --> pdb=" O GLN K 85 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA K 90 " --> pdb=" O ALA K 86 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP K 93 " --> pdb=" O GLN K 89 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU K 94 " --> pdb=" O ALA K 90 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU K 97 " --> pdb=" O ASP K 93 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP K 99 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA K 107 " --> pdb=" O ASN K 103 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU K 108 " --> pdb=" O GLN K 104 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE K 112 " --> pdb=" O GLU K 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 34 removed outlier: 3.640A pdb=" N LEU M 27 " --> pdb=" O ALA M 23 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG M 28 " --> pdb=" O ASP M 24 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE M 29 " --> pdb=" O GLU M 25 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU M 32 " --> pdb=" O ARG M 28 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS M 33 " --> pdb=" O PHE M 29 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU M 34 " --> pdb=" O LEU M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 removed outlier: 3.941A pdb=" N LYS M 67 " --> pdb=" O THR M 63 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN M 76 " --> pdb=" O LEU M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 249 through 254 removed outlier: 3.676A pdb=" N SER M 252 " --> pdb=" O ASP M 249 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY M 253 " --> pdb=" O ILE M 250 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 273 removed outlier: 3.554A pdb=" N ALA M 273 " --> pdb=" O LYS M 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 270 through 273' Processing helix chain 'M' and resid 292 through 305 removed outlier: 3.604A pdb=" N GLN M 298 " --> pdb=" O GLU M 294 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL M 303 " --> pdb=" O LEU M 299 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS M 304 " --> pdb=" O ASN M 300 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA M 305 " --> pdb=" O ALA M 301 " (cutoff:3.500A) Processing helix chain 'M' and resid 309 through 314 Processing helix chain 'M' and resid 315 through 324 removed outlier: 3.646A pdb=" N ILE M 319 " --> pdb=" O ASP M 315 " (cutoff:3.500A) Processing helix chain 'M' and resid 327 through 335 removed outlier: 4.025A pdb=" N VAL M 332 " --> pdb=" O GLU M 328 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE M 333 " --> pdb=" O THR M 329 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU M 334 " --> pdb=" O ALA M 330 " (cutoff:3.500A) Processing helix chain 'M' and resid 336 through 340 removed outlier: 3.671A pdb=" N GLN M 340 " --> pdb=" O LEU M 337 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 353 removed outlier: 3.863A pdb=" N THR M 353 " --> pdb=" O PHE M 349 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 358 Processing helix chain 'M' and resid 402 through 407 removed outlier: 3.701A pdb=" N ASN M 407 " --> pdb=" O TYR M 403 " (cutoff:3.500A) Processing helix chain 'M' and resid 448 through 460 removed outlier: 3.626A pdb=" N ASN M 452 " --> pdb=" O THR M 448 " (cutoff:3.500A) Processing helix chain 'M' and resid 496 through 502 Processing helix chain 'M' and resid 510 through 519 removed outlier: 3.515A pdb=" N ALA M 516 " --> pdb=" O SER M 512 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY M 519 " --> pdb=" O ALA M 515 " (cutoff:3.500A) Processing helix chain 'M' and resid 561 through 573 Processing helix chain 'M' and resid 632 through 640 Processing helix chain 'M' and resid 647 through 663 removed outlier: 4.018A pdb=" N ALA M 651 " --> pdb=" O ALA M 647 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET M 659 " --> pdb=" O VAL M 655 " (cutoff:3.500A) Processing helix chain 'M' and resid 667 through 677 removed outlier: 3.738A pdb=" N VAL M 673 " --> pdb=" O ALA M 669 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU M 674 " --> pdb=" O ALA M 670 " (cutoff:3.500A) Processing helix chain 'M' and resid 684 through 692 removed outlier: 3.715A pdb=" N LYS M 688 " --> pdb=" O ASN M 684 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET M 689 " --> pdb=" O LEU M 685 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU M 690 " --> pdb=" O LEU M 686 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN M 692 " --> pdb=" O LYS M 688 " (cutoff:3.500A) Processing helix chain 'M' and resid 701 through 719 removed outlier: 3.990A pdb=" N VAL M 708 " --> pdb=" O MET M 704 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS M 709 " --> pdb=" O MET M 705 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU M 711 " --> pdb=" O ARG M 707 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN M 713 " --> pdb=" O HIS M 709 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU M 714 " --> pdb=" O HIS M 710 " (cutoff:3.500A) Processing helix chain 'M' and resid 821 through 826 removed outlier: 3.793A pdb=" N GLU M 825 " --> pdb=" O PRO M 821 " (cutoff:3.500A) Processing helix chain 'M' and resid 872 through 877 Processing helix chain 'M' and resid 878 through 880 No H-bonds generated for 'chain 'M' and resid 878 through 880' Processing helix chain 'M' and resid 885 through 897 removed outlier: 3.645A pdb=" N SER M 889 " --> pdb=" O LEU M 885 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS M 895 " --> pdb=" O ALA M 891 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA M 896 " --> pdb=" O HIS M 892 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP M 897 " --> pdb=" O LEU M 893 " (cutoff:3.500A) Processing helix chain 'M' and resid 905 through 919 removed outlier: 3.523A pdb=" N LEU M 909 " --> pdb=" O SER M 905 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU M 910 " --> pdb=" O GLN M 906 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU M 911 " --> pdb=" O LYS M 907 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA M 912 " --> pdb=" O CYS M 908 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER M 916 " --> pdb=" O ALA M 912 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG M 917 " --> pdb=" O ASN M 913 " (cutoff:3.500A) Processing helix chain 'M' and resid 955 through 966 removed outlier: 4.142A pdb=" N VAL M 964 " --> pdb=" O LEU M 960 " (cutoff:3.500A) Processing helix chain 'M' and resid 995 through 1018 removed outlier: 4.462A pdb=" N ASP M1004 " --> pdb=" O LYS M1000 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET M1005 " --> pdb=" O ALA M1001 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS M1009 " --> pdb=" O MET M1005 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER M1012 " --> pdb=" O GLU M1008 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU M1013 " --> pdb=" O LYS M1009 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR M1016 " --> pdb=" O SER M1012 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR M1017 " --> pdb=" O LEU M1013 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY M1018 " --> pdb=" O MET M1014 " (cutoff:3.500A) Processing helix chain 'M' and resid 1022 through 1027 removed outlier: 3.677A pdb=" N LEU M1026 " --> pdb=" O GLU M1022 " (cutoff:3.500A) Processing helix chain 'M' and resid 1040 through 1068 removed outlier: 3.819A pdb=" N ASP M1046 " --> pdb=" O ARG M1042 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP M1049 " --> pdb=" O GLY M1045 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR M1052 " --> pdb=" O LYS M1048 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS M1068 " --> pdb=" O GLY M1064 " (cutoff:3.500A) Processing helix chain 'M' and resid 1072 through 1089 removed outlier: 4.370A pdb=" N ALA M1080 " --> pdb=" O LYS M1076 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER M1081 " --> pdb=" O LYS M1077 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA M1082 " --> pdb=" O LYS M1078 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR M1087 " --> pdb=" O TRP M1083 " (cutoff:3.500A) Processing helix chain 'M' and resid 1090 through 1093 removed outlier: 3.891A pdb=" N ARG M1093 " --> pdb=" O PRO M1090 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1090 through 1093' Processing helix chain 'M' and resid 1101 through 1105 removed outlier: 3.532A pdb=" N TRP M1104 " --> pdb=" O SER M1101 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE M1105 " --> pdb=" O PHE M1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1101 through 1105' Processing helix chain 'M' and resid 1106 through 1117 removed outlier: 3.515A pdb=" N LEU M1110 " --> pdb=" O VAL M1106 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU M1111 " --> pdb=" O GLY M1107 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP M1112 " --> pdb=" O ASP M1108 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE M1113 " --> pdb=" O VAL M1109 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS M1114 " --> pdb=" O LEU M1110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1238 through 1240 Processing sheet with id=AA2, first strand: chain 'A' and resid 1238 through 1240 removed outlier: 3.671A pdb=" N THR A 14 " --> pdb=" O LYS B1170 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASP B1168 " --> pdb=" O THR A 16 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 316 through 317 removed outlier: 3.545A pdb=" N LYS A 316 " --> pdb=" O PHE B1075 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 338 removed outlier: 3.635A pdb=" N SER A 435 " --> pdb=" O GLY A 338 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 434 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 436 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 324 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 338 removed outlier: 3.635A pdb=" N SER A 435 " --> pdb=" O GLY A 338 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 434 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 436 " --> pdb=" O VAL A 327 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 349 removed outlier: 3.705A pdb=" N ARG A 399 " --> pdb=" O VAL A 349 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 478 through 479 Processing sheet with id=AA8, first strand: chain 'A' and resid 529 through 531 removed outlier: 4.972A pdb=" N ILE A 529 " --> pdb=" O HIS H 94 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N HIS H 94 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY H 95 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS H 57 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE H 58 " --> pdb=" O PHE H 12 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG H 33 " --> pdb=" O VAL H 13 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLU H 31 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEU H 17 " --> pdb=" O ARG H 29 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG H 29 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU H 43 " --> pdb=" O VAL H 30 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 529 through 531 removed outlier: 4.972A pdb=" N ILE A 529 " --> pdb=" O HIS H 94 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N HIS H 94 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU H 97 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER H 115 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS H 99 " --> pdb=" O TYR H 113 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 557 through 559 Processing sheet with id=AB2, first strand: chain 'A' and resid 748 through 751 removed outlier: 3.795A pdb=" N GLY A 748 " --> pdb=" O ILE A 796 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 842 through 844 removed outlier: 3.705A pdb=" N TYR A 843 " --> pdb=" O ARG A 851 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 923 through 924 removed outlier: 3.527A pdb=" N GLN A 923 " --> pdb=" O LYS A1119 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 923 through 924 removed outlier: 3.527A pdb=" N GLN A 923 " --> pdb=" O LYS A1119 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A1084 " --> pdb=" O GLY A1118 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 954 through 955 removed outlier: 3.877A pdb=" N LYS A1077 " --> pdb=" O LEU A 954 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 960 through 967 removed outlier: 7.862A pdb=" N VAL A 960 " --> pdb=" O SER A 987 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N SER A 987 " --> pdb=" O VAL A 960 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR A 962 " --> pdb=" O HIS A 985 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 981 " --> pdb=" O ILE A 966 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS A 982 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 984 " --> pdb=" O ILE A1045 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A1024 " --> pdb=" O THR A1048 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1262 through 1264 Processing sheet with id=AB9, first strand: chain 'B' and resid 101 through 102 removed outlier: 4.331A pdb=" N GLY B 174 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL B 134 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU B 172 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.844A pdb=" N ALA B 476 " --> pdb=" O VAL B 216 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 398 through 401 removed outlier: 3.783A pdb=" N GLN B 220 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA B 219 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 228 through 230 removed outlier: 4.180A pdb=" N TRP B 235 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 249 " --> pdb=" O TYR B 271 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 539 through 540 removed outlier: 3.638A pdb=" N ARG B 629 " --> pdb=" O ILE B 662 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 539 through 540 Processing sheet with id=AC6, first strand: chain 'B' and resid 557 through 558 removed outlier: 3.886A pdb=" N VAL B 581 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N VAL B 574 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 617 " --> pdb=" O ASP B 612 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP B 612 " --> pdb=" O GLU B 617 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 742 through 745 removed outlier: 3.860A pdb=" N SER B 802 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE B 897 " --> pdb=" O LEU B 888 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU B 888 " --> pdb=" O PHE B 897 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA B 899 " --> pdb=" O VAL B 886 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL B 886 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N SER B 901 " --> pdb=" O GLN B 884 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 881 " --> pdb=" O MET B 854 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 808 through 811 removed outlier: 3.691A pdb=" N ALA B 898 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE B 897 " --> pdb=" O LEU B 888 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU B 888 " --> pdb=" O PHE B 897 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA B 899 " --> pdb=" O VAL B 886 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL B 886 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N SER B 901 " --> pdb=" O GLN B 884 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N VAL B 886 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS L 39 " --> pdb=" O VAL B 886 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 913 through 914 removed outlier: 7.380A pdb=" N ILE B 788 " --> pdb=" O GLY B 925 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU B 927 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N MET B 790 " --> pdb=" O LEU B 927 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE B 944 " --> pdb=" O ILE B 773 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 946 " --> pdb=" O ALA B 775 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 776 " --> pdb=" O PHE B1031 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE B1031 " --> pdb=" O VAL B 776 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 827 through 828 removed outlier: 3.968A pdb=" N ALA B 869 " --> pdb=" O THR B 865 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 859 through 861 removed outlier: 3.825A pdb=" N VAL B 860 " --> pdb=" O ILE B 873 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE B 873 " --> pdb=" O VAL B 860 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 1103 through 1108 removed outlier: 3.833A pdb=" N SER B1103 " --> pdb=" O VAL B1147 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B1147 " --> pdb=" O SER B1103 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 14 through 16 removed outlier: 5.876A pdb=" N ILE C 14 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU C 25 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU C 16 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE C 267 " --> pdb=" O MET C 189 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET C 189 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 187 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 58 removed outlier: 5.563A pdb=" N VAL C 48 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY C 172 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE C 50 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG C 170 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LYS C 164 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASN C 58 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLU C 162 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 108 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR C 126 " --> pdb=" O ARG C 107 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.842A pdb=" N LEU C 118 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 193 through 196 removed outlier: 4.000A pdb=" N ASP C 193 " --> pdb=" O SER C 260 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER C 260 " --> pdb=" O ASP C 193 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE C 195 " --> pdb=" O GLU C 258 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU C 258 " --> pdb=" O ILE C 195 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'E' and resid 55 through 58 removed outlier: 3.662A pdb=" N THR E 55 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE E 69 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS E 57 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N GLN E 66 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE E 98 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N TYR E 68 " --> pdb=" O ILE E 98 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL E 100 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE E 70 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA E 97 " --> pdb=" O HIS E 121 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU E 123 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU E 99 " --> pdb=" O GLU E 123 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE E 125 