Starting phenix.real_space_refine on Tue Dec 12 22:30:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhe_23337/12_2023/7lhe_23337_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhe_23337/12_2023/7lhe_23337.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhe_23337/12_2023/7lhe_23337_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhe_23337/12_2023/7lhe_23337_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhe_23337/12_2023/7lhe_23337_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhe_23337/12_2023/7lhe_23337.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhe_23337/12_2023/7lhe_23337.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhe_23337/12_2023/7lhe_23337_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhe_23337/12_2023/7lhe_23337_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 28 5.49 5 S 440 5.16 5 C 47047 2.51 5 N 12712 2.21 5 O 13460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 749": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2222": "OE1" <-> "OE2" Residue "A ASP 2242": "OD1" <-> "OD2" Residue "A TYR 2656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2673": "OD1" <-> "OD2" Residue "A PHE 2675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 749": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2222": "OE1" <-> "OE2" Residue "D ASP 2242": "OD1" <-> "OD2" Residue "D TYR 2656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2673": "OD1" <-> "OD2" Residue "D PHE 2675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 749": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2222": "OE1" <-> "OE2" Residue "C ASP 2242": "OD1" <-> "OD2" Residue "C TYR 2656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2673": "OD1" <-> "OD2" Residue "C PHE 2675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 749": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2222": "OE1" <-> "OE2" Residue "B ASP 2242": "OD1" <-> "OD2" Residue "B TYR 2656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2673": "OD1" <-> "OD2" Residue "B PHE 2675": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 73691 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 18148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2298, 18148 Classifications: {'peptide': 2298} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 37} Link IDs: {'CIS': 1, 'PTRANS': 67, 'TRANS': 2229} Chain breaks: 13 Unresolved chain link angles: 82 Unresolved non-hydrogen bonds: 461 Unresolved non-hydrogen angles: 575 Unresolved non-hydrogen dihedrals: 324 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 190 Chain: "D" Number of atoms: 18148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2298, 18148 Classifications: {'peptide': 2298} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 37} Link IDs: {'CIS': 1, 'PTRANS': 67, 'TRANS': 2229} Chain breaks: 13 Unresolved chain link angles: 82 Unresolved non-hydrogen bonds: 461 Unresolved non-hydrogen angles: 575 Unresolved non-hydrogen dihedrals: 324 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 190 Chain: "C" Number of atoms: 18148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2298, 18148 Classifications: {'peptide': 2298} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 37} Link IDs: {'CIS': 1, 'PTRANS': 67, 'TRANS': 2229} Chain breaks: 13 Unresolved chain link angles: 82 Unresolved non-hydrogen bonds: 461 Unresolved non-hydrogen angles: 575 Unresolved non-hydrogen dihedrals: 324 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 190 Chain: "B" Number of atoms: 18148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2298, 18148 Classifications: {'peptide': 2298} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 37} Link IDs: {'CIS': 1, 'PTRANS': 67, 'TRANS': 2229} Chain breaks: 13 Unresolved chain link angles: 82 Unresolved non-hydrogen bonds: 461 Unresolved non-hydrogen angles: 575 Unresolved non-hydrogen dihedrals: 324 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 190 Chain: "A" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 275 Unusual residues: {' ZN': 1, 'PLX': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 90 Chain: "D" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 235 Unusual residues: {' ZN': 1, 'PLX': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 78 Chain: "C" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 275 Unusual residues: {' ZN': 1, 'PLX': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 90 Chain: "B" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 314 Unusual residues: {' ZN': 1, 'PLX': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 103 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17089 SG CYS A2611 138.320 113.398 109.523 1.00105.09 S ATOM 17114 SG CYS A2614 137.709 114.962 105.865 1.00107.89 S ATOM 35237 SG CYS D2611 126.283 138.312 109.523 1.00105.09 S ATOM 35262 SG CYS D2614 124.719 137.701 105.864 1.00107.89 S ATOM 53385 SG CYS C2611 101.367 126.273 109.525 1.00105.09 S ATOM 53410 SG CYS C2614 101.978 124.709 105.867 1.00107.89 S ATOM 71533 SG CYS B2611 113.408 101.358 109.525 1.00105.09 S ATOM 71558 SG CYS B2614 114.971 101.969 105.867 1.00107.89 S Time building chain proxies: 27.98, per 1000 atoms: 0.38 Number of scatterers: 73691 At special positions: 0 Unit cell: (240.75, 240.75, 196.