Starting phenix.real_space_refine on Sat Mar 7 08:35:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tut_10595/03_2026/6tut_10595.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tut_10595/03_2026/6tut_10595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6tut_10595/03_2026/6tut_10595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tut_10595/03_2026/6tut_10595.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6tut_10595/03_2026/6tut_10595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tut_10595/03_2026/6tut_10595.map" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 7 6.06 5 S 212 5.16 5 C 25587 2.51 5 N 6932 2.21 5 O 7586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40324 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 10908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 10908 Classifications: {'peptide': 1390} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1326} Chain breaks: 5 Chain: "B" Number of atoms: 8657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8657 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 41, 'TRANS': 1055} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2647 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "D" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 857 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain breaks: 2 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1594 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 186} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1161 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "I" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 332 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 801 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1345 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 8, 'TRANS': 157} Chain breaks: 1 Chain: "N" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 968 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain breaks: 1 Chain: "O" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4433 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 19, 'TRANS': 531} Chain breaks: 1 Chain: "P" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1599 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "Q" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 503 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 6, 'TRANS': 72} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 3, 'ARG:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 71 Chain: "R" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1175 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain breaks: 1 Chain: "A" 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: "B" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" 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: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 492 SG CYS A 67 95.777 61.590 109.972 1.00 64.41 S ATOM 510 SG CYS A 70 92.568 60.168 108.326 1.00 59.03 S ATOM 557 SG CYS A 77 93.479 63.536 107.173 1.00 51.81 S ATOM 795 SG CYS A 107 80.440 95.862 141.450 1.00 65.56 S ATOM 818 SG CYS A 110 79.692 92.762 143.091 1.00 69.15 S ATOM 1184 SG CYS A 154 76.928 96.104 142.375 1.00 97.94 S ATOM 1208 SG CYS A 157 80.937 96.014 145.016 1.00 98.85 S ATOM 19138 SG CYS B1095 77.762 63.477 117.351 1.00 36.72 S ATOM 19161 SG CYS B1098 78.954 66.257 120.202 1.00 37.28 S ATOM 19227 SG CYS B1107 81.579 63.566 117.720 1.00 43.19 S ATOM 19247 SG CYS B1110 79.673 62.718 120.652 1.00 43.09 S ATOM 28293 SG CYS I 5 97.701 151.690 112.858 1.00 97.64 S ATOM 28312 SG CYS I 8 100.569 149.753 113.571 1.00 95.61 S ATOM 28440 SG CYS I 26 97.652 149.175 115.626 1.00115.81 S ATOM 28463 SG CYS I 29 100.846 152.559 116.302 1.00120.98 S ATOM 28640 SG CYS J 7 94.656 85.767 41.604 1.00 11.36 S ATOM 28663 SG CYS J 10 90.980 84.549 38.613 1.00 13.99 S ATOM 28943 SG CYS J 45 91.772 87.766 39.933 1.00 14.51 S ATOM 28949 SG CYS J 46 94.821 86.695 38.097 1.00 14.46 S ATOM 29986 SG CYS L 31 129.983 79.678 65.908 1.00 51.16 S ATOM 30110 SG CYS L 48 133.080 77.767 66.245 1.00 64.65 S ATOM 30133 SG CYS L 51 133.538 82.585 66.401 1.00 70.20 S Time building chain proxies: 8.28, per 1000 atoms: 0.21 Number of scatterers: 40324 At special positions: 0 Unit cell: (158.232, 181.134, 200.913, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 7 29.99 S 212 16.00 O 7586 8.00 N 6932 7.00 C 25587 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: 3.91 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 77 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 67 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 70 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 107 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 157 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 110 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1098 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1110 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 26 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN J 100 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " Number of angles added : 27 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9612 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 60 sheets defined 38.4% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 removed outlier: 3.657A pdb=" N ILE A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 116 through 128 removed outlier: 3.617A pdb=" N GLN A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 190 through 202 removed outlier: 3.858A pdb=" N LYS A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.744A pdb=" N LEU A 211 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG A 213 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 215 " --> pdb=" O GLU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 removed outlier: 3.788A pdb=" N ASN A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 283 through 306 removed outlier: 3.559A pdb=" N GLU A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 removed outlier: 3.549A pdb=" N GLU A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.580A pdb=" N LEU A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 423 removed outlier: 3.510A pdb=" N LEU A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 455 Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 524 through 534 removed outlier: 3.699A pdb=" N ALA A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 removed outlier: 3.835A pdb=" N THR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 561 " --> pdb=" O PHE A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 583 removed outlier: 3.642A pdb=" N GLN A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 615 removed outlier: 3.548A pdb=" N PHE A 610 " --> pdb=" O GLY A 606 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 612 " --> pdb=" O GLN A 608 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 649 removed outlier: 3.852A pdb=" N ASP A 649 " --> pdb=" O SER A 646 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 646 through 649' Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 686 through 701 Processing helix chain 'A' and resid 704 through 709 Processing helix chain 'A' and resid 713 through 718 removed outlier: 4.102A pdb=" N VAL A 717 " --> pdb=" O GLY A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 747 removed outlier: 3.514A pdb=" N LYS A 726 " --> pdb=" O ASP A 722 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU A 728 " --> pdb=" O LYS A 724 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 741 " --> pdb=" O LYS A 737 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR A 743 " --> pdb=" O ASP A 739 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LEU A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS A 747 " --> pdb=" O THR A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 771 removed outlier: 3.687A pdb=" N LEU A 769 " --> pdb=" O LYS A 765 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 770 " --> pdb=" O ILE A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 783 Processing helix chain 'A' and resid 789 through 797 Processing helix chain 'A' and resid 802 through 811 Processing helix chain 'A' and resid 841 through 846 Processing helix chain 'A' and resid 857 through 873 removed outlier: 3.520A pdb=" N LEU A 862 " --> pdb=" O PRO A 858 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 894 removed outlier: 3.502A pdb=" N THR A 879 " --> pdb=" O THR A 875 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY A 883 " --> pdb=" O THR A 879 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER A 886 " --> pdb=" O THR A 882 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 888 " --> pdb=" O TYR A 884 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER A 892 " --> pdb=" O ARG A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 Processing helix chain 'A' and resid 922 through 926 removed outlier: 3.801A pdb=" N MET A 926 " --> pdb=" O PRO A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 946 removed outlier: 3.602A pdb=" N THR A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 967 removed outlier: 3.704A pdb=" N MET A 960 " --> pdb=" O PRO A 956 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A 966 " --> pdb=" O THR A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 995 Processing helix chain 'A' and resid 996 through 997 No H-bonds generated for 'chain 'A' and resid 996 through 997' Processing helix chain 'A' and resid 998 through 1025 removed outlier: 3.578A pdb=" N ILE A1012 " --> pdb=" O LEU A1008 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1060 Processing helix chain 'A' and resid 1066 through 1081 Processing helix chain 'A' and resid 1088 through 1099 removed outlier: 3.690A pdb=" N ILE A1097 " --> pdb=" O GLY A1093 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY A1098 " --> pdb=" O ALA A1094 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A1099 " --> pdb=" O GLN A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1131 removed outlier: 3.535A pdb=" N ILE A1126 " --> pdb=" O GLY A1122 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN A1131 " --> pdb=" O LYS A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1201 through 1213 removed outlier: 3.910A pdb=" N ILE A1205 " --> pdb=" O THR A1201 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A1206 " --> pdb=" O ILE A1202 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER A1213 " --> pdb=" O ILE A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1220 No H-bonds generated for 'chain 'A' and resid 1218 through 1220' Processing helix chain 'A' and resid 1256 through 1266 removed outlier: 3.608A pdb=" N ARG A1265 " --> pdb=" O GLN A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1306 Processing helix chain 'A' and resid 1318 through 1327 removed outlier: 3.670A pdb=" N VAL A1325 " --> pdb=" O GLU A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1343 removed outlier: 3.628A pdb=" N SER A1334 " --> pdb=" O ALA A1330 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG A1337 " --> pdb=" O TYR A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1346 No H-bonds generated for 'chain 'A' and resid 1344 through 1346' Processing helix chain 'A' and resid 1352 through 1362 removed outlier: 3.744A pdb=" N LEU A1358 " --> pdb=" O HIS A1354 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET A1362 " --> pdb=" O LEU A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1380 Processing helix chain 'A' and resid 1383 through 1390 removed outlier: 3.521A pdb=" N SER A1388 " --> pdb=" O LEU A1384 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A1389 " --> pdb=" O GLN A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1402 removed outlier: 3.531A pdb=" N ALA A1400 " --> pdb=" O LEU A1396 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1418 removed outlier: 3.663A pdb=" N ILE A1415 " --> pdb=" O VAL A1411 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1428 removed outlier: 4.339A pdb=" N PHE A1428 " --> pdb=" O THR A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1456 removed outlier: 3.910A pdb=" N GLU A1454 " --> pdb=" O SER A1450 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.557A pdb=" N ASP B 43 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS B 44 " --> pdb=" O ALA B 41 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TRP