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL E 101 " --> pdb=" O PHE E 125 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 143 through 145 Processing sheet with id=AE1, first strand: chain 'I' and resid 15 through 18 removed outlier: 3.696A pdb=" N LYS I 17 " --> pdb=" O LEU I 26 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU I 26 " --> pdb=" O LYS I 17 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.732A pdb=" N PHE I 87 " --> pdb=" O PHE I 100 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA I 89 " --> pdb=" O THR I 98 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 19 through 23 removed outlier: 3.567A pdb=" N THR K 34 " --> pdb=" O SER K 20 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP K 22 " --> pdb=" O SER K 32 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE K 71 " --> pdb=" O VAL K 35 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N HIS K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 39 through 43 removed outlier: 3.784A pdb=" N ALA M 41 " --> pdb=" O GLN M 60 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA M 57 " --> pdb=" O ILE M 14 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 218 through 221 removed outlier: 3.517A pdb=" N MET M 218 " --> pdb=" O VAL M 195 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS M 155 " --> pdb=" O PHE M 192 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N CYS M 153 " --> pdb=" O ARG M 194 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TRP M 148 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLY M 131 " --> pdb=" O TRP M 148 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU M 127 " --> pdb=" O VAL M 113 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY M 131 " --> pdb=" O ILE M 109 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE M 109 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL M 110 " --> pdb=" O GLU M 240 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU M 240 " --> pdb=" O VAL M 110 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR M 112 " --> pdb=" O CYS M 238 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA M 180 " --> pdb=" O CYS M 169 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR M 166 " --> pdb=" O ARG M 258 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASP M 260 " --> pdb=" O THR M 166 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER M 168 " --> pdb=" O ASP M 260 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 124 through 125 Processing sheet with id=AE7, first strand: chain 'M' and resid 391 through 400 removed outlier: 3.542A pdb=" N LEU M 394 " --> pdb=" O ARG M 383 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ARG M 383 " --> pdb=" O LEU M 394 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N CYS M 381 " --> pdb=" O PRO M 396 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU M 398 " --> pdb=" O MET M 379 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N MET M 379 " --> pdb=" O LEU M 398 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N ARG M 417 " --> pdb=" O SER M 380 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN M 382 " --> pdb=" O ARG M 417 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N THR M 419 " --> pdb=" O GLN M 382 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA M 384 " --> pdb=" O THR M 419 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N TRP M 485 " --> pdb=" O LEU M 472 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 435 through 438 removed outlier: 3.724A pdb=" N SER M 437 " --> pdb=" O LYS M 444 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS M 444 " --> pdb=" O SER M 437 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 557 through 560 removed outlier: 5.910A pdb=" N GLY M 558 " --> pdb=" O ALA M 593 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE M 581 " --> pdb=" O ILE M 592 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLN M 582 " --> pdb=" O THR M 621 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR M 621 " --> pdb=" O GLN M 582 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 732 through 735 removed outlier: 3.732A pdb=" N PHE M 814 " --> pdb=" O CYS M 734 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 779 through 780 765 hydrogen bonds defined for protein. 2145 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: 14.55 Time building geometry restraints manager: 9.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 10468 1.35 - 1.46: 7186 1.46 - 1.58: 14396 1.58 - 1.70: 0 1.70 - 1.82: 304 Bond restraints: 32354 Sorted by residual: bond pdb=" C LEU A1131 " pdb=" N PRO A1132 " ideal model delta sigma weight residual 1.331 1.381 -0.050 7.90e-03 1.60e+04 3.93e+01 bond pdb=" C ASP A 771 " pdb=" N PRO A 772 " ideal model delta sigma weight residual 1.337 1.381 -0.044 1.24e-02 6.50e+03 1.25e+01 bond pdb=" N CYS I 32 " pdb=" CA CYS I 32 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.30e-02 5.92e+03 7.43e+00 bond pdb=" N CYS I 10 " pdb=" CA CYS I 10 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.77e+00 bond pdb=" C GLU B 682 " pdb=" N PRO B 683 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.70e+00 ... (remaining 32349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 43320 2.59 - 5.18: 467 5.18 - 7.77: 74 7.77 - 10.35: 8 10.35 - 12.94: 3 Bond angle restraints: 43872 Sorted by residual: angle pdb=" C GLU M 36 " pdb=" N ASP M 37 " pdb=" CA ASP M 37 " ideal model delta sigma weight residual 122.46 128.91 -6.45 1.41e+00 5.03e-01 2.09e+01 angle pdb=" C VAL F 89 " pdb=" N GLU F 90 " pdb=" CA GLU F 90 " ideal model delta sigma weight residual 122.46 128.86 -6.40 1.41e+00 5.03e-01 2.06e+01 angle pdb=" N ILE B 685 " pdb=" CA ILE B 685 " pdb=" C ILE B 685 " ideal model delta sigma weight residual 113.71 109.53 4.18 9.50e-01 1.11e+00 1.94e+01 angle pdb=" C ASP B 563 " pdb=" N THR B 564 " pdb=" CA THR B 564 " ideal model delta sigma weight residual 121.54 129.91 -8.37 1.91e+00 2.74e-01 1.92e+01 angle pdb=" C LEU A 633 " pdb=" N GLN A 634 " pdb=" CA GLN A 634 " ideal model delta sigma weight residual 121.54 129.62 -8.08 1.91e+00 2.74e-01 1.79e+01 ... (remaining 43867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 17813 17.91 - 35.82: 1389 35.82 - 53.73: 228 53.73 - 71.64: 39 71.64 - 89.55: 14 Dihedral angle restraints: 19483 sinusoidal: 7216 harmonic: 12267 Sorted by residual: dihedral pdb=" CA PRO B 360 " pdb=" C PRO B 360 " pdb=" N GLY B 361 " pdb=" CA GLY B 361 " ideal model delta harmonic sigma weight residual -180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA ASP M 547 " pdb=" CB ASP M 547 " pdb=" CG ASP M 547 " pdb=" OD1 ASP M 547 " ideal model delta sinusoidal sigma weight residual -30.00 -89.38 59.38 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP C 96 " pdb=" CB ASP C 96 " pdb=" CG ASP C 96 " pdb=" OD1 ASP C 96 " ideal model delta sinusoidal sigma weight residual -30.00 -87.41 57.41 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 19480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4091 0.055 - 0.109: 800 0.109 - 0.164: 158 0.164 - 0.219: 20 0.219 - 0.274: 2 Chirality restraints: 5071 Sorted by residual: chirality pdb=" CB ILE A 872 " pdb=" CA ILE A 872 " pdb=" CG1 ILE A 872 " pdb=" CG2 ILE A 872 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB VAL B 548 " pdb=" CA VAL B 548 " pdb=" CG1 VAL B 548 " pdb=" CG2 VAL B 548 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL B 765 " pdb=" CA VAL B 765 " pdb=" CG1 VAL B 765 " pdb=" CG2 VAL B 765 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 5068 not shown) Planarity restraints: 5644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 45 " 0.043 5.00e-02 4.00e+02 6.47e-02 6.69e+00 pdb=" N PRO C 46 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 46 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 46 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR M 387 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO M 388 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO M 388 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO M 388 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 990 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO B 991 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 991 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 991 " -0.031 5.00e-02 4.00e+02 ... (remaining 5641 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 229 2.64 - 3.20: 24508 3.20 - 3.77: 44495 3.77 - 4.33: 59988 4.33 - 4.90: 100411 Nonbonded interactions: 229631 Sorted by model distance: nonbonded pdb=" OD1 ASP A 447 " pdb="MG MG A1602 " model vdw 2.070 2.170 nonbonded pdb=" OD2 ASP A 451 " pdb="MG MG A1602 " model vdw 2.071 2.170 nonbonded pdb=" OD1 ASP A 449 " pdb="MG MG A1602 " model vdw 2.073 2.170 nonbonded pdb=" OD1 ASP M 830 " pdb="MG MG M2001 " model vdw 2.082 2.170 nonbonded pdb=" OD1 ASP M 832 " pdb="MG MG M2001 " model vdw 2.083 2.170 ... (remaining 229626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.220 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 79.520 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.170 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 : 0.009 0.681 32382 Z= 0.314 Angle : 0.902 58.839 43901 Z= 0.423 Chirality : 0.047 0.274 5071 Planarity : 0.005 0.065 5644 Dihedral : 13.151 89.550 11523 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.19 % Allowed : 6.19 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.29 (0.09), residues: 4151 helix: -4.35 (0.07), residues: 1144 sheet: -2.94 (0.19), residues: 572 loop : -3.35 (0.09), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 51 HIS 0.004 0.000 HIS B 877 PHE 0.012 0.001 PHE A 758 TYR 0.013 0.001 TYR A 605 ARG 0.002 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.25396 ( 753) hydrogen bonds : angle 8.68260 ( 2145) metal coordination : bond 0.28084 ( 28) metal coordination : angle 21.74327 ( 29) covalent geometry : bond 0.00283 (32354) covalent geometry : angle 0.70778 (43872) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 3737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 677 time to evaluate : 3.