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 440 16.00 P 28 15.00 O 13460 8.00 N 12712 7.00 C 47047 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 - 3.50 Amino acid : False - 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.84 Conformation dependent library (CDL) restraints added in 9.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2805 " pdb="ZN ZN A2805 " - pdb=" NE2 HIS A2631 " pdb="ZN ZN A2805 " - pdb=" ND1 HIS A2636 " pdb="ZN ZN A2805 " - pdb=" SG CYS A2614 " pdb="ZN ZN A2805 " - pdb=" SG CYS A2611 " pdb=" ZN B2809 " pdb="ZN ZN B2809 " - pdb=" ND1 HIS B2636 " pdb="ZN ZN B2809 " - pdb=" NE2 HIS B2631 " pdb="ZN ZN B2809 " - pdb=" SG CYS B2614 " pdb="ZN ZN B2809 " - pdb=" SG CYS B2611 " pdb=" ZN C2806 " pdb="ZN ZN C2806 " - pdb=" NE2 HIS C2631 " pdb="ZN ZN C2806 " - pdb=" ND1 HIS C2636 " pdb="ZN ZN C2806 " - pdb=" SG CYS C2614 " pdb="ZN ZN C2806 " - pdb=" SG CYS C2611 " pdb=" ZN D2805 " pdb="ZN ZN D2805 " - pdb=" NE2 HIS D2631 " pdb="ZN ZN D2805 " - pdb=" ND1 HIS D2636 " pdb="ZN ZN D2805 " - pdb=" SG CYS D2614 " pdb="ZN ZN D2805 " - pdb=" SG CYS D2611 " Number of angles added : 5 18160 Ramachandran restraints generated. 9080 Oldfield, 0 Emsley, 9080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17568 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 352 helices and 36 sheets defined 48.3% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 21.16 Creating SS restraints... Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 88 through 107 removed outlier: 3.776A pdb=" N GLU A 106 " --> pdb=" O GLN A 102 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 462 removed outlier: 3.576A pdb=" N ASP A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS A 462 " --> pdb=" O GLY A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 485 removed outlier: 3.780A pdb=" N THR A 474 " --> pdb=" O ARG A 470 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 512 Processing helix chain 'A' and resid 516 through 531 Proline residue: A 526 - end of helix Processing helix chain 'A' and resid 537 through 543 Processing helix chain 'A' and resid 547 through 562 removed outlier: 3.618A pdb=" N ILE A 552 " --> pdb=" O PRO A 548 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 555 " --> pdb=" O HIS A 551 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N CYS A 556 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR A 557 " --> pdb=" O CYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 577 removed outlier: 3.813A pdb=" N GLN A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 598 Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 612 through 620 Processing helix chain 'A' and resid 629 through 636 Processing helix chain 'A' and resid 646 through 656 removed outlier: 3.758A pdb=" N GLU A 650 " --> pdb=" O PRO A 646 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 651 " --> pdb=" O VAL A 647 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A 653 " --> pdb=" O GLN A 649 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LYS A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 661 No H-bonds generated for 'chain 'A' and resid 659 through 661' Processing helix chain 'A' and resid 713 through 719 removed outlier: 3.540A pdb=" N GLN A 717 " --> pdb=" O ARG A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 741 Processing helix chain 'A' and resid 754 through 757 No H-bonds generated for 'chain 'A' and resid 754 through 757' Processing helix chain 'A' and resid 762 through 767 Processing helix chain 'A' and resid 776 through 787 removed outlier: 3.613A pdb=" N CYS A 782 " --> pdb=" O ARG A 778 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS A 787 " --> pdb=" O ARG A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 850 removed outlier: 4.563A pdb=" N GLN A 835 " --> pdb=" O GLU A 831 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N THR A 836 " --> pdb=" O ARG A 832 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE A 839 " --> pdb=" O GLN A 835 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 840 " --> pdb=" O THR A 836 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 841 " --> pdb=" O MET A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 875 removed outlier: 5.084A pdb=" N GLU A 865 " --> pdb=" O LYS A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 894 removed outlier: 3.631A pdb=" N LEU A 885 " --> pdb=" O PHE A 881 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG A 886 " --> pdb=" O SER A 882 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 890 " --> pdb=" O ARG A 886 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ALA A 893 " --> pdb=" O LYS A 889 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 894 " --> pdb=" O ILE A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 1003 removed outlier: 3.776A pdb=" N LEU A 982 " --> pdb=" O LEU A 978 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN A 983 " --> pdb=" O GLN A 979 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 986 " --> pdb=" O LEU A 982 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1040 removed outlier: 3.746A pdb=" N GLU A1031 " --> pdb=" O ALA A1027 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N HIS A1032 " --> pdb=" O LEU A1028 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A1033 " --> pdb=" O ASP