B 45 " --> pdb=" O GLN B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 46 through 55 removed outlier: 4.102A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 69 removed outlier: 4.491A pdb=" N SER B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 169 through 174 removed outlier: 3.534A pdb=" N LYS B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 276 through 293 removed outlier: 3.695A pdb=" N ASP B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASN B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER B 290 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.957A pdb=" N ILE B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 330 removed outlier: 3.718A pdb=" N GLU B 325 " --> pdb=" O GLN B 321 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 362 removed outlier: 3.726A pdb=" N ARG B 355 " --> pdb=" O MET B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 379 through 408 removed outlier: 3.563A pdb=" N GLU B 389 " --> pdb=" O SER B 385 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LYS B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 440 removed outlier: 3.955A pdb=" N HIS B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN B 427 " --> pdb=" O ASN B 423 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ASN B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 429 " --> pdb=" O HIS B 425 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B 431 " --> pdb=" O ASN B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 removed outlier: 4.015A pdb=" N ALA B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 removed outlier: 3.537A pdb=" N GLN B 493 " --> pdb=" O GLN B 490 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 494 " --> pdb=" O PRO B 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 490 through 494' Processing helix chain 'B' and resid 526 through 536 removed outlier: 3.597A pdb=" N TYR B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 552 removed outlier: 4.503A pdb=" N HIS B 550 " --> pdb=" O ALA B 547 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU B 551 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN B 552 " --> pdb=" O LEU B 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 547 through 552' Processing helix chain 'B' and resid 567 through 581 removed outlier: 3.662A pdb=" N LEU B 578 " --> pdb=" O GLN B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 632 removed outlier: 3.511A pdb=" N LEU B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP B 632 " --> pdb=" O ARG B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.508A pdb=" N LYS B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.516A pdb=" N ILE B 666 " --> pdb=" O GLU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 681 removed outlier: 3.530A pdb=" N LEU B 681 " --> pdb=" O PHE B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 694 Processing helix chain 'B' and resid 695 through 707 removed outlier: 3.518A pdb=" N ASN B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 700 " --> pdb=" O SER B 696 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N CYS B 703 " --> pdb=" O ASN B 699 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 704 " --> pdb=" O THR B 700 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS B 707 " --> pdb=" O CYS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 744 removed outlier: 3.539A pdb=" N ILE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 749 removed outlier: 3.619A pdb=" N LYS B 748 " --> pdb=" O ASP B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.533A pdb=" N ARG B 780 " --> pdb=" O SER B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 822 Processing helix chain 'B' and resid 954 through 971 removed outlier: 3.961A pdb=" N MET B 958 " --> pdb=" O THR B 954 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 995 removed outlier: 4.000A pdb=" N LYS B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 990 " --> pdb=" O ASP B 986 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL B 992 " --> pdb=" O SER B 988 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY B 995 " --> pdb=" O LEU B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1034 Processing helix chain 'B' and resid 1066 through 1073 Processing helix chain 'B' and resid 1075 through 1084 removed outlier: 3.618A pdb=" N LEU B1079 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1123 through 1133 Processing helix chain 'C' and resid 32 through 40 removed outlier: 3.785A pdb=" N LYS C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 93 through 102 Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.584A pdb=" N LEU C 113 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.522A pdb=" N PHE C 219 " --> pdb=" O HIS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.547A pdb=" N LYS C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 330 removed outlier: 3.789A pdb=" N PHE C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 27 removed outlier: 3.511A pdb=" N VAL D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 62 removed outlier: 3.632A pdb=" N ARG D 60 " --> pdb=" O GLN D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 67 Processing helix chain 'D' and resid 105 through 110 removed outlier: 4.474A pdb=" N LYS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 105 through 110' Processing helix chain 'D' and resid 111 through 114 removed outlier: 3.543A pdb=" N LYS D 114 " --> pdb=" O ASN D 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 111 through 114' Processing helix chain 'D' and resid 116 through 126 removed outlier: 3.945A pdb=" N LEU D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 138 removed outlier: 3.670A pdb=" N VAL D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'E' and resid 2 through 26 removed outlier: 3.735A pdb=" N VAL E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET E 22 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL E 23 " --> pdb=" O VAL E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 35 removed outlier: 3.638A pdb=" N GLU E 34 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.864A pdb=" N LYS E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 102 removed outlier: 4.046A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN E 101 " --> pdb=" O VAL E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 122 removed outlier: 3.890A pdb=" N MET E 121 " --> pdb=" O PRO E 118 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS E 122 " --> pdb=" O SER E 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 118 through 122' Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.520A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 removed outlier: 3.541A pdb=" N LYS E 166 " --> pdb=" O ARG E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 86 through 103 removed outlier: 3.539A pdb=" N ALA F 91 " --> pdb=" O LYS F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 20 removed outlier: 4.175A pdb=" N HIS G 19 " --> pdb=" O ASP G 16 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG G 20 " --> pdb=" O GLN G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.614A pdb=" N GLN G 29 " --> pdb=" O ALA G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'G' and resid 162 through 174 removed outlier: 3.583A pdb=" N GLU G 167 " --> pdb=" O PRO G 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU G 168 " --> pdb=" O LYS G 164 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU G 170 " --> pdb=" O ARG G 166 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU G 174 " --> pdb=" O GLU G 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 20 No H-bonds generated for 'chain 'I' and resid 18 through 20' Processing helix chain 'J' and resid 14 through 17 Processing helix chain 'J' and resid 18 through 27 removed outlier: 3.741A pdb=" N ASN J 23 " --> pdb=" O GLU J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 40 removed outlier: 3.651A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.983A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR J 52 " --> pdb=" O ARG J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 81 removed outlier: 4.151A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 140 removed outlier: 3.616A pdb=" N LYS K 122 " --> pdb=" O GLN K 118 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU K 124 " --> pdb=" O GLY K 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 140 removed outlier: 3.951A pdb=" N GLU M 139 " --> pdb=" O LYS M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 192 removed outlier: 4.032A pdb=" N ASP M 187 " --> pdb=" O PHE M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 230 through 239 removed outlier: 3.781A pdb=" N ALA M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU M 239 " --> pdb=" O LYS M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 258 removed outlier: 3.732A pdb=" N LYS M 256 " --> pdb=" O PHE M 252 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 262 Processing helix chain 'N' and resid 275 through 296 removed outlier: 3.714A pdb=" N GLN N 288 " --> pdb=" O ASN N 284 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU N 291 " --> pdb=" O HIS N 287 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS N 293 " --> pdb=" O HIS N 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 321 through 329 removed outlier: 3.590A pdb=" N ASP N 327 " --> pdb=" O GLU N 323 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET N 328 " --> pdb=" O GLU N 324 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU N 329 " --> pdb=" O LYS N 325 " (cutoff:3.500A) Processing helix chain 'O' and resid 38 through 42 removed outlier: 3.601A pdb=" N LEU O 42 " --> pdb=" O GLN O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 50 Processing helix chain 'O' and resid 50 through 55 Processing helix chain 'O' and resid 60 through 72 removed outlier: 3.526A pdb=" N MET O 67 " --> pdb=" O SER O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 83 removed outlier: 3.561A pdb=" N LEU O 79 " --> pdb=" O SER O 75 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU O 81 " --> pdb=" O ARG O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 99 removed outlier: 3.596A pdb=" N THR O 94 " --> pdb=" O SER O 90 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL O 96 " --> pdb=" O LYS O 92 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER O 97 " --> pdb=" O THR O 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 132 removed outlier: 4.271A pdb=" N LEU O 130 " --> pdb=" O GLY O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 132 through 144 removed outlier: 3.974A pdb=" N ILE O 137 " --> pdb=" O SER O 133 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR O 142 " --> pdb=" O ASP O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 151 through 165 removed outlier: 4.513A pdb=" N ALA O 157 " --> pdb=" O LYS O 153 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU O 158 " --> pdb=" O GLN O 154 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN O 162 " --> pdb=" O GLU O 158 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE O 164 " --> pdb=" O VAL O 160 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER O 165 " --> pdb=" O GLN O 161 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 178 removed outlier: 3.605A pdb=" N SER O 177 " --> pdb=" O ASP O 173 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL O 178 " --> pdb=" O TYR O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 197 removed outlier: 3.886A pdb=" N THR O 186 " --> pdb=" O SER O 182 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL O 192 " --> pdb=" O SER O 188 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET O 197 " --> pdb=" O GLN O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 205 through 209 removed outlier: 3.760A pdb=" N THR O 209 " --> pdb=" O LEU O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 222 removed outlier: 3.661A pdb=" N PHE O 217 " --> pdb=" O ASP O 213 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS O 222 " --> pdb=" O LEU O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 233 through 258 removed outlier: 3.871A pdb=" N ASN O 244 " --> pdb=" O GLN O 240 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR O 247 " --> pdb=" O MET O 243 " (cutoff:3.500A) Proline residue: O 256 - end of helix Processing helix chain 'O' and resid 286 through 301 removed