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.5888 (m90) cc_final: 0.5680 (m-70) REVERT: A 336 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8004 (mt-10) REVERT: A 477 LEU cc_start: 0.8342 (mt) cc_final: 0.8103 (mt) REVERT: A 581 LEU cc_start: 0.8809 (mt) cc_final: 0.8493 (mt) REVERT: A 613 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7618 (mp10) REVERT: A 835 LEU cc_start: 0.8935 (tp) cc_final: 0.8712 (tp) REVERT: B 421 LYS cc_start: 0.7804 (mmtt) cc_final: 0.7484 (mtmt) REVERT: B 716 LEU cc_start: 0.9422 (tt) cc_final: 0.9222 (tt) REVERT: B 1018 TYR cc_start: 0.8969 (m-10) cc_final: 0.8572 (m-10) REVERT: B 1027 ARG cc_start: 0.8485 (mtm110) cc_final: 0.8161 (ttm170) REVERT: B 1061 ARG cc_start: 0.7969 (mmt-90) cc_final: 0.7709 (mpt-90) REVERT: B 1079 GLU cc_start: 0.7980 (mp0) cc_final: 0.7444 (mm-30) REVERT: H 126 ASP cc_start: 0.8516 (p0) cc_final: 0.8024 (p0) REVERT: H 129 HIS cc_start: 0.6742 (m90) cc_final: 0.6322 (m-70) REVERT: I 33 ASP cc_start: 0.7632 (m-30) cc_final: 0.7383 (p0) REVERT: J 58 LYS cc_start: 0.8992 (ttmt) cc_final: 0.8514 (mtmm) REVERT: K 65 HIS cc_start: 0.7782 (m90) cc_final: 0.7515 (m90) REVERT: K 84 MET cc_start: 0.8740 (tpt) cc_final: 0.8506 (tpp) REVERT: L 30 ARG cc_start: 0.7264 (mpt180) cc_final: 0.5884 (mtp180) REVERT: M 11 THR cc_start: 0.9046 (m) cc_final: 0.8840 (m) REVERT: M 423 GLU cc_start: 0.5890 (tp30) cc_final: 0.5598 (tp30) REVERT: M 557 ILE cc_start: 0.6181 (mm) cc_final: 0.5970 (mm) REVERT: M 559 LYS cc_start: 0.6351 (mptt) cc_final: 0.5627 (mttt) REVERT: M 616 ARG cc_start: 0.6455 (mtt180) cc_final: 0.6222 (mmt180) REVERT: M 1084 TYR cc_start: 0.5604 (t80) cc_final: 0.4586 (m-80) REVERT: M 1102 PHE cc_start: 0.5842 (t80) cc_final: 0.5238 (t80) outliers start: 6 outliers final: 2 residues processed: 681 average time/residue: 0.5421 time to fit residues: 576.4038 Evaluate side-chains 446 residues out of total 3737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 444 time to evaluate : 3.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain H residue 47 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 351 optimal weight: 5.9990 chunk 315 optimal weight: 0.2980 chunk 174 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 326 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 chunk 377 optimal weight: 2.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 ASN A 505 ASN A 638 ASN A 655 ASN A 658 GLN ** A 743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN B 66 ASN B 220 GLN B 246 ASN B 355 HIS B 510 HIS ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN B 784 GLN B 804 GLN B 828 GLN B 896 ASN B1003 GLN B1093 HIS E 102 GLN E 126 GLN H 94 HIS I 12 ASN I 80 GLN K 76 HIS K 103 ASN M 84 HIS M 304 HIS M 692 GLN M1119 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.164369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.152748 restraints weight = 44069.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.140010 restraints weight = 83236.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.136580 restraints weight = 85171.617| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 32382 Z= 0.175 Angle : 0.622 25.713 43901 Z= 0.298 Chirality : 0.044 0.259 5071 Planarity : 0.004 0.052 5644 Dihedral : 4.169 26.560 4514 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.89 % Allowed : 14.55 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.10), residues: 4151 helix: -3.08 (0.11), residues: 1217 sheet: -2.53 (0.19), residues: 605 loop : -2.99 (0.10), residues: 2329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 623 HIS 0.009 0.001 HIS B 688 PHE 0.019 0.002 PHE A1217 TYR 0.022 0.002 TYR M 293 ARG 0.007 0.001 ARG M 142 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 753) hydrogen bonds : angle 5.34501 ( 2145) metal coordination : bond 0.02561 ( 28) metal coordination : angle 9.73703 ( 29) covalent geometry : bond 0.00411 (32354) covalent geometry : angle 0.57000 (43872) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 457 time to evaluate : 3.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8201 (mt-10) REVERT: A 613 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8093 (mp10) REVERT: A 1219 GLN cc_start: 0.7041 (tm-30) cc_final: 0.6722 (tm-30) REVERT: B 232 ASN cc_start: 0.7771 (t0) cc_final: 0.7334 (t0) REVERT: B 421 LYS cc_start: 0.7637 (mmtt) cc_final: 0.7227 (ttmt) REVERT: B 581 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8169 (t) REVERT: B 1037 TYR cc_start: 0.9062 (m-10) cc_final: 0.8843 (m-80) REVERT: B 1061 ARG cc_start: 0.8026 (mmt-90) cc_final: 0.7746 (mpt-90) REVERT: C 271 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6857 (mt-10) REVERT: C 293 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8651 (mt) REVERT: E 11 TYR cc_start: 0.7559 (t80) cc_final: 0.7298 (t80) REVERT: E 26 TYR cc_start: 0.7284 (OUTLIER) cc_final: 0.4632 (t80) REVERT: E 28 ILE cc_start: 0.5888 (mp) cc_final: 0.5576 (tp) REVERT: H 126 ASP cc_start: 0.8559 (p0) cc_final: 0.7951 (p0) REVERT: H 129 HIS cc_start: 0.6771 (m90) cc_final: 0.6263 (m-70) REVERT: I 113 ARG cc_start: 0.8220 (ttt90) cc_final: 0.7786 (ttt-90) REVERT: J 48 MET cc_start: 0.8576 (mmm) cc_final: 0.7737 (mtt) REVERT: K 84 MET cc_start: 0.8740 (tpt) cc_final: 0.8267 (tpp) REVERT: M 128 LYS cc_start: 0.8610 (ttpt) cc_final: 0.7876 (ptmm) REVERT: M 423 GLU cc_start: 0.6713 (tp30) cc_final: 0.6396 (tp30) REVERT: M 449 ASN cc_start: 0.8871 (t0) cc_final: 0.8656 (t0) REVERT: M 559 LYS cc_start: 0.6383 (mptt) cc_final: 0.5661 (mttm) REVERT: M 616 ARG cc_start: 0.6688 (mtt180) cc_final: 0.6327 (mmt180) REVERT: M 674 LEU cc_start: 0.6041 (tp) cc_final: 0.5832 (tp) REVERT: M 1014 MET cc_start: 0.6797 (tpt) cc_final: 0.6482 (tpt) REVERT: M 1084 TYR cc_start: 0.6022 (t80) cc_final: 0.4826 (m-80) outliers start: 61 outliers final: 39 residues processed: 498 average time/residue: 0.4559 time to fit residues: 363.1866 Evaluate side-chains 440 residues out of total 3737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 398 time to evaluate : 3.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 1002 GLU Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain E residue 26 TYR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain I residue 34 HIS Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 334 LEU Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 624 THR Chi-restraints excluded: chain M residue 794 VAL Chi-restraints excluded: chain M residue 942 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 364 optimal weight: 9.9990 chunk 345 optimal weight: 0.8980 chunk 156 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 285 optimal weight: 0.3980 chunk 299 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 224 optimal weight: 0.0670 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN A 485 ASN A 501 ASN A 545 GLN A 655 ASN ** A 743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 HIS B 725 GLN B 949 HIS B1003 GLN ** E 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.166392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.150296 restraints weight = 44144.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.142516 restraints weight = 82855.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.139909 restraints weight = 63470.662| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 32382 Z= 0.094 Angle : 0.517 18.495 43901 Z= 0.249 Chirality : 0.041 0.260 5071 Planarity : 0.003 0.047 5644 Dihedral : 3.828 24.645 4514 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.17 % Allowed : 17.03 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.11), residues: 4151 helix: -2.30 (0.13), residues: 1203 sheet: -2.18 (0.20), residues: 579 loop : -2.73 (0.11), residues: 2369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 623 HIS 0.003 0.001 HIS B 877 PHE 0.019 0.001 PHE A 308 TYR 0.016 0.001 TYR M 951 ARG 0.005 0.000 ARG E 197 Details of bonding type rmsd hydrogen bonds : bond 0.03150 ( 753) hydrogen bonds : angle 4.84091 ( 2145) metal coordination : bond 0.01742 ( 28) metal coordination : angle 7.26690 ( 29) covalent geometry : bond 0.00218 (32354) covalent geometry : angle 0.48256 (43872) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 422 time to evaluate : 3.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8056 (tpp) cc_final: 0.7789 (tpp) REVERT: A 336 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8190 (mt-10) REVERT: A 613 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7656 (mp10) REVERT: A 728 MET cc_start: 0.8892 (mtm) cc_final: 0.8545 (mtp) REVERT: A 1136 MET cc_start: 0.7651 (ptp) cc_final: 0.7423 (ptp) REVERT: A 1217 PHE cc_start: 0.7514 (t80) cc_final: 0.7018 (t80) REVERT: B 232 ASN cc_start: 0.7759 (t0) cc_final: 0.7259 (t0) REVERT: B 421 LYS cc_start: 0.7589 (mmtt) cc_final: 0.7250 (ttmt) REVERT: B 581 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8146 (t) REVERT: C 33 MET cc_start: 0.8531 (tpt) cc_final: 0.8251 (tpt) REVERT: C 45 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8858 (m) REVERT: E 26 TYR cc_start: 0.7203 (OUTLIER) cc_final: 0.4842 (t80) REVERT: E 28 ILE cc_start: 0.5995 (mp) cc_final: 0.5721 (tp) REVERT: F 109 LYS cc_start: 0.7761 (mmmt) cc_final: 0.6797 (tppt) REVERT: H 100 ILE cc_start: 0.7919 (mt) cc_final: 0.7646 (tt) REVERT: H 126 ASP cc_start: 0.8508 (p0) cc_final: 0.7929 (p0) REVERT: H 129 HIS cc_start: 0.6556 (m90) cc_final: 0.6243 (m-70) REVERT: I 113 ARG cc_start: 0.8176 (ttt90) cc_final: 0.7780 (ttt-90) REVERT: J 48 MET cc_start: 0.8325 (mmm) cc_final: 0.7464 (mtt) REVERT: K 45 ILE cc_start: 0.8821 (tt) cc_final: 0.8583 (tt) REVERT: K 84 MET cc_start: 0.8738 (tpt) cc_final: 0.8487 (tpp) REVERT: M 128 LYS cc_start: 0.8668 (ttpt) cc_final: 0.8163 (ptmm) REVERT: M 559 LYS cc_start: 0.6349 (mptt) cc_final: 0.5675 (mttm) REVERT: M 616 ARG cc_start: 0.6637 (mtt180) cc_final: 0.6336 (mmt180) REVERT: M 674 LEU cc_start: 0.5953 (tp) cc_final: 0.5696 (tp) REVERT: M 731 LEU cc_start: 0.7907 (pt) cc_final: 0.7559 (pt) REVERT: M 1047 MET cc_start: 0.7592 (tpt) cc_final: 0.7115 (tpt) REVERT: M 1050 ARG cc_start: 0.7421 (ptt-90) cc_final: 0.7003 (ptt-90) REVERT: M 1084 TYR cc_start: 0.5749 (t80) cc_final: 0.4606 (m-80) outliers start: 70 outliers final: 41 residues processed: 472 average time/residue: 0.4408 time to fit residues: 332.6799 Evaluate side-chains 431 residues out of total 3737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 387 time to evaluate : 3.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 485 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 1002 GLU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain E residue 26 TYR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain I residue 34 HIS Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain M residue 24 ASP Chi-restraints excluded: chain M residue 123 PHE Chi-restraints excluded: chain M residue 334 LEU Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 591 VAL Chi-restraints excluded: chain M residue 624 THR Chi-restraints excluded: chain M residue 746 VAL Chi-restraints excluded: chain M residue 932 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 202 optimal weight: 6.9990 chunk 294 optimal weight: 7.9990 chunk 191 optimal weight: 0.9980 chunk 32 optimal weight: 0.0370 chunk 314 optimal weight: 8.9990 chunk 58 optimal weight: 0.0040 chunk 136 optimal weight: 8.9990 chunk 341 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 178 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 overall best weight: 1.3672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 HIS A 462 GLN ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN ** A 743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN B1003 GLN ** E 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 HIS M 306 GLN ** M 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.163690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.147760 restraints weight = 44178.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 79)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.139789 restraints weight = 82203.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.137469 restraints weight = 62792.030| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 32382 Z= 0.113 Angle : 0.513 16.675 43901 Z= 0.251 Chirality : 0.041 0.231 5071 Planarity : 0.003 0.049 5644 Dihedral : 3.835 23.920 4513 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.79 % Allowed : 18.14 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.12), residues: 4151 helix: -1.87 (0.14), residues: 1194 sheet: -2.06 (0.20), residues: 612 loop : -2.57 (0.11), residues: 2345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 623 HIS 0.004 0.001 HIS B 877 PHE 0.013 0.001 PHE M 210 TYR 0.018 0.001 TYR E 11 ARG 0.005 0.000 ARG E 197 Details of bonding type rmsd hydrogen bonds : bond 0.02886 ( 753) hydrogen bonds : angle 4.55382 ( 2145) metal coordination : bond 0.01459 ( 28) metal coordination : angle 6.61327 ( 29) covalent geometry : bond 0.00269 (32354) covalent geometry : angle 0.48463 (43872) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 403 time to evaluate : 3.912 Fit side-chains REVERT: A 309 MET cc_start: 0.8048 (tpp) cc_final: 0.7787 (tpp) REVERT: A 336 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8216 (mt-10) REVERT: A 436 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8152 (pp) REVERT: A 728 MET cc_start: 0.8917 (mtm) cc_final: 0.8598 (mtp) REVERT: A 986 ILE cc_start: 0.8766 (mm) cc_final: 0.8492 (mt) REVERT: B 232 ASN cc_start: 0.7803 (t0) cc_final: 0.7313 (t0) REVERT: B 295 MET cc_start: 0.8205 (tpp) cc_final: 0.7931 (tpp) REVERT: B 421 LYS cc_start: 0.7507 (mmtt) cc_final: 0.7175 (ttmt) REVERT: B 581 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8301 (t) REVERT: C 45 VAL cc_start: 0.9135 (OUTLIER) cc_final: 0.8876 (m) REVERT: C 249 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8207 (tm-30) REVERT: E 11 TYR cc_start: 0.7377 (t80) cc_final: 0.7068 (t80) REVERT: E 26 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.4882 (t80) REVERT: E 57 LYS cc_start: 0.6344 (tppt) cc_final: 0.6102 (tppt) REVERT: F 102 MET cc_start: 0.7444 (tpp) cc_final: 0.7087 (mpp) REVERT: F 109 LYS cc_start: 0.7810 (mmmt) cc_final: 0.6918 (tppt) REVERT: H 126 ASP cc_start: 0.8510 (p0) cc_final: 0.7973 (p0) REVERT: H 129 HIS cc_start: 0.6570 (m90) cc_final: 0.6191 (m-70) REVERT: I 113 ARG cc_start: 0.8279 (ttt90) cc_final: 0.7900 (ttt-90) REVERT: I 114 GLU cc_start: 0.7696 (tp30) cc_final: 0.7495 (tp30) REVERT: J 48 MET cc_start: 0.8464 (mmm) cc_final: 0.7555 (mtt) REVERT: K 84 MET cc_start: 0.8787 (tpt) cc_final: 0.8538 (tpp) REVERT: M 128 LYS cc_start: 0.8732 (ttpt) cc_final: 0.8233 (ptmm) REVERT: M 154 TYR cc_start: 0.7998 (m-80) cc_final: 0.7770 (m-80) REVERT: M 559 LYS cc_start: 0.6436 (mptt) cc_final: 0.5687 (mttm) REVERT: M 616 ARG cc_start: 0.6711 (mtt180) cc_final: 0.6366 (mmt180) REVERT: M 674 LEU cc_start: 0.6144 (tp) cc_final: 0.5910 (tp) REVERT: M 731 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7657 (pt) REVERT: M 1047 MET cc_start: 0.7656 (tpt) cc_final: 0.7179 (tpt) REVERT: M 1050 ARG cc_start: 0.7406 (ptt-90) cc_final: 0.7027 (ptt-90) REVERT: M 1084 TYR cc_start: 0.5795 (t80) cc_final: 0.4568 (m-80) outliers start: 90 outliers final: 61 residues processed: 468 average time/residue: 0.4503 time to fit residues: 338.0831 Evaluate side-chains 443 residues out of total 3737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 377 time to evaluate : 5.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 1002 GLU Chi-restraints excluded: chain B residue 1017 VAL Chi-restraints excluded: chain B residue 1084 ILE Chi-restraints excluded: chain B residue 1169 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain E residue 26 TYR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain I residue 34 HIS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain M residue 24 ASP Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 123 PHE Chi-restraints excluded: chain M residue 153 CYS Chi-restraints excluded: chain M residue 250 ILE Chi-restraints excluded: chain M residue 334 LEU Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 583 ILE Chi-restraints excluded: chain M residue 591 VAL Chi-restraints excluded: chain M residue 624 THR Chi-restraints excluded: chain M residue 731 LEU Chi-restraints excluded: chain M residue 746 VAL Chi-restraints excluded: chain M residue 794 VAL Chi-restraints excluded: chain M residue 956 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 228 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 262 optimal weight: 0.9980 chunk 283 optimal weight: 9.9990 chunk 346 optimal weight: 8.9990 chunk 236 optimal weight: 6.9990 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 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 ASN ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 ASN ** A 743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1141 HIS ** E 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.160445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.144311 restraints weight = 43986.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.137222 restraints weight = 83559.