outlier: 3.537A pdb=" N ILE O 297 " --> pdb=" O SER O 293 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN O 298 " --> pdb=" O LYS O 294 " (cutoff:3.500A) Processing helix chain 'O' and resid 307 through 319 removed outlier: 3.635A pdb=" N VAL O 311 " --> pdb=" O VAL O 307 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR O 319 " --> pdb=" O ALA O 315 " (cutoff:3.500A) Processing helix chain 'O' and resid 330 through 334 removed outlier: 3.689A pdb=" N THR O 333 " --> pdb=" O LEU O 330 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY O 334 " --> pdb=" O THR O 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 330 through 334' Processing helix chain 'O' and resid 339 through 353 removed outlier: 3.507A pdb=" N LYS O 343 " --> pdb=" O LEU O 339 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU O 353 " --> pdb=" O ALA O 349 " (cutoff:3.500A) Processing helix chain 'O' and resid 364 through 369 removed outlier: 3.784A pdb=" N ALA O 367 " --> pdb=" O ILE O 364 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG O 368 " --> pdb=" O ASP O 365 " (cutoff:3.500A) Processing helix chain 'O' and resid 449 through 463 removed outlier: 3.654A pdb=" N ILE O 459 " --> pdb=" O SER O 455 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU O 460 " --> pdb=" O HIS O 456 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA O 461 " --> pdb=" O LEU O 457 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER O 462 " --> pdb=" O LYS O 458 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER O 463 " --> pdb=" O ILE O 459 " (cutoff:3.500A) Processing helix chain 'O' and resid 483 through 500 removed outlier: 3.706A pdb=" N LYS O 488 " --> pdb=" O MET O 484 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N SER O 489 " --> pdb=" O PRO O 485 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU O 493 " --> pdb=" O SER O 489 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR O 494 " --> pdb=" O SER O 490 " (cutoff:3.500A) Processing helix chain 'O' and resid 501 through 515 removed outlier: 3.866A pdb=" N MET O 505 " --> pdb=" O GLY O 501 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG O 506 " --> pdb=" O PRO O 502 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG O 512 " --> pdb=" O SER O 508 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN O 514 " --> pdb=" O CYS O 510 " (cutoff:3.500A) Processing helix chain 'O' and resid 518 through 526 removed outlier: 3.743A pdb=" N ASN O 523 " --> pdb=" O GLU O 519 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER O 524 " --> pdb=" O LYS O 520 " (cutoff:3.500A) Processing helix chain 'O' and resid 529 through 537 Processing helix chain 'O' and resid 537 through 542 removed outlier: 3.939A pdb=" N ARG O 542 " --> pdb=" O ALA O 538 " (cutoff:3.500A) Processing helix chain 'O' and resid 569 through 599 removed outlier: 3.663A pdb=" N SER O 573 " --> pdb=" O LYS O 569 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE O 576 " --> pdb=" O HIS O 572 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET O 577 " --> pdb=" O SER O 573 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU O 581 " --> pdb=" O MET O 577 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU O 589 " --> pdb=" O MET O 585 " (cutoff:3.500A) Processing helix chain 'O' and resid 599 through 609 Processing helix chain 'O' and resid 620 through 649 removed outlier: 4.036A pdb=" N LEU O 624 " --> pdb=" O LEU O 620 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN O 625 " --> pdb=" O PRO O 621 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLN O 626 " --> pdb=" O SER O 622 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG O 633 " --> pdb=" O MET O 629 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE O 638 " --> pdb=" O GLU O 634 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU O 647 " --> pdb=" O ARG O 643 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 101 Processing helix chain 'P' and resid 109 through 113 Processing helix chain 'P' and resid 119 through 131 removed outlier: 3.739A pdb=" N LEU P 125 " --> pdb=" O VAL P 121 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS P 126 " --> pdb=" O LEU P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 189 removed outlier: 3.708A pdb=" N LEU P 178 " --> pdb=" O PHE P 174 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU P 179 " --> pdb=" O ILE P 175 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR P 180 " --> pdb=" O ASN P 176 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE P 181 " --> pdb=" O SER P 177 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN P 189 " --> pdb=" O PHE P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 192 through 196 removed outlier: 3.768A pdb=" N LYS P 196 " --> pdb=" O ASN P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 218 through 228 removed outlier: 5.391A pdb=" N GLU P 223 " --> pdb=" O GLN P 219 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR P 226 " --> pdb=" O LEU P 222 " (cutoff:3.500A) Processing helix chain 'P' and resid 239 through 244 Processing helix chain 'P' and resid 265 through 270 removed outlier: 3.779A pdb=" N GLN P 270 " --> pdb=" O SER P 267 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 63 removed outlier: 3.599A pdb=" N VAL Q 56 " --> pdb=" O ARG Q 52 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS Q 57 " --> pdb=" O SER Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1084 through 1088 Processing helix chain 'Q' and resid 1090 through 1094 removed outlier: 3.754A pdb=" N ASN Q1093 " --> pdb=" O ARG Q1090 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1105 through 1112 removed outlier: 3.659A pdb=" N GLY Q1111 " --> pdb=" O ASP Q1107 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 16 removed outlier: 3.574A pdb=" N LEU R 16 " --> pdb=" O VAL R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 246 removed outlier: 3.892A pdb=" N TYR R 237 " --> pdb=" O LYS R 233 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE R 239 " --> pdb=" O PHE R 235 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA R 240 " --> pdb=" O ALA R 236 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE R 241 " --> pdb=" O TYR R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 277 removed outlier: 3.572A pdb=" N LYS R 270 " --> pdb=" O THR R 266 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU R 275 " --> pdb=" O PHE R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 295 removed outlier: 3.720A pdb=" N GLU R 288 " --> pdb=" O GLU R 284 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN R 291 " --> pdb=" O TRP R 287 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET R 294 " --> pdb=" O ILE R 290 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 removed outlier: 6.510A pdb=" N GLU A 3 " --> pdb=" O ILE G 38 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU G 44 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA G 74 " --> pdb=" O SER G 5 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE G 2 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 2 through 5 removed outlier: 6.777A pdb=" N LYS G 6 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA G 74 " --> pdb=" O SER G 5 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ASN G 69 " --> pdb=" O VAL G 54 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL G 54 " --> pdb=" O ASN G 69 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR G 71 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG G 73 " --> pdb=" O ASP G 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1405 through 1406 removed outlier: 6.628A pdb=" N ARG B1142 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU A 16 " --> pdb=" O ARG B1140 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ARG B1140 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE A 18 " --> pdb=" O ALA B1138 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ALA B1138 " --> pdb=" O PHE A 18 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 33 removed outlier: 5.140A pdb=" N SER A 30 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N HIS A 83 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL A 32 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LYS A 85 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 10.390A pdb=" N LEU A 86 " --> pdb=" O PRO A 262 " (cutoff:3.500A) removed outlier: 11.115A pdb=" N LEU A 88 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N TYR A 260 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 90 " --> pdb=" O TRP A 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 40 through 41 removed outlier: 3.777A pdb=" N ALA A 47 " --> pdb=" O ASP A 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 163 through 165 removed outlier: 3.579A pdb=" N VAL A 163 " --> pdb=" O ASP A 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 370 through 373 removed outlier: 3.630A pdb=" N LEU B1060 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1036 through 1038 removed outlier: 7.927A pdb=" N PHE A 498 " --> pdb=" O ARG A 378 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 380 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEU A 500 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N SER A 382 " --> pdb=" O LEU A 500 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 403 through 407 removed outlier: 3.567A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N HIS A 465 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA A 430 " --> pdb=" O HIS A 465 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AB2, first strand: chain 'A' and resid 625 through 629 removed outlier: 6.389A pdb=" N ILE A 653 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 814 through 815 Processing sheet with id=AB4, first strand: chain 'A' and resid 897 through 898 Processing sheet with id=AB5, first strand: chain 'A' and resid 1141 through 1142 Processing sheet with id=AB6, first strand: chain 'A' and resid 1144 through 1145 removed outlier: 4.640A pdb=" N VAL A1144 " --> pdb=" O ILE A1310 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 6.703A pdb=" N THR A1164 " --> pdb=" O VAL A1272 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1170 through 1177 removed outlier: 6.963A pdb=" N ARG A1187 " --> pdb=" O PHE A1171 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL A1173 " --> pdb=" O GLN A1185 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLN A1185 " --> pdb=" O VAL A1173 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASP A1175 " --> pdb=" O PHE A1183 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE A1183 " --> pdb=" O ASP A1175 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER A1182 " --> pdb=" O VAL A1234 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A1229 " --> pdb=" O ILE A1225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 143 through 147 Processing sheet with id=AC1, first strand: chain 'B' and resid 82 through 83 removed outlier: 7.374A pdb=" N ASP B 132 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE B 98 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N TYR B 130 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL B 100 " --> pdb=" O PRO B 128 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ALA B 127 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ARG B 151 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ILE B 129 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 133 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LYS B 145 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TYR B 135 " --> pdb=" O MET B 143 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N MET B 143 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG B 137 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ILE B 141 " --> pdb=" O ARG B 137 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC3, first strand: chain 'B' and resid 375 through 378 removed outlier: 6.718A pdb=" N VAL B 196 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 206 through 207 removed outlier: 3.539A pdb=" N ILE B 206 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 235 through 236 Processing sheet with id=AC6, first strand: chain 'B' and resid 442 through 444 removed outlier: 3.641A pdb=" N MET B 449 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AC8, first strand: chain 'B' and resid 619 through 620 Processing sheet