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.135291 restraints weight = 64497.512| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 32382 Z= 0.145 Angle : 0.552 18.474 43901 Z= 0.270 Chirality : 0.043 0.221 5071 Planarity : 0.004 0.052 5644 Dihedral : 4.105 24.481 4513 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.53 % Allowed : 18.42 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.12), residues: 4151 helix: -1.70 (0.14), residues: 1212 sheet: -1.97 (0.20), residues: 632 loop : -2.42 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 623 HIS 0.007 0.001 HIS B 877 PHE 0.020 0.001 PHE M 469 TYR 0.017 0.001 TYR A 605 ARG 0.005 0.000 ARG B 954 Details of bonding type rmsd hydrogen bonds : bond 0.03047 ( 753) hydrogen bonds : angle 4.57147 ( 2145) metal coordination : bond 0.01513 ( 28) metal coordination : angle 7.02337 ( 29) covalent geometry : bond 0.00347 (32354) covalent geometry : angle 0.52147 (43872) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 401 time to evaluate : 4.550 Fit side-chains revert: symmetry clash REVERT: A 307 ARG cc_start: 0.7669 (tpp-160) cc_final: 0.7442 (tpp-160) REVERT: A 309 MET cc_start: 0.8076 (tpp) cc_final: 0.7854 (tpp) REVERT: A 336 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8355 (mt-10) REVERT: A 436 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8297 (pp) REVERT: A 760 PHE cc_start: 0.9536 (OUTLIER) cc_final: 0.8918 (m-80) REVERT: A 1136 MET cc_start: 0.7776 (ptp) cc_final: 0.7557 (ptp) REVERT: A 1219 GLN cc_start: 0.6990 (tm-30) cc_final: 0.6685 (tm-30) REVERT: B 232 ASN cc_start: 0.7905 (t0) cc_final: 0.7527 (t0) REVERT: B 421 LYS cc_start: 0.7408 (mmtt) cc_final: 0.7198 (ttmt) REVERT: B 581 VAL cc_start: 0.8797 (OUTLIER) cc_final: 0.8479 (t) REVERT: B 658 ILE cc_start: 0.9169 (pt) cc_final: 0.8711 (mt) REVERT: B 897 PHE cc_start: 0.8833 (m-80) cc_final: 0.8600 (m-80) REVERT: E 11 TYR cc_start: 0.7356 (t80) cc_final: 0.7140 (t80) REVERT: E 26 TYR cc_start: 0.7625 (OUTLIER) cc_final: 0.5212 (t80) REVERT: F 102 MET cc_start: 0.7445 (tpp) cc_final: 0.6989 (mpp) REVERT: F 109 LYS cc_start: 0.7777 (mmmt) cc_final: 0.6857 (tppt) REVERT: I 113 ARG cc_start: 0.8307 (ttt90) cc_final: 0.7895 (ttt-90) REVERT: J 48 MET cc_start: 0.8364 (mmm) cc_final: 0.7519 (mtt) REVERT: K 84 MET cc_start: 0.8766 (tpt) cc_final: 0.8515 (tpp) REVERT: M 128 LYS cc_start: 0.8735 (ttpt) cc_final: 0.8239 (ptmm) REVERT: M 559 LYS cc_start: 0.6550 (mptt) cc_final: 0.5857 (mttm) REVERT: M 564 PHE cc_start: 0.7135 (t80) cc_final: 0.6700 (t80) REVERT: M 704 MET cc_start: 0.7753 (tmm) cc_final: 0.7390 (ppp) REVERT: M 731 LEU cc_start: 0.8136 (pt) cc_final: 0.7672 (pt) REVERT: M 1047 MET cc_start: 0.7623 (tpt) cc_final: 0.7100 (tpt) REVERT: M 1050 ARG cc_start: 0.7456 (ptt-90) cc_final: 0.7073 (ptt-90) REVERT: M 1084 TYR cc_start: 0.5556 (t80) cc_final: 0.4391 (m-80) outliers start: 114 outliers final: 85 residues processed: 485 average time/residue: 0.5802 time to fit residues: 462.4347 Evaluate side-chains 477 residues out of total 3737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 388 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1002 GLU Chi-restraints excluded: chain B residue 1017 VAL Chi-restraints excluded: chain B residue 1084 ILE Chi-restraints excluded: chain B residue 1169 THR Chi-restraints excluded: chain B residue 1171 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 26 TYR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 34 HIS Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 123 PHE Chi-restraints excluded: chain M residue 153 CYS Chi-restraints excluded: chain M residue 233 THR Chi-restraints excluded: chain M residue 250 ILE Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 482 ASN Chi-restraints excluded: chain M residue 583 ILE Chi-restraints excluded: chain M residue 591 VAL Chi-restraints excluded: chain M residue 624 THR Chi-restraints excluded: chain M residue 746 VAL Chi-restraints excluded: chain M residue 794 VAL Chi-restraints excluded: chain M residue 942 PHE Chi-restraints excluded: chain M residue 956 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 9 optimal weight: 9.9990 chunk 21 optimal weight: 0.0770 chunk 366 optimal weight: 5.9990 chunk 137 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 387 optimal weight: 0.8980 chunk 281 optimal weight: 20.0000 chunk 383 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 297 optimal weight: 4.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 ASN ** A 743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN ** E 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.159886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.143391 restraints weight = 43684.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.137314 restraints weight = 81877.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.135497 restraints weight = 67535.595| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 32382 Z= 0.121 Angle : 0.521 16.342 43901 Z= 0.256 Chirality : 0.042 0.208 5071 Planarity : 0.003 0.051 5644 Dihedral : 4.015 25.947 4513 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.53 % Allowed : 18.85 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.12), residues: 4151 helix: -1.54 (0.14), residues: 1223 sheet: -1.87 (0.20), residues: 629 loop : -2.37 (0.12), residues: 2299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 623 HIS 0.006 0.001 HIS B 877 PHE 0.015 0.001 PHE M 311 TYR 0.013 0.001 TYR A 605 ARG 0.009 0.000 ARG B 954 Details of bonding type rmsd hydrogen bonds : bond 0.02809 ( 753) hydrogen bonds : angle 4.46174 ( 2145) metal coordination : bond 0.01473 ( 28) metal coordination : angle 6.44897 ( 29) covalent geometry : bond 0.00291 (32354) covalent geometry : angle 0.49433 (43872) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 408 time to evaluate : 3.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8048 (tpp) cc_final: 0.7835 (tpp) REVERT: A 336 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8322 (mt-10) REVERT: A 436 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8219 (pp) REVERT: A 836 MET cc_start: 0.8655 (tpt) cc_final: 0.8313 (tpt) REVERT: A 1219 GLN cc_start: 0.6975 (tm-30) cc_final: 0.6676 (tm-30) REVERT: B 60 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8546 (tp) REVERT: B 232 ASN cc_start: 0.7868 (t0) cc_final: 0.7506 (t0) REVERT: B 421 LYS cc_start: 0.7449 (mmtt) cc_final: 0.7228 (ttmt) REVERT: B 581 VAL cc_start: 0.8791 (OUTLIER) cc_final: 0.8508 (t) REVERT: B 658 ILE cc_start: 0.9166 (pt) cc_final: 0.8671 (mt) REVERT: E 11 TYR cc_start: 0.7445 (t80) cc_final: 0.7195 (t80) REVERT: E 26 TYR cc_start: 0.7659 (OUTLIER) cc_final: 0.5328 (t80) REVERT: F 102 MET cc_start: 0.7505 (tpp) cc_final: 0.7050 (mpp) REVERT: F 109 LYS cc_start: 0.7748 (mmmt) cc_final: 0.6825 (tppt) REVERT: H 7 MET cc_start: 0.5935 (mmp) cc_final: 0.5603 (mtt) REVERT: H 129 HIS cc_start: 0.6290 (m-70) cc_final: 0.5948 (m-70) REVERT: I 113 ARG cc_start: 0.8353 (ttt90) cc_final: 0.7923 (ttt-90) REVERT: J 48 MET cc_start: 0.8178 (mmm) cc_final: 0.7358 (mtt) REVERT: K 84 MET cc_start: 0.8754 (tpt) cc_final: 0.8551 (tpp) REVERT: M 128 LYS cc_start: 0.8693 (ttpt) cc_final: 0.8208 (ptmm) REVERT: M 325 MET cc_start: 0.3547 (ttp) cc_final: 0.3138 (ttp) REVERT: M 559 LYS cc_start: 0.6510 (mptt) cc_final: 0.5900 (mttm) REVERT: M 663 MET cc_start: 0.5891 (ppp) cc_final: 0.5641 (ppp) REVERT: M 704 MET cc_start: 0.7638 (tmm) cc_final: 0.7285 (ppp) REVERT: M 731 LEU cc_start: 0.8170 (pt) cc_final: 0.7843 (pt) REVERT: M 1047 MET cc_start: 0.7524 (tpt) cc_final: 0.7169 (tpt) REVERT: M 1050 ARG cc_start: 0.7461 (ptt-90) cc_final: 0.7235 (ptt-90) REVERT: M 1084 TYR cc_start: 0.5460 (t80) cc_final: 0.4659 (m-80) outliers start: 114 outliers final: 87 residues processed: 493 average time/residue: 0.4409 time to fit residues: 351.0297 Evaluate side-chains 485 residues out of total 3737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 394 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 485 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1002 GLU Chi-restraints excluded: chain B residue 1017 VAL Chi-restraints excluded: chain B residue 1084 ILE Chi-restraints excluded: chain B residue 1169 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 26 TYR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 34 HIS Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 123 PHE Chi-restraints excluded: chain M residue 153 CYS Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 233 THR Chi-restraints excluded: chain M residue 250 ILE Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 482 ASN Chi-restraints excluded: chain M residue 591 VAL Chi-restraints excluded: chain M residue 624 THR Chi-restraints excluded: chain M residue 746 VAL Chi-restraints excluded: chain M residue 782 THR Chi-restraints excluded: chain M residue 794 VAL Chi-restraints excluded: chain M residue 956 VAL Chi-restraints excluded: chain M residue 968 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 227 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 394 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 287 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 299 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 202 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN ** E 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.160454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.144448 restraints weight = 44145.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.137691 restraints weight = 85033.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.134191 restraints weight = 68612.657| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32382 Z= 0.122 Angle : 0.527 15.975 43901 Z= 0.259 Chirality : 0.042 0.202 5071 Planarity : 0.003 0.054 5644 Dihedral : 3.995 25.956 4513 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.44 % Allowed : 19.47 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.12), residues: 4151 helix: -1.38 (0.15), residues: 1214 sheet: -1.78 (0.20), residues: 630 loop : -2.31 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 623 HIS 0.006 0.001 HIS B 877 PHE 0.017 0.001 PHE B 569 TYR 0.018 0.001 TYR M1084 ARG 0.008 0.000 ARG B 954 Details of bonding type rmsd hydrogen bonds : bond 0.02773 ( 753) hydrogen bonds : angle 4.38726 ( 2145) metal coordination : bond 0.01375 ( 28) metal coordination : angle 6.31667 ( 29) covalent geometry : bond 0.00294 (32354) covalent geometry : angle 0.50204 (43872) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 402 time to evaluate : 3.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 728 MET cc_start: 0.8984 (mtm) cc_final: 0.8753 (mtp) REVERT: A 760 PHE cc_start: 0.9552 (OUTLIER) cc_final: 0.8776 (m-80) REVERT: A 986 ILE cc_start: 0.8900 (mm) cc_final: 0.8697 (mt) REVERT: A 1136 MET cc_start: 0.7718 (ptp) cc_final: 0.7507 (ptp) REVERT: A 1219 GLN cc_start: 0.7017 (tm-30) cc_final: 0.6672 (tm-30) REVERT: B 60 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8542 (tp) REVERT: B 232 ASN cc_start: 0.7849 (t0) cc_final: 0.7499 (t0) REVERT: B 421 LYS cc_start: 0.7430 (mmtt) cc_final: 0.7189 (ttmt) REVERT: B 581 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8570 (t) REVERT: B 658 ILE cc_start: 0.9117 (pt) cc_final: 0.8652 (mt) REVERT: E 11 TYR cc_start: 0.7365 (t80) cc_final: 0.7117 (t80) REVERT: E 26 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.5382 (t80) REVERT: E 56 LEU cc_start: 0.5577 (tp) cc_final: 0.4410 (pp) REVERT: F 92 GLU cc_start: 0.8462 (pm20) cc_final: 0.7930 (pm20) REVERT: F 102 MET cc_start: 0.7406 (tpp) cc_final: 0.6988 (mpp) REVERT: F 109 LYS cc_start: 0.7739 (mmmt) cc_final: 0.6795 (tppt) REVERT: H 7 MET cc_start: 0.5924 (mmp) cc_final: 0.5637 (mtt) REVERT: H 39 MET cc_start: 0.8032 (mtp) cc_final: 0.7814 (mtt) REVERT: H 129 HIS cc_start: 0.6347 (m-70) cc_final: 0.5931 (m-70) REVERT: I 113 ARG cc_start: 0.8342 (ttt90) cc_final: 0.7926 (ttt-90) REVERT: J 48 MET cc_start: 0.8152 (mmm) cc_final: 0.7384 (mtt) REVERT: K 84 MET cc_start: 0.8771 (tpt) cc_final: 0.8569 (tpp) REVERT: M 154 TYR cc_start: 0.7954 (m-80) cc_final: 0.7729 (m-80) REVERT: M 559 LYS cc_start: 0.6537 (mptt) cc_final: 0.5984 (mttt) REVERT: M 731 LEU cc_start: 0.8146 (pt) cc_final: 0.7840 (pt) REVERT: M 1047 MET cc_start: 0.7497 (tpt) cc_final: 0.7105 (tpt) REVERT: M 1050 ARG cc_start: 0.7465 (ptt-90) cc_final: 0.7223 (ptt-90) REVERT: M 1084 TYR cc_start: 0.4707 (t80) cc_final: 0.4344 (m-80) outliers start: 111 outliers final: 95 residues processed: 483 average time/residue: 0.4257 time to fit residues: 332.5760 Evaluate side-chains 488 residues out of total 3737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 389 time to evaluate : 4.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1002 GLU Chi-restraints excluded: chain B residue 1017 VAL Chi-restraints excluded: chain B residue 1064 VAL Chi-restraints excluded: chain B residue 1084 ILE Chi-restraints excluded: chain B residue 1169 THR Chi-restraints excluded: chain B residue 1171 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 26 TYR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 34 HIS Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 153 CYS Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 233 THR Chi-restraints excluded: chain M residue 250 ILE Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 482 ASN Chi-restraints excluded: chain M residue 521 LEU Chi-restraints excluded: chain M residue 583 ILE Chi-restraints excluded: chain M residue 591 VAL Chi-restraints excluded: chain M residue 624 THR Chi-restraints excluded: chain M residue 746 VAL Chi-restraints excluded: chain M residue 782 THR Chi-restraints excluded: chain M residue 794 VAL Chi-restraints excluded: chain M residue 956 VAL Chi-restraints excluded: chain M residue 968 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 379 optimal weight: 6.9990 chunk 368 optimal weight: 30.0000 chunk 340 optimal weight: 8.9990 chunk 327 optimal weight: 20.0000 chunk 150 optimal weight: 6.9990 chunk 242 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 385 optimal weight: 8.9990 chunk 380 optimal weight: 0.9980 chunk 365 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN ** A 743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN ** E 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 411 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.154848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.138190 restraints weight = 44549.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.131530 restraints weight = 90202.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.129599 restraints weight = 66797.905| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 32382 Z= 0.227 Angle : 0.641 20.669 43901 Z= 0.316 Chirality : 0.046 0.213 5071 Planarity : 0.004 0.091 5644 Dihedral : 4.660 27.371 4513 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 3.78 % Allowed : 19.72 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.12), residues: 4151 helix: -1.55 (0.14), residues: 1232 sheet: -1.88 (0.20), residues: 610 loop : -2.43 (0.12), residues: 2309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1139 HIS 0.010 0.001 HIS B 877 PHE 0.020 0.002 PHE A 574 TYR 0.024 0.002 TYR A 718 ARG 0.006 0.001 ARG E 88 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 753) hydrogen bonds : angle 4.78809 ( 2145) metal coordination : bond 0.01591 ( 28) metal coordination : angle 7.81907 ( 29) covalent geometry : bond 0.00549 (32354) covalent geometry : angle 0.60932 (43872) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 406 time to evaluate : 3.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.7951 (tpp) cc_final: 0.7721 (mpp) REVERT: A 436 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8267 (pp) REVERT: A 728 MET cc_start: 0.8935 (mtm) cc_final: 0.8702 (mtp) REVERT: A 760 PHE cc_start: 0.9587 (OUTLIER) cc_final: 0.8981 (m-80) REVERT: A 836 MET cc_start: 0.8668 (tpt) cc_final: 0.8366 (tpt) REVERT: A 1180 ARG cc_start: 0.8601 (mmm-85) cc_final: 0.8156 (ttm110) REVERT: B 232 ASN cc_start: 0.7904 (t0) cc_final: 0.7614 (t0) REVERT: B 421 LYS cc_start: 0.7412 (mmtt) cc_final: 0.7204 (ttmt) REVERT: B 581 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8661 (t) REVERT: B 858 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7399 (t0) REVERT: B 928 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8048 (mt-10) REVERT: B 999 GLU cc_start: 0.7577 (tp30) cc_final: 0.7365 (mm-30) REVERT: E 26 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.5539 (t80) REVERT: F 102 MET cc_start: 0.7358 (tpp) cc_final: 0.6905 (mpp) REVERT: H 7 MET cc_start: 0.6137 (mmp) cc_final: 0.5785 (mtt) REVERT: I 113 ARG cc_start: 0.8393 (ttt90) cc_final: 0.8010 (ttt-90) REVERT: J 48 MET cc_start: 0.8312 (mmm) cc_final: 0.7521 (mtt) REVERT: M 559 LYS cc_start: 0.6679 (mptt) cc_final: 0.5970 (mttm) REVERT: M 704 MET cc_start: 0.7846 (tmm) cc_final: 0.7476 (ppp) REVERT: M 731 LEU cc_start: 0.8201 (pt) cc_final: 0.7937 (pt) REVERT: M 1084 TYR cc_start: 0.4652 (t80) cc_final: 0.4405 (m-80) outliers start: 122 outliers final: 96 residues processed: 496 average time/residue: 0.4196 time to fit residues: 337.1612 Evaluate side-chains 490 residues out of total 3737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 389 time to evaluate : 3.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1002 GLU Chi-restraints excluded: chain B residue 1017 VAL Chi-restraints excluded: chain B residue 1064 VAL Chi-restraints excluded: chain B residue 1084 ILE Chi-restraints excluded: chain B residue 1171 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 26 TYR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 34 HIS Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 123 PHE Chi-restraints excluded: chain M residue 153 CYS Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 233 THR Chi-restraints excluded: chain M residue 250 ILE Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 482 ASN Chi-restraints excluded: chain M residue 583 ILE Chi-restraints excluded: chain M residue 591 VAL Chi-restraints excluded: chain M residue 624 THR Chi-restraints excluded: chain M residue 746 VAL Chi-restraints excluded: chain M residue 782 THR Chi-restraints excluded: chain M residue 794 VAL Chi-restraints excluded: chain M residue 909 LEU Chi-restraints excluded: chain M residue 956 VAL Chi-restraints excluded: chain M residue 1012 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 134 optimal weight: 0.7980 chunk 383 optimal weight: 10.0000 chunk 6 optimal weight: 50.0000 chunk 18 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 255 optimal weight: 3.9990 chunk 245 optimal weight: 0.0030 chunk 154 optimal weight: 0.5980 chunk 240 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN B 355 HIS B1091 ASN ** E 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 HIS ** M 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.160774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.144125 restraints weight = 43931.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.137793 restraints weight = 87006.