with id=AC9, first strand: chain 'B' and resid 560 through 561 removed outlier: 6.455A pdb=" N GLY B 554 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE B 601 " --> pdb=" O GLY B 554 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TYR B 556 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 709 through 710 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 709 through 710 current: chain 'B' and resid 942 through 944 removed outlier: 6.815A pdb=" N LEU B 771 " --> pdb=" O ILE B 924 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N VAL B 926 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 773 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LYS B 911 " --> pdb=" O LEU B1027 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.957A pdb=" N ALA B 894 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN B 883 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ASN B 903 " --> pdb=" O SER B 879 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N SER B 879 " --> pdb=" O ASN B 903 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.957A pdb=" N ALA B 894 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN B 883 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ASN B 903 " --> pdb=" O SER B 879 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N SER B 879 " --> pdb=" O ASN B 903 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AD5, first strand: chain 'B' and resid 805 through 806 Processing sheet with id=AD6, first strand: chain 'B' and resid 841 through 843 removed outlier: 4.473A pdb=" N ILE B 843 " --> pdb=" O VAL B 871 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1101 through 1102 removed outlier: 4.067A pdb=" N ASP B1093 " --> pdb=" O GLY B1102 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 12 through 13 removed outlier: 3.697A pdb=" N ILE C 7 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU C 291 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN C 301 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA C 225 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLU C 303 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 41 through 47 removed outlier: 3.638A pdb=" N ASN C 43 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU C 47 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 167 through 170 removed outlier: 4.309A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N SER C 203 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE C 85 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS C 205 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL C 83 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N HIS C 207 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL L 65 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AE3, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AE4, first strand: chain 'E' and resid 61 through 62 removed outlier: 6.953A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 87 through 88 removed outlier: 3.999A pdb=" N VAL E 88 " --> pdb=" O ASN E 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.995A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 98 through 100 removed outlier: 7.361A pdb=" N LYS G 98 " --> pdb=" O SER G 90 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY G 87 " --> pdb=" O ILE G 146 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU G 197 " --> pdb=" O GLU G 151 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU G 153 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA G 195 " --> pdb=" O GLU G 153 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 98 through 100 removed outlier: 7.361A pdb=" N LYS G 98 " --> pdb=" O SER G 90 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY G 87 " --> pdb=" O ILE G 146 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 120 through 122 removed outlier: 4.024A pdb=" N TRP G 128 " --> pdb=" O PHE G 140 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 27 through 30 removed outlier: 6.646A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY H 127 " --> pdb=" O ILE H 112 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 23 through 25 Processing sheet with id=AF3, first strand: chain 'I' and resid 14 through 16 Processing sheet with id=AF4, first strand: chain 'K' and resid 60 through 66 removed outlier: 6.688A pdb=" N ASN K 102 " --> pdb=" O TYR K 91 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR K 91 " --> pdb=" O ASN K 102 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG K 104 " --> pdb=" O CYS K 89 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N CYS K 89 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLN K 106 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 70 through 74 removed outlier: 6.595A pdb=" N VAL N 365 " --> pdb=" O ILE M 71 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU M 73 " --> pdb=" O ILE N 363 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE N 363 " --> pdb=" O GLU M 73 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU N 371 " --> pdb=" O ILE N 382 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE N 382 " --> pdb=" O LEU N 371 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 77 through 78 removed outlier: 6.975A pdb=" N LYS M 77 " --> pdb=" O LEU M 170 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE M 162 " --> pdb=" O TYR M 169 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 243 through 244 removed outlier: 4.224A pdb=" N THR M 147 " --> pdb=" O PHE M 182 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL M 151 " --> pdb=" O GLN M 178 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN M 178 " --> pdb=" O VAL M 151 " (cutoff:3.500A) removed outlier: 11.305A pdb=" N ARG M 93 " --> pdb=" O PRO M 181 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ASP N 393 " --> pdb=" O ARG N 411 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ARG N 411 " --> pdb=" O ASP N 393 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE N 395 " --> pdb=" O LEU N 409 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR M 246 " --> pdb=" O ALA N 406 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU N 408 " --> pdb=" O THR M 246 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA M 248 " --> pdb=" O LEU N 408 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N GLY N 410 " --> pdb=" O ALA M 248 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 108 through 110 removed outlier: 3.925A pdb=" N GLU O 109 " --> pdb=" O THR O 117 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 200 through 202 Processing sheet with id=AG1, first strand: chain 'O' and resid 361 through 362 removed outlier: 3.547A pdb=" N PHE O 361 " --> pdb=" O TYR O 476 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 549 through 550 Processing sheet with id=AG3, first strand: chain 'P' and resid 105 through 106 removed outlier: 3.805A pdb=" N ILE P 147 " --> pdb=" O VAL P 137 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 216 through 217 removed outlier: 3.843A pdb=" N SER P 216 " --> pdb=" O TYR P 261 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR P 261 " --> pdb=" O SER P 216 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'R' and resid 17 through 20 removed outlier: 3.520A pdb=" N CYS R 23 " --> pdb=" O THR R 20 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'R' and resid 17 through 20 removed outlier: 3.520A pdb=" N CYS R 23 " --> pdb=" O THR R 20 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP R 319 " --> pdb=" O CYS R 340 " (cutoff:3.500A) 1422 hydrogen bonds defined for protein. 3936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.68 Time building geometry restraints manager: 5.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6905 1.31 - 1.44: 10184 1.44 - 1.57: 23614 1.57 - 1.69: 2 1.69 - 1.82: 341 Bond restraints: 41046 Sorted by residual: bond pdb=" CB PRO A 507 " pdb=" CG PRO A 507 " ideal model delta sigma weight residual 1.492 1.352 0.140 5.00e-02 4.00e+02 7.88e+00 bond pdb=" CB VAL A 652 " pdb=" CG1 VAL A 652 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.48e+00 bond pdb=" C LEU B 489 " pdb=" N GLN B 490 " ideal model delta sigma weight residual 1.339 1.188 0.151 5.57e-02 3.22e+02 7.40e+00 bond pdb=" C PRO A 858 " pdb=" N PRO A 859 " ideal model delta sigma weight residual 1.337 1.370 -0.032 1.24e-02 6.50e+03 6.85e+00 bond pdb=" CB ARG C 293 " pdb=" CG ARG C 293 " ideal model delta sigma weight residual 1.520 1.442 0.078 3.00e-02 1.11e+03 6.68e+00 ... (remaining 41041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 54556 3.56 - 7.12: 756 7.12 - 10.69: 103 10.69 - 14.25: 8 14.25 - 17.81: 4 Bond angle restraints: 55427 Sorted by residual: angle pdb=" N PRO Q1092 " pdb=" CA PRO Q1092 " pdb=" CB PRO Q1092 " ideal model delta sigma weight residual 103.52 110.26 -6.74 1.06e+00 8.90e-01 4.04e+01 angle pdb=" C LYS L 49 " pdb=" N ASP L 50 " pdb=" CA ASP L 50 " ideal model delta sigma weight residual 126.32 135.72 -9.40 1.74e+00 3.30e-01 2.92e+01 angle pdb=" C PHE B 637 " pdb=" N ASP B 638 " pdb=" CA ASP B 638 " ideal model delta sigma weight residual 125.66 135.47 -9.81 1.85e+00 2.92e-01 2.81e+01 angle pdb=" C ALA C 286 " pdb=" N ASP C 287 " pdb=" CA ASP C 287 " ideal model delta sigma weight residual 126.32 135.36 -9.04 1.74e+00 3.30e-01 2.70e+01 angle pdb=" C GLN B 837 " pdb=" N SER B 838 " pdb=" CA SER B 838 " ideal model delta sigma weight residual 122.82 130.05 -7.23 1.42e+00 4.96e-01 2.59e+01 ... (remaining 55422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.40: 23343 15.40 - 30.80: 1442 30.80 - 46.21: 359 46.21 - 61.61: 24 61.61 - 77.01: 21 Dihedral angle restraints: 25189 sinusoidal: 10347 harmonic: 14842 Sorted by residual: dihedral pdb=" CA SER B 223 " pdb=" C SER B 223 " pdb=" N THR B 224 " pdb=" CA THR B 224 " ideal model delta harmonic sigma weight residual 180.00 -134.74 -45.26 0 5.00e+00 4.00e-02 8.20e+01 dihedral pdb=" CA ASP A1043 " pdb=" C ASP A1043 " pdb=" N PRO A1044 " pdb=" CA PRO A1044 " ideal model delta harmonic sigma weight residual -180.00 -136.23 -43.77 0 5.00e+00 4.00e-02 7.66e+01 dihedral pdb=" CA GLN A 477 " pdb=" C GLN A 477 " pdb=" N PRO A 478 " pdb=" CA PRO A 478 " ideal model delta harmonic sigma weight residual 0.00 33.50 -33.50 0 5.00e+00 4.00e-02 4.49e+01 ... (remaining 25186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 5153 0.082 - 0.163: 998 0.163 - 0.245: 105 0.245 - 0.326: 12 0.326 - 0.408: 3 Chirality restraints: 6271 Sorted by residual: chirality pdb=" CB ILE F 130 " pdb=" CA ILE F 130 " pdb=" CG1 ILE F 130 " pdb=" CG2 ILE F 130 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CB ILE B 565 " pdb=" CA ILE B 565 " pdb=" CG1 ILE B 565 " pdb=" CG2 ILE B 565 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CB ILE I 35 " pdb=" CA ILE I 35 " pdb=" CG1 ILE I 35 " pdb=" CG2 ILE I 35 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 6268 not shown) Planarity restraints: 7125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 300 " 0.021 2.00e-02 2.50e+03 2.60e-02 1.18e+01 pdb=" CG PHE C 300 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE C 300 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE C 300 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 300 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE C 300 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 300 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 127 " 0.049 5.00e-02 4.00e+02 7.46e-02 8.89e+00 pdb=" N PRO E 128 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO E 128 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 128 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS I 29 " 0.046 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO I 30 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO I 30 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO I 30 " 0.039 5.00e-02 4.00e+02 ... (remaining 7122 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 718 2.66 - 3.22: 36752 3.22 - 3.78: 62505 3.78 - 4.34: 87486 4.34 - 4.90: 142543 Nonbonded interactions: 330004 Sorted by model distance: nonbonded pdb=" O ARG J 6 " pdb="ZN ZN J 101 " model vdw 2.096 2.230 nonbonded pdb=" OG1 THR E 18 " pdb=" O LEU E 140 " model vdw 2.238 3.040 nonbonded pdb=" OG SER O 642 " pdb=" OE1 GLU Q 51 " model vdw 2.245 3.040 nonbonded pdb=" OG SER B 462 " pdb=" O ALA B 709 " model vdw 2.250 3.040 nonbonded pdb=" OG SER M 138 " pdb=" OE1 GLU M 139 " model vdw 2.265 3.040 ... (remaining 329999 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.990 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: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 43.990 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.648 41069 Z= 0.453 Angle : 1.173 47.587 55454 Z= 0.581 Chirality : 0.065 0.408 6271 Planarity : 0.007 0.075 7125 Dihedral : 11.161 77.012 15577 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.08 % Favored : 91.82 % Rotamer: Outliers : 0.36 % Allowed : 4.98 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.90 (0.09), residues: 5012 helix: -4.17 (0.06), residues: 1798 sheet: -2.63 (0.18), residues: 680 loop : -2.66 (0.10), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A1125 TYR 0.034 0.003 TYR B 553 PHE 0.058 0.004 PHE C 300 TRP 0.043 0.004 TRP A 316 HIS 0.027 0.003 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00969 (41046) covalent geometry : angle 1.09712 (55427) hydrogen bonds : bond 0.27784 ( 1376) hydrogen bonds : angle 10.06932 ( 3936) metal coordination : bond 0.25130 ( 23) metal coordination : angle 18.80220 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 4510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 672 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 HIS cc_start: 0.8119 (t-170) cc_final: 0.7738 (m90) REVERT: B 296 TYR cc_start: 0.7947 (m-80) cc_final: 0.7540 (m-80) REVERT: B 417 ASP cc_start: 0.7461 (p0) cc_final: 0.7256 (p0) REVERT: B 428 ASN cc_start: 0.8007 (t160) cc_final: 0.7712 (t0) REVERT: B 907 GLU cc_start: 0.7956 (tt0) cc_final: 0.7740 (mt-10) REVERT: D 14 TYR cc_start: 0.8156 (t80) cc_final: 0.7906 (m-10) REVERT: D 18 LYS cc_start: 0.8974 (ttpt) cc_final: 0.8524 (mttp) REVERT: E 41 ASP cc_start: 0.6900 (p0) cc_final: 0.5936 (p0) REVERT: G 36 ASN cc_start: 0.7914 (t0) cc_final: 0.7367 (t0) REVERT: G 49 TYR cc_start: 0.8898 (t80) cc_final: 0.8678 (t80) REVERT: J 26 GLN cc_start: 0.7652 (tm-30) cc_final: 0.7446 (tm-30) REVERT: M 190 ASN cc_start: 0.8469 (t0) cc_final: 0.8210 (t0) REVERT: M 257 ASP cc_start: 0.8447 (t0) cc_final: 0.8184 (t0) REVERT: N 321 VAL cc_start: 0.8680 (p) cc_final: 0.8319 (t) REVERT: N 392 GLN cc_start: 0.7378 (tm130) cc_final: 0.7150 (tm-30) REVERT: O 197 MET cc_start: 0.7690 (ppp) cc_final: 0.7217 (ppp) REVERT: P 94 TYR cc_start: 0.6519 (m-10) cc_final: 0.5807 (m-10) REVERT: P 148 TYR cc_start: 0.8116 (m-80) cc_final: 0.7904 (m-80) REVERT: R 30 ASP cc_start: 0.8561 (p0) cc_final: 0.8133 (p0) REVERT: R 288 GLU cc_start: 0.8726 (mp0) cc_final: 0.8405 (mp0) REVERT: R 302 PHE cc_start: 0.8782 (m-80) cc_final: 0.8460 (m-80) REVERT: R 314 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8304 (tm-30) REVERT: R 326 TYR cc_start: 0.8647 (t80) cc_final: 0.8445 (t80) REVERT: R 327 ASN cc_start: 0.7018 (t0) cc_final: 0.6505 (t0) outliers start: 16 outliers final: 10 residues processed: 685 average time/residue: 0.2816 time to fit residues: 303.2613 Evaluate side-chains 449 residues out of total 4510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 439 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain M residue 163 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 494 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN A 207 HIS A 281 ASN ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN A 518 ASN A 523 GLN A 540 ASN A 630 ASN A 675 HIS A 695 ASN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 929 ASN A1013 ASN A1149 ASN ** A1174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1354 HIS ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 ASN B 619 GLN B 655 ASN B 699 ASN B 774 ASN B 903 ASN B 947 HIS B1036 HIS B1077 GLN C 32 ASN C 53 ASN C 93 GLN C 161 HIS C 216 HIS D 122 GLN E 61 GLN E 101 GLN E 106 GLN E 146 HIS E 174 GLN F 104 ASN G 112 GLN K 74 ASN K 95 HIS K 106 GLN M 158 GLN O 43 ASN O 128 HIS O 143 GLN O 152 HIS O 229 ASN O 544 ASN O 549 GLN O 652 GLN ** R 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 308 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.113219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.077540 restraints weight = 87049.115| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.24 r_work: 0.2983 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 41069 Z= 0.159 Angle : 0.710 16.770 55454 Z= 0.363 Chirality : 0.047 0.189 6271 Planarity : 0.005 0.069 7125 Dihedral : 6.248 43.958 5525 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.11 % Favored : 93.85 % Rotamer: Outliers : 1.77 % Allowed : 8.92 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.48 (0.10), residues: 5012 helix: -2.40 (0.10), residues: 1794 sheet: -2.41 (0.18), residues: 695 loop : -2.14 (0.11), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 280 TYR 0.021 0.002 TYR B 658 PHE 0.037 0.002 PHE B 678 TRP 0.029 0.002 TRP A 316 HIS 0.012 0.002 HIS R 249 Details of bonding type rmsd covalent geometry : bond 0.00357 (41046) covalent geometry : angle 0.69772 (55427) hydrogen bonds : bond 0.04712 ( 1376) hydrogen bonds : angle 5.88693 ( 3936) metal coordination : bond 0.01095 ( 23) metal coordination : angle 5.95896 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 4510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 491 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 HIS cc_start: 0.8465 (t-170) cc_final: 0.7888 (m90) REVERT: A 890 MET cc_start: 0.9149 (tpt) cc_final: 0.8846 (tpt) REVERT: A 1196 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8674 (pp) REVERT: A 1227 LYS cc_start: 0.8921 (ptpp) cc_final: 0.8710 (ptmt) REVERT: B 137 ARG cc_start: 0.8369 (tmm-80) cc_final: 0.7936 (tmm-80) REVERT: B 296 TYR cc_start: 0.7974 (m-80) cc_final: 0.7707 (m-80) REVERT: B 428 ASN cc_start: 0.8334 (t0) cc_final: 0.8074 (t0) REVERT: B 771 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8809 (pp) REVERT: B 907 GLU cc_start: 0.8402 (tt0) cc_final: 0.8091 (mt-10) REVERT: C 266 TYR cc_start: 0.8406 (p90) cc_final: 0.8188 (p90) REVERT: D 14 TYR cc_start: 0.8522 (t80) cc_final: 0.8085 (m-10) REVERT: D 18 LYS cc_start: 0.9092 (ttpt) cc_final: 0.8822 (mttp) REVERT: D 157 ILE cc_start: 0.8162 (mm) cc_final: 0.7960 (mm) REVERT: E 121 MET cc_start: 0.8469 (mpp) cc_final: 0.7955 (mpp) REVERT: G 36 ASN cc_start: 0.8113 (t0) cc_final: 0.7797 (t0) REVERT: G 49 TYR cc_start: 0.8999 (t80) cc_final: 0.8660 (t80) REVERT: J 26 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8096 (tm-30) REVERT: M 257 ASP cc_start: 0.9036 (t0) cc_final: 0.8639 (t0) REVERT: N 292 ARG cc_start: 0.8625 (mtm110) cc_final: 0.8107 (mtm-85) REVERT: N 391 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8350 (pp) REVERT: N 422 ILE cc_start: 0.8817 (mm) cc_final: 0.8601 (mm) REVERT: O 37 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8810 (tt) REVERT: O 197 MET cc_start: 0.7776 (ppp) cc_final: 0.7026 (ppp) REVERT: O 516 LEU cc_start: 0.8652 (tp) cc_final: 0.8407 (mt) REVERT: P 148 TYR cc_start: 0.8584 (m-80) cc_final: 0.8251 (m-80) REVERT: P 149 MET cc_start: 0.8141 (tpt) cc_final: 0.7175 (tpt) REVERT: P 184 ARG cc_start: 0.7989 (tpm170) cc_final: 0.7750 (tpm170) REVERT: P 250 ASP cc_start: 0.8773 (t0) cc_final: 0.8366 (t0) REVERT: R 284 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8403 (tp30) REVERT: R 288 GLU cc_start: 0.8723 (mp0) cc_final: 0.7932 (mp0) REVERT: R 293 HIS cc_start: 0.8672 (m90) cc_final: 0.8271 (m90) REVERT: R 302 PHE cc_start: 0.9109 (m-80) cc_final: 0.8507 (m-80) REVERT: R 314 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8209 (tm-30) REVERT: R 326 TYR cc_start: 0.8798 (t80) cc_final: 0.7887 (t80) outliers start: 79 outliers final: 43 residues processed: 546 average time/residue: 0.2563 time to fit residues: 226.9635 Evaluate side-chains 467 residues out of total 4510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 420 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 887 ARG Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 248 ASP Chi-restraints excluded: chain R residue 270 LYS Chi-restraints excluded: chain R residue 325 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 407 optimal weight: 7.9990 chunk 235 optimal weight: 2.9990 chunk 438 optimal weight: 20.0000 chunk 431 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 405 optimal weight: 5.9990 chunk 347 optimal weight: 0.4980 chunk 241 optimal weight: 2.9990 chunk 270 optimal weight: 0.0980 chunk 327 optimal weight: 0.9980 chunk 465 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 941 HIS A1149 ASN ** A1174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 ASN ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN H 139 ASN ** O 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 249 HIS R 327 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.113070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.077456 restraints weight = 86732.928| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.23 r_work: 0.2977 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 41069 Z= 0.142 Angle : 0.651 16.682 55454 Z= 0.330 Chirality : 0.046 0.198 6271 Planarity : 0.005 0.067 7125 Dihedral : 5.751 41.187 5523 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.95 % Favored : 94.01 % Rotamer: Outliers : 2.17 % Allowed : 9.97 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.11), residues: 5012 helix: -1.48 (0.11), residues: 1804 sheet: -2.16 (0.18), residues: 685 loop : -1.91 (0.12), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 152 TYR 0.024 0.001 TYR R 326 PHE 0.031 0.002 PHE B 678 TRP 0.022 0.002 TRP M 140 HIS 0.007 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00324 (41046) covalent geometry : angle 0.63991 (55427) hydrogen bonds : bond 0.03965 ( 1376) hydrogen bonds : angle 5.29250 ( 3936) metal coordination : bond 0.00608 ( 23) metal coordination : angle 5.53387 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 4510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 464 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 HIS cc_start: 0.8537 (t-170) cc_final: 0.7967 (m90) REVERT: A 298 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8726 (mp) REVERT: A 890 MET cc_start: 0.9157 (tpt) cc_final: 0.8896 (tpt) REVERT: A 1196 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8703 (pp) REVERT: A 1227 LYS cc_start: 0.8996 (ptpp) cc_final: 0.8721 (ptmt) REVERT: A 1373 ARG cc_start: 0.7043 (mtt-85) cc_final: 0.6774 (mtt-85) REVERT: B 227 ARG cc_start: 0.6822 (mmm160) cc_final: 0.6556 (mmm160) REVERT: B 428 ASN cc_start: 0.8409 (t0) cc_final: 0.8127 (t0) REVERT: B 477 PHE cc_start: 0.4700 (t80) cc_final: 0.4440 (t80) REVERT: B 771 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8788 (pp) REVERT: B 907 GLU cc_start: 0.8424 (tt0) cc_final: 0.8063 (mt-10) REVERT: D 13 ASP cc_start: 0.8680 (m-30) cc_final: 0.8451 (m-30) REVERT: D 113 PHE cc_start: 0.7707 (m-80) cc_final: 0.7194 (m-80) REVERT: E 1 MET cc_start: 0.8731 (tmm) cc_final: 0.8134 (tmm) REVERT: G 36 ASN cc_start: 0.8336 (t0) cc_final: 0.7958 (t0) REVERT: G 130 TRP cc_start: 0.7905 (t60) cc_final: 0.7688 (t60) REVERT: J 26 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8126 (tm-30) REVERT: M 257 ASP cc_start: 0.8978 (t0) cc_final: 0.8638 (t0) REVERT: N 312 ARG cc_start: 0.8333 (ttp-170) cc_final: 0.8056 (ttp-170) REVERT: N 422 ILE cc_start: 0.8619 (mm) cc_final: 0.8400 (mm) REVERT: O 37 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8775 (tt) REVERT: O 197 MET cc_start: 0.7881 (ppp) cc_final: 0.7016 (ppp) REVERT: P 148 TYR cc_start: 0.8646 (m-80) cc_final: 0.8403 (m-80) REVERT: P 149 MET cc_start: 0.8077 (tpt) cc_final: 0.7127 (tpt) REVERT: P 184 ARG cc_start: 0.8047 (tpm170) cc_final: 0.7786 (tpm170) REVERT: P 250 ASP cc_start: 0.8908 (t0) cc_final: 0.8543 (t0) REVERT: R 284 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8369 (tp30) REVERT: R 288 GLU cc_start: 0.8749 (mp0) cc_final: 0.7921 (mp0) REVERT: R 302 PHE cc_start: 0.9050 (m-80) cc_final: 0.8467 (m-80) REVERT: R 314 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8274 (tm-30) outliers start: 97 outliers final: 55 residues processed: 531 average time/residue: 0.2469 time to fit residues: 213.9833 Evaluate side-chains 480 residues out of total 4510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 421 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1395 HIS Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1109 