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.135351 restraints weight = 63936.486| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 32382 Z= 0.093 Angle : 0.537 17.346 43901 Z= 0.261 Chirality : 0.041 0.194 5071 Planarity : 0.003 0.074 5644 Dihedral : 4.074 26.422 4513 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.72 % Allowed : 21.18 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.12), residues: 4151 helix: -1.27 (0.15), residues: 1223 sheet: -1.67 (0.21), residues: 613 loop : -2.26 (0.12), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M1065 HIS 0.005 0.001 HIS A 352 PHE 0.016 0.001 PHE B 569 TYR 0.018 0.001 TYR M1084 ARG 0.008 0.000 ARG B 954 Details of bonding type rmsd hydrogen bonds : bond 0.02653 ( 753) hydrogen bonds : angle 4.40668 ( 2145) metal coordination : bond 0.01443 ( 28) metal coordination : angle 6.84186 ( 29) covalent geometry : bond 0.00216 (32354) covalent geometry : angle 0.50779 (43872) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 418 time to evaluate : 3.697 Fit side-chains revert: symmetry clash REVERT: A 334 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8548 (mm) REVERT: A 352 HIS cc_start: 0.8366 (m-70) cc_final: 0.8129 (m-70) REVERT: A 436 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8189 (pp) REVERT: A 728 MET cc_start: 0.8935 (mtm) cc_final: 0.8711 (mtp) REVERT: A 1219 GLN cc_start: 0.7097 (tm-30) cc_final: 0.6802 (tm-30) REVERT: B 232 ASN cc_start: 0.7789 (t0) cc_final: 0.7487 (t0) REVERT: B 421 LYS cc_start: 0.7427 (mmtt) cc_final: 0.7201 (ttmt) REVERT: B 581 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8552 (t) REVERT: B 658 ILE cc_start: 0.9160 (pt) cc_final: 0.8704 (mt) REVERT: B 858 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7363 (t0) REVERT: B 928 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7993 (mt-10) REVERT: E 26 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.5402 (t80) REVERT: E 89 MET cc_start: 0.4146 (ttt) cc_final: 0.3701 (ptt) REVERT: F 72 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8046 (ttt180) REVERT: H 7 MET cc_start: 0.5848 (mmp) cc_final: 0.5547 (mtt) REVERT: H 129 HIS cc_start: 0.6117 (m90) cc_final: 0.5862 (m-70) REVERT: I 45 ARG cc_start: 0.6757 (mtp180) cc_final: 0.6526 (mtp180) REVERT: I 113 ARG cc_start: 0.8258 (ttt90) cc_final: 0.7888 (ttt-90) REVERT: J 48 MET cc_start: 0.8169 (mmm) cc_final: 0.7513 (mtt) REVERT: M 559 LYS cc_start: 0.6539 (mptt) cc_final: 0.5920 (mttm) REVERT: M 704 MET cc_start: 0.7751 (tmm) cc_final: 0.7451 (ppp) REVERT: M 731 LEU cc_start: 0.8062 (pt) cc_final: 0.7772 (pt) REVERT: M 738 MET cc_start: 0.2065 (ptt) cc_final: 0.1805 (ptt) REVERT: M 1084 TYR cc_start: 0.4589 (t80) cc_final: 0.4354 (m-80) outliers start: 88 outliers final: 73 residues processed: 481 average time/residue: 0.4429 time to fit residues: 344.0546 Evaluate side-chains 471 residues out of total 3737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 392 time to evaluate : 3.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 1017 VAL Chi-restraints excluded: chain B residue 1064 VAL Chi-restraints excluded: chain B residue 1084 ILE Chi-restraints excluded: chain B residue 1171 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 26 TYR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 34 HIS Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 153 CYS Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 309 SER Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 482 ASN Chi-restraints excluded: chain M residue 583 ILE Chi-restraints excluded: chain M residue 591 VAL Chi-restraints excluded: chain M residue 624 THR Chi-restraints excluded: chain M residue 746 VAL Chi-restraints excluded: chain M residue 794 VAL Chi-restraints excluded: chain M residue 956 VAL Chi-restraints excluded: chain M residue 1012 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 312 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 365 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 84 optimal weight: 30.0000 chunk 392 optimal weight: 0.1980 chunk 44 optimal weight: 6.9990 chunk 208 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 HIS ** B 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.156986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140528 restraints weight = 44393.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.134044 restraints weight = 85401.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.131345 restraints weight = 64221.372| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 32382 Z= 0.186 Angle : 0.616 23.545 43901 Z= 0.299 Chirality : 0.044 0.358 5071 Planarity : 0.004 0.077 5644 Dihedral : 4.408 26.536 4513 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.07 % Allowed : 20.99 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.12), residues: 4151 helix: -1.40 (0.14), residues: 1239 sheet: -1.80 (0.20), residues: 629 loop : -2.35 (0.12), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1139 HIS 0.008 0.001 HIS B 513 PHE 0.018 0.002 PHE M 311 TYR 0.018 0.002 TYR M1084 ARG 0.006 0.001 ARG B 954 Details of bonding type rmsd hydrogen bonds : bond 0.03186 ( 753) hydrogen bonds : angle 4.63835 ( 2145) metal coordination : bond 0.01407 ( 28) metal coordination : angle 8.14358 ( 29) covalent geometry : bond 0.00450 (32354) covalent geometry : angle 0.57906 (43872) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 388 time to evaluate : 3.493 Fit side-chains revert: symmetry clash REVERT: A 309 MET cc_start: 0.7866 (tpp) cc_final: 0.7657 (mpp) REVERT: A 334 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8684 (mm) REVERT: A 336 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8171 (mt-10) REVERT: A 352 HIS cc_start: 0.8425 (m-70) cc_final: 0.8201 (m-70) REVERT: A 436 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8367 (pp) REVERT: A 728 MET cc_start: 0.8937 (mtm) cc_final: 0.8699 (mtp) REVERT: A 760 PHE cc_start: 0.9573 (OUTLIER) cc_final: 0.8831 (m-80) REVERT: A 836 MET cc_start: 0.8667 (tpt) cc_final: 0.8310 (tpt) REVERT: A 1180 ARG cc_start: 0.8551 (mmm-85) cc_final: 0.8102 (ttm110) REVERT: A 1219 GLN cc_start: 0.7260 (tm-30) cc_final: 0.6949 (tm-30) REVERT: B 232 ASN cc_start: 0.7853 (t0) cc_final: 0.7546 (t0) REVERT: B 421 LYS cc_start: 0.7454 (mmtt) cc_final: 0.7185 (ttmt) REVERT: B 581 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8718 (t) REVERT: B 658 ILE cc_start: 0.9196 (pt) cc_final: 0.8748 (mt) REVERT: B 858 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7489 (t0) REVERT: B 928 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7965 (mt-10) REVERT: E 26 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.5551 (t80) REVERT: E 57 LYS cc_start: 0.6528 (ptmm) cc_final: 0.5480 (ptmm) REVERT: E 89 MET cc_start: 0.4499 (ttt) cc_final: 0.3827 (ptt) REVERT: F 72 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8040 (ttt180) REVERT: H 7 MET cc_start: 0.5975 (mmp) cc_final: 0.5504 (mtt) REVERT: I 113 ARG cc_start: 0.8336 (ttt90) cc_final: 0.7946 (ttt-90) REVERT: J 48 MET cc_start: 0.8387 (mmm) cc_final: 0.7459 (mtt) REVERT: M 559 LYS cc_start: 0.6666 (mptt) cc_final: 0.5959 (mttm) REVERT: M 663 MET cc_start: 0.5836 (ppp) cc_final: 0.5449 (ppp) REVERT: M 704 MET cc_start: 0.7766 (tmm) cc_final: 0.7450 (ppp) REVERT: M 731 LEU cc_start: 0.8144 (pt) cc_final: 0.7862 (pt) REVERT: M 1084 TYR cc_start: 0.4565 (t80) cc_final: 0.4160 (m-80) outliers start: 99 outliers final: 84 residues processed: 460 average time/residue: 0.4461 time to fit residues: 330.1904 Evaluate side-chains 476 residues out of total 3737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 385 time to evaluate : 3.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 1002 GLU Chi-restraints excluded: chain B residue 1017 VAL Chi-restraints excluded: chain B residue 1064 VAL Chi-restraints excluded: chain B residue 1084 ILE Chi-restraints excluded: chain B residue 1171 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 26 TYR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 34 HIS Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 115 PHE Chi-restraints excluded: chain M residue 123 PHE Chi-restraints excluded: chain M residue 153 CYS Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 309 SER Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 482 ASN Chi-restraints excluded: chain M residue 583 ILE Chi-restraints excluded: chain M residue 591 VAL Chi-restraints excluded: chain M residue 620 VAL Chi-restraints excluded: chain M residue 624 THR Chi-restraints excluded: chain M residue 746 VAL Chi-restraints excluded: chain M residue 782 THR Chi-restraints excluded: chain M residue 794 VAL Chi-restraints excluded: chain M residue 956 VAL Chi-restraints excluded: chain M residue 1058 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 334 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 374 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 chunk 280 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 393 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 90 optimal weight: 0.0270 chunk 20 optimal weight: 3.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 GLN B 355 HIS B1091 ASN ** E 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 HIS ** M 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.161432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.143720 restraints weight = 43914.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.141093 restraints weight = 90134.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.141404 restraints weight = 90689.095| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 32382 Z= 0.089 Angle : 0.521 14.822 43901 Z= 0.257 Chirality : 0.041 0.360 5071 Planarity : 0.003 0.069 5644 Dihedral : 3.899 25.832 4513 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.54 % Allowed : 21.58 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.13), residues: 4151 helix: -1.10 (0.15), residues: 1226 sheet: -1.57 (0.21), residues: 634 loop : -2.18 (0.12), residues: 2291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 840 HIS 0.004 0.001 HIS A 352 PHE 0.019 0.001 PHE M 311 TYR 0.019 0.001 TYR A 605 ARG 0.007 0.000 ARG B 954 Details of bonding type rmsd hydrogen bonds : bond 0.02554 ( 753) hydrogen bonds : angle 4.30658 ( 2145) metal coordination : bond 0.01345 ( 28) metal coordination : angle 5.69990 ( 29) covalent geometry : bond 0.00205 (32354) covalent geometry : angle 0.50051 (43872) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11132.12 seconds wall clock time: 196 minutes 45.62 seconds (11805.62 seconds total)