THR Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 325 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 72 optimal weight: 0.9980 chunk 438 optimal weight: 20.0000 chunk 384 optimal weight: 7.9990 chunk 276 optimal weight: 2.9990 chunk 403 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 317 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 401 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 284 optimal weight: 7.9990 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 465 HIS ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 HIS A1149 ASN ** A1174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 GLN ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN B 299 GLN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 880 HIS B 994 GLN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN K 102 ASN M 158 GLN ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.111791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.075639 restraints weight = 86701.823| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.11 r_work: 0.2948 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 41069 Z= 0.191 Angle : 0.671 17.076 55454 Z= 0.339 Chirality : 0.047 0.191 6271 Planarity : 0.005 0.064 7125 Dihedral : 5.641 43.027 5520 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.21 % Favored : 93.75 % Rotamer: Outliers : 2.53 % Allowed : 10.71 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.11), residues: 5012 helix: -1.05 (0.12), residues: 1806 sheet: -2.00 (0.18), residues: 695 loop : -1.80 (0.12), residues: 2511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 130 TYR 0.022 0.002 TYR G 120 PHE 0.030 0.002 PHE B 678 TRP 0.024 0.002 TRP M 140 HIS 0.011 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00451 (41046) covalent geometry : angle 0.66047 (55427) hydrogen bonds : bond 0.03792 ( 1376) hydrogen bonds : angle 5.12778 ( 3936) metal coordination : bond 0.00754 ( 23) metal coordination : angle 5.41959 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 4510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 433 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 HIS cc_start: 0.8578 (t-170) cc_final: 0.7984 (m90) REVERT: A 890 MET cc_start: 0.9151 (tpt) cc_final: 0.8858 (tpt) REVERT: A 1196 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8719 (pp) REVERT: A 1227 LYS cc_start: 0.9017 (ptpp) cc_final: 0.8723 (ptmt) REVERT: A 1373 ARG cc_start: 0.7087 (mtt-85) cc_final: 0.6768 (mtt-85) REVERT: B 227 ARG cc_start: 0.6648 (mmm160) cc_final: 0.6287 (mmm160) REVERT: B 234 ILE cc_start: 0.8707 (pt) cc_final: 0.8269 (tp) REVERT: B 428 ASN cc_start: 0.8475 (t0) cc_final: 0.8194 (t0) REVERT: B 771 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8830 (pp) REVERT: B 907 GLU cc_start: 0.8460 (tt0) cc_final: 0.8061 (mt-10) REVERT: B 908 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8547 (mp) REVERT: D 13 ASP cc_start: 0.8647 (m-30) cc_final: 0.8373 (m-30) REVERT: D 137 ILE cc_start: 0.9325 (mm) cc_final: 0.9030 (mm) REVERT: E 1 MET cc_start: 0.8698 (tmm) cc_final: 0.8320 (tmm) REVERT: G 9 ASP cc_start: 0.8548 (t0) cc_final: 0.8249 (t0) REVERT: G 36 ASN cc_start: 0.8396 (t0) cc_final: 0.7880 (t0) REVERT: G 120 TYR cc_start: 0.8900 (p90) cc_final: 0.8553 (p90) REVERT: G 137 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.6602 (tptp) REVERT: I 27 ARG cc_start: 0.8484 (mtp85) cc_final: 0.8227 (mtp85) REVERT: J 26 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8100 (tm-30) REVERT: M 257 ASP cc_start: 0.8986 (t0) cc_final: 0.8653 (t0) REVERT: N 299 ASN cc_start: 0.8137 (m110) cc_final: 0.7737 (m-40) REVERT: O 37 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8840 (tt) REVERT: O 197 MET cc_start: 0.7888 (ppp) cc_final: 0.7517 (ppp) REVERT: P 149 MET cc_start: 0.8199 (tpt) cc_final: 0.7319 (tpt) REVERT: P 184 ARG cc_start: 0.8068 (tpm170) cc_final: 0.7800 (tpm170) REVERT: P 250 ASP cc_start: 0.8917 (t0) cc_final: 0.8474 (t0) REVERT: R 235 PHE cc_start: 0.6683 (m-10) cc_final: 0.6339 (m-10) REVERT: R 284 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8317 (tp30) REVERT: R 288 GLU cc_start: 0.8746 (mp0) cc_final: 0.7939 (mp0) REVERT: R 314 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8267 (tm-30) outliers start: 113 outliers final: 77 residues processed: 516 average time/residue: 0.2538 time to fit residues: 216.3543 Evaluate side-chains 492 residues out of total 4510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 410 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 1043 ASP Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1277 ASP Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1395 HIS Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain B residue 1109 THR Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 457 LEU Chi-restraints excluded: chain O residue 528 MET Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 325 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 76 optimal weight: 1.9990 chunk 379 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 217 optimal weight: 0.6980 chunk 149 optimal weight: 10.0000 chunk 345 optimal weight: 0.3980 chunk 492 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 213 optimal weight: 0.8980 chunk 268 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 805 ASN ** A1174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN H 139 ASN K 83 ASN M 158 GLN M 234 HIS ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 456 HIS ** O 572 HIS ** 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 = 0.113271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.077724 restraints weight = 86845.350| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.11 r_work: 0.2996 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 41069 Z= 0.121 Angle : 0.610 15.902 55454 Z= 0.308 Chirality : 0.045 0.190 6271 Planarity : 0.004 0.062 7125 Dihedral : 5.334 39.437 5519 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.33 % Favored : 94.63 % Rotamer: Outliers : 2.62 % Allowed : 11.34 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.11), residues: 5012 helix: -0.65 (0.12), residues: 1794 sheet: -1.90 (0.18), residues: 699 loop : -1.64 (0.12), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 152 TYR 0.021 0.001 TYR R 326 PHE 0.027 0.001 PHE B 678 TRP 0.022 0.001 TRP M 140 HIS 0.008 0.001 HIS D 133 Details of bonding type rmsd covalent geometry : bond 0.00274 (41046) covalent geometry : angle 0.60054 (55427) hydrogen bonds : bond 0.03321 ( 1376) hydrogen bonds : angle 4.85425 ( 3936) metal coordination : bond 0.00799 ( 23) metal coordination : angle 4.78209 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 4510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 449 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 HIS cc_start: 0.8587 (t-170) cc_final: 0.8013 (m90) REVERT: A 285 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8014 (mt) REVERT: A 890 MET cc_start: 0.9135 (tpt) cc_final: 0.8922 (tpt) REVERT: A 1196 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8722 (pp) REVERT: A 1448 PHE cc_start: 0.7429 (t80) cc_final: 0.7146 (t80) REVERT: B 227 ARG cc_start: 0.6612 (mmm160) cc_final: 0.6332 (mmm160) REVERT: B 234 ILE cc_start: 0.8614 (pt) cc_final: 0.8259 (tp) REVERT: B 370 ASP cc_start: 0.8292 (p0) cc_final: 0.7936 (p0) REVERT: B 477 PHE cc_start: 0.4698 (t80) cc_final: 0.4488 (t80) REVERT: B 771 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8821 (pp) REVERT: B 824 LEU cc_start: 0.8505 (tp) cc_final: 0.8149 (mp) REVERT: B 907 GLU cc_start: 0.8383 (tt0) cc_final: 0.8113 (mt-10) REVERT: D 137 ILE cc_start: 0.9320 (mm) cc_final: 0.9000 (mm) REVERT: E 1 MET cc_start: 0.8606 (tmm) cc_final: 0.8182 (tmm) REVERT: E 144 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8053 (pp) REVERT: G 9 ASP cc_start: 0.8537 (t0) cc_final: 0.8276 (t0) REVERT: G 36 ASN cc_start: 0.8330 (t0) cc_final: 0.7937 (t0) REVERT: H 87 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7335 (tpm170) REVERT: I 27 ARG cc_start: 0.8419 (mtp85) cc_final: 0.8139 (mtp85) REVERT: J 26 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8010 (tm-30) REVERT: M 175 ARG cc_start: 0.7924 (mtp85) cc_final: 0.7714 (mtp85) REVERT: M 185 TYR cc_start: 0.7913 (p90) cc_final: 0.7390 (p90) REVERT: M 257 ASP cc_start: 0.8985 (t0) cc_final: 0.8641 (t0) REVERT: N 299 ASN cc_start: 0.8023 (m110) cc_final: 0.7678 (m-40) REVERT: N 391 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.7983 (pp) REVERT: N 395 ILE cc_start: 0.8636 (mp) cc_final: 0.8392 (mt) REVERT: O 37 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8735 (tt) REVERT: O 197 MET cc_start: 0.7900 (ppp) cc_final: 0.7554 (ppp) REVERT: P 149 MET cc_start: 0.8115 (tpt) cc_final: 0.7218 (tpt) REVERT: P 184 ARG cc_start: 0.8059 (tpm170) cc_final: 0.7770 (tpm170) REVERT: P 250 ASP cc_start: 0.8898 (t0) cc_final: 0.8428 (t0) REVERT: R 235 PHE cc_start: 0.6445 (m-10) cc_final: 0.6046 (m-10) REVERT: R 284 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8351 (tp30) REVERT: R 288 GLU cc_start: 0.8738 (mp0) cc_final: 0.7909 (mp0) REVERT: R 314 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8327 (tm-30) outliers start: 117 outliers final: 74 residues processed: 531 average time/residue: 0.2491 time to fit residues: 219.6919 Evaluate side-chains 496 residues out of total 4510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 415 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 1043 ASP Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1298 TYR Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1395 HIS Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain B residue 1109 THR Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 325 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 454 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 233 optimal weight: 0.0980 chunk 479 optimal weight: 6.9990 chunk 458 optimal weight: 3.9990 chunk 430 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 484 optimal weight: 3.9990 chunk 63 optimal weight: 0.0030 overall best weight: 1.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN M 167 GLN N 289 HIS ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 327 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.112188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.075793 restraints weight = 86996.747| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.27 r_work: 0.2965 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 41069 Z= 0.166 Angle : 0.636 15.925 55454 Z= 0.319 Chirality : 0.046 0.259 6271 Planarity : 0.004 0.062 7125 Dihedral : 5.302 39.527 5519 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.97 % Favored : 93.99 % Rotamer: Outliers : 2.64 % Allowed : 11.86 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.12), residues: 5012 helix: -0.48 (0.12), residues: 1801 sheet: -1.82 (0.19), residues: 693 loop : -1.57 (0.12), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 280 TYR 0.015 0.001 TYR G 139 PHE 0.028 0.001 PHE B 678 TRP 0.029 0.001 TRP M 140 HIS 0.009 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00391 (41046) covalent geometry : angle 0.62647 (55427) hydrogen bonds : bond 0.03436 ( 1376) hydrogen bonds : angle 4.79445 ( 3936) metal coordination : bond 0.00812 ( 23) metal coordination : angle 5.09419 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 4510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 425 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 HIS cc_start: 0.8588 (t-170) cc_final: 0.8037 (m90) REVERT: A 285 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7933 (mt) REVERT: A 890 MET cc_start: 0.9126 (tpt) cc_final: 0.8851 (tpt) REVERT: A 1196 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8731 (pp) REVERT: B 227 ARG cc_start: 0.6507 (mmm160) cc_final: 0.6247 (mmm160) REVERT: B 234 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8339 (tp) REVERT: B 269 MET cc_start: 0.8424 (mmm) cc_final: 0.8161 (mmm) REVERT: B 370 ASP cc_start: 0.8295 (p0) cc_final: 0.7940 (p0) REVERT: B 771 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8898 (pp) REVERT: B 907 GLU cc_start: 0.8442 (tt0) cc_final: 0.8107 (mt-10) REVERT: B 908 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8564 (mp) REVERT: D 137 ILE cc_start: 0.9326 (mm) cc_final: 0.9010 (mm) REVERT: E 1 MET cc_start: 0.8635 (tmm) cc_final: 0.8235 (tmm) REVERT: E 121 MET cc_start: 0.8472 (mpp) cc_final: 0.8230 (mpp) REVERT: E 144 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8045 (pp) REVERT: G 36 ASN cc_start: 0.8367 (t0) cc_final: 0.7950 (t0) REVERT: G 120 TYR cc_start: 0.8894 (p90) cc_final: 0.8456 (p90) REVERT: H 35 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8332 (mm110) REVERT: H 87 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7302 (tpm170) REVERT: I 27 ARG cc_start: 0.8493 (mtp85) cc_final: 0.8151 (mtp85) REVERT: J 26 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8110 (tm-30) REVERT: M 185 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7360 (p90) REVERT: M 257 ASP cc_start: 0.9003 (t0) cc_final: 0.8696 (t0) REVERT: N 292 ARG cc_start: 0.8637 (mtm110) cc_final: 0.8400 (mtm110) REVERT: N 299 ASN cc_start: 0.7992 (m110) cc_final: 0.7660 (m-40) REVERT: N 391 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7908 (pp) REVERT: N 395 ILE cc_start: 0.8649 (mp) cc_final: 0.8406 (mt) REVERT: O 37 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8830 (tt) REVERT: O 107 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8541 (tp) REVERT: O 197 MET cc_start: 0.7926 (ppp) cc_final: 0.7508 (ppp) REVERT: O 577 MET cc_start: 0.8981 (tpp) cc_final: 0.8578 (ttt) REVERT: P 149 MET cc_start: 0.8163 (tpt) cc_final: 0.7299 (tpt) REVERT: P 184 ARG cc_start: 0.8019 (tpm170) cc_final: 0.7726 (tpm170) REVERT: P 250 ASP cc_start: 0.8890 (t0) cc_final: 0.8386 (t0) REVERT: R 235 PHE cc_start: 0.6403 (m-10) cc_final: 0.6006 (m-10) REVERT: R 284 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8347 (tp30) REVERT: R 288 GLU cc_start: 0.8825 (mp0) cc_final: 0.7945 (mp0) REVERT: R 302 PHE cc_start: 0.8936 (m-80) cc_final: 0.8549 (m-80) REVERT: R 314 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8294 (tm-30) outliers start: 118 outliers final: 88 residues processed: 509 average time/residue: 0.2381 time to fit residues: 201.5729 Evaluate side-chains 512 residues out of total 4510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 413 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 1043 ASP Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1277 ASP Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1395 HIS Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain B residue 1109 THR Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain O residue 457 LEU Chi-restraints excluded: chain O residue 528 MET Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 270 LYS Chi-restraints excluded: chain R residue 325 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 235 optimal weight: 0.4980 chunk 282 optimal weight: 8.9990 chunk 207 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 478 optimal weight: 8.9990 chunk 413 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 419 optimal weight: 0.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 HIS A1149 ASN ** A1174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 HIS ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.112193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.075613 restraints weight = 86811.792| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.24 r_work: 0.2970 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 41069 Z= 0.165 Angle : 0.629 16.160 55454 Z= 0.316 Chirality : 0.046 0.250 6271 Planarity : 0.004 0.062 7125 Dihedral : 5.258 39.542 5519 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.69 % Favored : 94.27 % Rotamer: Outliers : 2.80 % Allowed : 12.30 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.12), residues: 5012 helix: -0.33 (0.12), residues: 1799 sheet: -1.68 (0.19), residues: 699 loop : -1.50 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 6 TYR 0.015 0.001 TYR R 335 PHE 0.029 0.002 PHE M 106 TRP 0.042 0.001 TRP M 140 HIS 0.008 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00391 (41046) covalent geometry : angle 0.61943 (55427) hydrogen bonds : bond 0.03382 ( 1376) hydrogen bonds : angle 4.73156 ( 3936) metal coordination : bond 0.00753 ( 23) metal coordination : angle 4.92879 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 4510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 427 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 HIS cc_start: 0.8602 (t-170) cc_final: 0.8057 (m90) REVERT: A 285 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7927 (mt) REVERT: A 890 MET cc_start: 0.9120 (tpt) cc_final: 0.8839 (tpt) REVERT: A 1196 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8743 (pp) REVERT: A 1304 MET cc_start: 0.9196 (mtp) cc_final: 0.8940 (mtp) REVERT: B 227 ARG cc_start: 0.6521 (mmm160) cc_final: 0.6296 (mmm160) REVERT: B 234 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8452 (tp) REVERT: B 269 MET cc_start: 0.8432 (mmm) cc_final: 0.8183 (mmm) REVERT: B 370 ASP cc_start: 0.8257 (p0) cc_final: 0.7924 (p0) REVERT: B 771 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8881 (pp) REVERT: B 907 GLU cc_start: 0.8420 (tt0) cc_final: 0.7990 (mt-10) REVERT: B 908 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8578 (mp) REVERT: B 928 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7122 (tm130) REVERT: D 137 ILE cc_start: 0.9301 (mm) cc_final: 0.9005 (mm) REVERT: E 1 MET cc_start: 0.8639 (tmm) cc_final: 0.8264 (tmm) REVERT: E 46 TYR cc_start: 0.7934 (m-80) cc_final: 0.7497 (m-80) REVERT: E 144 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8017 (pp) REVERT: G 36 ASN cc_start: 0.8390 (t0) cc_final: 0.7865 (t0) REVERT: H 27 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: H 35 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8324 (mm110) REVERT: H 87 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7266 (tpm170) REVERT: I 27 ARG cc_start: 0.8502 (mtp85) cc_final: 0.8245 (mtp85) REVERT: J 26 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8110 (tm-30) REVERT: M 185 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.7393 (p90) REVERT: M 257 ASP cc_start: 0.9009 (t0) cc_final: 0.8712 (t0) REVERT: N 299 ASN cc_start: 0.7928 (m110) cc_final: 0.7640 (m-40) REVERT: N 391 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7899 (pp) REVERT: N 395 ILE cc_start: 0.8638 (mp) cc_final: 0.8401 (mt) REVERT: O 37 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8834 (tt) REVERT: O 107 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8548 (tp) REVERT: O 197 MET cc_start: 0.7943 (ppp) cc_final: 0.7521 (ppp) REVERT: O 577 MET cc_start: 0.8952 (tpp) cc_final: 0.8515 (ttt) REVERT: P 149 MET cc_start: 0.8198 (tpt) cc_final: 0.7401 (tpt) REVERT: P 184 ARG cc_start: 0.8041 (tpm170) cc_final: 0.7738 (tpm170) REVERT: P 232 ASN cc_start: 0.7244 (p0) cc_final: 0.6961 (p0) REVERT: P 250 ASP cc_start: 0.8876 (t0) cc_final: 0.8319 (t0) REVERT: R 10 GLU cc_start: 0.8649 (tp30) cc_final: 0.8322 (tp30) REVERT: R 14 GLN cc_start: 0.8032 (mt0) cc_final: 0.7542 (mp10) REVERT: R 235 PHE cc_start: 0.6448 (m-10) cc_final: 0.5677 (m-10) REVERT: R 284 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8342 (tp30) REVERT: R 288 GLU cc_start: 0.8814 (mp0) cc_final: 0.7929 (mp0) REVERT: R 302 PHE cc_start: 0.8931 (m-80) cc_final: 0.8577 (m-80) REVERT: R 314 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8336 (tm-30) outliers start: 125 outliers final: 91 residues processed: 519 average time/residue: 0.2398 time to fit residues: 206.2267 Evaluate side-chains 518 residues out of total 4510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 414 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1277 ASP Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1343 MET Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 928 GLN Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1082 ARG Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain B residue 1109 THR Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain O residue 457 LEU Chi-restraints excluded: chain O residue 528 MET Chi-restraints excluded: chain P residue 259 ASP Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 270 LYS Chi-restraints excluded: chain R residue 325 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 240 optimal weight: 1.9990 chunk 275 optimal weight: 0.7980 chunk 319 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 490 optimal weight: 0.9990 chunk 338 optimal weight: 7.9990 chunk 324 optimal weight: 0.0470 chunk 497 optimal weight: 4.9990 chunk 290 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 289 optimal weight: 10.0000 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1149 ASN ** A1174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 HIS ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN D 111 ASN H 139 ASN N 289 HIS ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 572 HIS ** 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 = 0.3844 r_free = 0.3844 target = 0.112919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.076905 restraints weight = 86687.214| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.19 r_work: 0.2993 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 41069 Z= 0.127 Angle : 0.609 15.434 55454 Z= 0.306 Chirality : 0.045 0.215 6271 Planarity : 0.004 0.061 7125 Dihedral : 5.098 38.931 5519 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.61 % Favored : 94.35 % Rotamer: Outliers : 2.49 % Allowed : 13.13 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.12), residues: 5012 helix: -0.16 (0.13), residues: 1803 sheet: -1.66 (0.20), residues: 668 loop : -1.44 (0.12), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 130 TYR 0.012 0.001 TYR G 49 PHE 0.027 0.001 PHE B 678 TRP 0.053 0.001 TRP M 140 HIS 0.006 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00291 (41046) covalent geometry : angle 0.60056 (55427) hydrogen bonds : bond 0.03147 ( 1376) hydrogen bonds : angle 4.61205 ( 3936) metal coordination : bond 0.00606 ( 23) metal coordination : angle 4.56305 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 4510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 437 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8322 (mmp) cc_final: 0.7916 (mmt) REVERT: A 156 HIS cc_start: 0.8630 (t-170) cc_final: 0.8069 (m90) REVERT: A 285 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7887 (mt) REVERT: A 890 MET cc_start: 0.9143 (tpt) cc_final: 0.8917 (tpt) REVERT: B 234 ILE cc_start: 0.8749 (pt) cc_final: 0.8405 (tp) REVERT: B 269 MET cc_start: 0.8410 (mmm) cc_final: 0.8162 (mmm) REVERT: B 370 ASP cc_start: 0.8273 (p0) cc_final: 0.7922 (p0) REVERT: B 824 LEU cc_start: 0.8473 (tp) cc_final: 0.8092 (mp) REVERT: B 907 GLU cc_start: 0.8401 (tt0) cc_final: 0.8062 (mt-10) REVERT: B 908 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8528 (mp) REVERT: B 928 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7082 (tm130) REVERT: D 137 ILE cc_start: 0.9290 (mm) cc_final: 0.8962 (mm) REVERT: D 153 MET cc_start: 0.8694 (mmp) cc_final: 0.8473 (mmp) REVERT: E 1 MET cc_start: 0.8461 (tmm) cc_final: 0.8167 (tmm) REVERT: E 144 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.7973 (pp) REVERT: G 36 ASN cc_start: 0.8355 (t0) cc_final: 0.7832 (t0) REVERT: H 27 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: H 35 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8269 (mm110) REVERT: H 87 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7169 (tpm170) REVERT: I 27 ARG cc_start: 0.8443 (mtp85) cc_final: 0.8139 (mtp85) REVERT: J 26 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8034 (tm-30) REVERT: M 185 TYR cc_start: 0.7919 (OUTLIER) cc_final: 0.7456 (p90) REVERT: M 257 ASP cc_start: 0.9013 (t0) cc_final: 0.8701 (t0) REVERT: N 299 ASN cc_start: 0.7855 (m110) cc_final: 0.7620 (m110) REVERT: N 391 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7847 (pp) REVERT: N 395 ILE cc_start: 0.8622 (mp) cc_final: 0.8394 (mt) REVERT: O 37 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8796 (tt) REVERT: O 197 MET cc_start: 0.7960 (ppp) cc_final: 0.7566 (ppp) REVERT: O 577 MET cc_start: 0.8868 (tpp) cc_final: 0.8450 (ttt) REVERT: P 149 MET cc_start: 0.8214 (tpt) cc_final: 0.7415 (tpt) REVERT: P 184 ARG cc_start: 0.8016 (tpm170) cc_final: 0.7703 (tpm170) REVERT: P 250 ASP cc_start: 0.8866 (t0) cc_final: 0.8327 (t0) REVERT: R 235 PHE cc_start: 0.6431 (m-10) cc_final: 0.5674 (m-10) REVERT: R 258 ASP cc_start: 0.7214 (m-30) cc_final: 0.6831 (t0) REVERT: R 284 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8333 (tp30) REVERT: R 288 GLU cc_start: 0.8814 (mp0) cc_final: 0.7915 (mp0) REVERT: R 302 PHE cc_start: 0.8932 (m-80) cc_final: 0.8599 (m-80) REVERT: R 314 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8318 (tm-30) outliers start: 111 outliers final: 86 residues processed: 514 average time/residue: 0.2518 time to fit residues: 214.6678 Evaluate side-chains 503 residues out of total 4510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 408 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1277 ASP Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1343 MET Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 928 GLN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain B residue 1109 THR Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain O residue 528 MET Chi-restraints excluded: chain O residue 585 MET Chi-restraints excluded: chain P residue 259 ASP Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 270 LYS Chi-restraints excluded: chain R residue 325 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 177 optimal weight: 1.9990 chunk 480 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 174 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 263 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 chunk 350 optimal weight: 0.0570 chunk 152 optimal weight: 0.9980 chunk 318 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS A1149 ASN ** A1174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN H 139 ASN ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.113336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.076956 restraints weight = 86642.054| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.15 r_work: 0.2985 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 41069 Z= 0.116 Angle : 0.608 14.440 55454 Z= 0.305 Chirality : 0.044 0.195 6271 Planarity : 0.004 0.062 7125 Dihedral : 4.994 39.322 5519 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.53 % Favored : 94.43 % Rotamer: Outliers : 2.29 % Allowed : 13.33 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.12), residues: 5012 helix: -0.02 (0.13), residues: 1801 sheet: -1.60 (0.20), residues: 679 loop : -1.39 (0.12), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 292 TYR 0.010 0.001 TYR Q 58 PHE 0.026 0.001 PHE D 113 TRP 0.064 0.001 TRP M 140 HIS 0.009 0.001 HIS D 133 Details of bonding type rmsd covalent geometry : bond 0.00264 (41046) covalent geometry : angle 0.60074 (55427) hydrogen bonds : bond 0.03037 ( 1376) hydrogen bonds : angle 4.53072 ( 3936) metal coordination : bond 0.00538 ( 23) metal coordination : angle 4.33008 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 4510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 433 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 HIS cc_start: 0.8638 (t-170) cc_final: 0.8098 (m90) REVERT: A 285 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7873 (mt) REVERT: B 234 ILE cc_start: 0.8751 (pt) cc_final: 0.8459 (tp) REVERT: B 269 MET cc_start: 0.8365 (mmm) cc_final: 0.8123 (mmm) REVERT: B 370 ASP cc_start: 0.8308 (p0) cc_final: 0.7951 (p0) REVERT: B 824 LEU cc_start: 0.8529 (tp) cc_final: 0.8193 (mp) REVERT: B 907 GLU cc_start: 0.8442 (tt0) cc_final: 0.8091 (mt-10) REVERT: B 908 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8488 (mp) REVERT: B 928 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7059 (tm130) REVERT: D 107 MET cc_start: 0.8426 (ptm) cc_final: 0.7422 (ttt) REVERT: D 137 ILE cc_start: 0.9291 (mm) cc_final: 0.9016 (mm) REVERT: E 144 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.7999 (pp) REVERT: G 36 ASN cc_start: 0.8344 (t0) cc_final: 0.7938 (t0) REVERT: H 14 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7787 (tm-30) REVERT: H 35 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8279 (mm110) REVERT: I 27 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8171 (mtp85) REVERT: J 26 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8079 (tm-30) REVERT: M 185 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7565 (p90) REVERT: M 257 ASP cc_start: 0.9017 (t0) cc_final: 0.8678 (t0) REVERT: N 391 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.7896 (pp) REVERT: N 395 ILE cc_start: 0.8652 (mp) cc_final: 0.8421 (mt) REVERT: O 37 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8731 (tt) REVERT: O 107 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8564 (tp) REVERT: O 197 MET cc_start: 0.7973 (ppp) cc_final: 0.7134 (ppp) REVERT: O 577 MET cc_start: 0.8882 (tpp) cc_final: 0.8600 (ttt) REVERT: P 149 MET cc_start: 0.8163 (tpt) cc_final: 0.7373 (tpt) REVERT: P 184 ARG cc_start: 0.8004 (tpm170) cc_final: 0.7450 (tpm170) REVERT: P 232 ASN cc_start: 0.7265 (p0) cc_final: 0.6976 (p0) REVERT: P 250 ASP cc_start: 0.8840 (t0) cc_final: 0.8293 (t0) REVERT: R 235 PHE cc_start: 0.6518 (m-10) cc_final: 0.5849 (m-10) REVERT: R 258 ASP cc_start: 0.7133 (m-30) cc_final: 0.6791 (t0) REVERT: R 284 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8359 (tp30) REVERT: R 288 GLU cc_start: 0.8779 (mp0) cc_final: 0.7870 (mp0) REVERT: R 302 PHE cc_start: 0.8908 (m-80) cc_final: 0.8589 (m-80) REVERT: R 314 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8332 (tm-30) outliers start: 102 outliers final: 80 residues processed: 503 average time/residue: 0.2548 time to fit residues: 211.8124 Evaluate side-chains 498 residues out of total 4510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 410 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1343 MET Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 928 GLN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain B residue 1109 THR Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain O residue 528 MET Chi-restraints excluded: chain O residue 585 MET Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 259 ASP Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 270 LYS Chi-restraints excluded: chain R residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 185 optimal weight: 3.9990 chunk 171 optimal weight: 0.0020 chunk 165 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 464 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 449 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 249 optimal weight: 0.8980 overall best weight: 1.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.111982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.075914 restraints weight = 86414.220| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.33 r_work: 0.2971 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 41069 Z= 0.175 Angle : 0.649 15.413 55454 Z= 0.324 Chirality : 0.046 0.218 6271 Planarity : 0.004 0.062 7125 Dihedral : 5.091 39.785 5519 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.87 % Favored : 94.09 % Rotamer: Outliers : 2.24 % Allowed : 13.42 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.12), residues: 5012 helix: -0.05 (0.13), residues: 1810 sheet: -1.58 (0.19), residues: 694 loop : -1.39 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 292 TYR 0.015 0.001 TYR G 67 PHE 0.029 0.002 PHE B 678 TRP 0.086 0.002 TRP M 140 HIS 0.007 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00417 (41046) covalent geometry : angle 0.63999 (55427) hydrogen bonds : bond 0.03322 ( 1376) hydrogen bonds : angle 4.59405 ( 3936) metal coordination : bond 0.00804 ( 23) metal coordination : angle 4.85444 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 4510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 409 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8367 (mmp) cc_final: 0.8007 (mmt) REVERT: A 156 HIS cc_start: 0.8618 (t-170) cc_final: 0.8107 (m90) REVERT: A 285 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7812 (mt) REVERT: B 234 ILE cc_start: 0.8759 (pt) cc_final: 0.8441 (tp) REVERT: B 269 MET cc_start: 0.8383 (mmm) cc_final: 0.8140 (mmm) REVERT: B 370 ASP cc_start: 0.8262 (p0) cc_final: 0.7914 (p0) REVERT: B 907 GLU cc_start: 0.8428 (tt0) cc_final: 0.8078 (mt-10) REVERT: B 908 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8604 (mp) REVERT: B 928 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7076 (tm130) REVERT: B 977 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8747 (m) REVERT: D 137 ILE cc_start: 0.9273 (mm) cc_final: 0.8976 (mm) REVERT: E 144 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.7988 (pp) REVERT: G 36 ASN cc_start: 0.8414 (t0) cc_final: 0.7847 (t0) REVERT: H 14 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7881 (tm-30) REVERT: H 35 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8342 (mm110) REVERT: J 26 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8031 (tm-30) REVERT: M 257 ASP cc_start: 0.9005 (t0) cc_final: 0.8687 (t0) REVERT: N 391 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7877 (pp) REVERT: N 395 ILE cc_start: 0.8677 (mp) cc_final: 0.8440 (mt) REVERT: O 37 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8900 (tt) REVERT: O 107 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8518 (tp) REVERT: O 197 MET cc_start: 0.7910 (ppp) cc_final: 0.7448 (ppp) REVERT: O 577 MET cc_start: 0.8923 (tpp) cc_final: 0.8413 (ttt) REVERT: P 149 MET cc_start: 0.8164 (tpt) cc_final: 0.7384 (tpt) REVERT: P 184 ARG cc_start: 0.7996 (tpm170) cc_final: 0.7687 (tpm170) REVERT: P 250 ASP cc_start: 0.8830 (t0) cc_final: 0.8278 (t0) REVERT: R 235 PHE cc_start: 0.6515 (m-10) cc_final: 0.5863 (m-10) REVERT: R 258 ASP cc_start: 0.7147 (m-30) cc_final: 0.6807 (t0) REVERT: R 284 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8350 (tp30) REVERT: R 288 GLU cc_start: 0.8826 (mp0) cc_final: 0.7850 (mp0) REVERT: R 302 PHE cc_start: 0.8935 (m-80) cc_final: 0.8610 (m-80) REVERT: R 314 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8308 (tm-30) outliers start: 100 outliers final: 87 residues processed: 485 average time/residue: 0.2476 time to fit residues: 200.2418 Evaluate side-chains 498 residues out of total 4510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 403 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1277 ASP Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1343 MET Chi-restraints excluded: chain A residue 1395 HIS Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 928 GLN Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain B residue 1109 THR Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 528 MET Chi-restraints excluded: chain O residue 585 MET Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 172 ILE Chi-restraints excluded: chain P residue 259 ASP Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 270 LYS Chi-restraints excluded: chain R residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 199 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 283 optimal weight: 5.9990 chunk 361 optimal weight: 0.7980 chunk 229 optimal weight: 2.9990 chunk 258 optimal weight: 0.5980 chunk 226 optimal weight: 0.9990 chunk 259 optimal weight: 4.9990 chunk 392 optimal weight: 10.0000 chunk 243 optimal weight: 0.8980 chunk 391 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 HIS A1149 ASN ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 21 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.112900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.077569 restraints weight = 86768.199| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.21 r_work: 0.2990 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 41069 Z= 0.122 Angle : 0.616 15.000 55454 Z= 0.308 Chirality : 0.044 0.187 6271 Planarity : 0.004 0.062 7125 Dihedral : 4.949 39.248 5519 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.39 % Favored : 94.55 % Rotamer: Outliers : 2.06 % Allowed : 13.72 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.12), residues: 5012 helix: 0.09 (0.13), residues: 1799 sheet: -1.48 (0.20), residues: 682 loop : -1.34 (0.12), residues: 2531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 292 TYR 0.012 0.001 TYR O 132 PHE 0.026 0.001 PHE B 678 TRP 0.083 0.001 TRP M 140 HIS 0.005 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00280 (41046) covalent geometry : angle 0.60902 (55427) hydrogen bonds : bond 0.03033 ( 1376) hydrogen bonds : angle 4.48586 ( 3936) metal coordination : bond 0.00552 ( 23) metal coordination : angle 4.33496 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14145.36 seconds wall clock time: 241 minutes 48.66 seconds (14508.66 seconds total)