A1029 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU A1034 " --> pdb=" O PHE A1030 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU A1035 " --> pdb=" O GLU A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1068 removed outlier: 3.541A pdb=" N VAL A1063 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A1064 " --> pdb=" O PHE A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1086 Processing helix chain 'A' and resid 1089 through 1100 Processing helix chain 'A' and resid 1113 through 1124 removed outlier: 3.817A pdb=" N SER A1124 " --> pdb=" O ASP A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1188 removed outlier: 4.144A pdb=" N LYS A1177 " --> pdb=" O TYR A1173 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU A1178 " --> pdb=" O ARG A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1206 removed outlier: 4.278A pdb=" N LEU A1204 " --> pdb=" O GLN A1200 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU A1205 " --> pdb=" O GLN A1201 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG A1206 " --> pdb=" O GLN A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1218 Processing helix chain 'A' and resid 1231 through 1244 removed outlier: 4.063A pdb=" N ARG A1235 " --> pdb=" O GLN A1231 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU A1236 " --> pdb=" O GLU A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1258 removed outlier: 3.674A pdb=" N LEU A1254 " --> pdb=" O GLN A1250 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS A1257 " --> pdb=" O ALA A1253 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N HIS A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1270 through 1276 Processing helix chain 'A' and resid 1292 through 1294 No H-bonds generated for 'chain 'A' and resid 1292 through 1294' Processing helix chain 'A' and resid 1296 through 1299 No H-bonds generated for 'chain 'A' and resid 1296 through 1299' Processing helix chain 'A' and resid 1306 through 1309 No H-bonds generated for 'chain 'A' and resid 1306 through 1309' Processing helix chain 'A' and resid 1312 through 1315 No H-bonds generated for 'chain 'A' and resid 1312 through 1315' Processing helix chain 'A' and resid 1327 through 1336 removed outlier: 3.626A pdb=" N ALA A1332 " --> pdb=" O ASP A1328 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLU A1333 " --> pdb=" O MET A1329 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU A1334 " --> pdb=" O VAL A1330 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL A1335 " --> pdb=" O MET A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1367 removed outlier: 3.826A pdb=" N ASP A1366 " --> pdb=" O ASP A1363 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A1367 " --> pdb=" O ARG A1364 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1363 through 1367' Processing helix chain 'A' and resid 1374 through 1377 No H-bonds generated for 'chain 'A' and resid 1374 through 1377' Processing helix chain 'A' and resid 1380 through 1383 No H-bonds generated for 'chain 'A' and resid 1380 through 1383' Processing helix chain 'A' and resid 1395 through 1399 Processing helix chain 'A' and resid 1404 through 1413 removed outlier: 4.474A pdb=" N VAL A1409 " --> pdb=" O ASP A1405 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL A1410 " --> pdb=" O ILE A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1417 through 1431 Processing helix chain 'A' and resid 1441 through 1462 removed outlier: 3.884A pdb=" N HIS A1446 " --> pdb=" O TYR A1442 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET A1447 " --> pdb=" O THR A1443 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP A1448 " --> pdb=" O SER A1444 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS A1449 " --> pdb=" O ASN A1445 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A1450 " --> pdb=" O HIS A1446 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A1457 " --> pdb=" O ASN A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1600 through 1629 removed outlier: 3.534A pdb=" N GLN A1605 " --> pdb=" O ILE A1601 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG A1614 " --> pdb=" O ALA A1610 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LEU A1615 " --> pdb=" O LEU A1611 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ARG A1616 " --> pdb=" O GLU A1612 " (cutoff:3.500A) Proline residue: A1617 - end of helix removed outlier: 3.798A pdb=" N GLN A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A1624 " --> pdb=" O GLN A1620 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL A1625 " --> pdb=" O ALA A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1652 through 1660 Processing helix chain 'A' and resid 1670 through 1683 Processing helix chain 'A' and resid 1726 through 1744 removed outlier: 3.679A pdb=" N HIS A1730 " --> pdb=" O GLN A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1792 through 1802 removed outlier: 3.742A pdb=" N GLN A1796 " --> pdb=" O LEU A1792 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N CYS A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1811 removed outlier: 3.578A pdb=" N VAL A1808 " --> pdb=" O ALA A1804 " (cutoff:3.500A) Processing helix chain 'A' and resid 1818 through 1832 Processing helix chain 'A' and resid 1837 through 1847 removed outlier: 3.505A pdb=" N HIS A1841 " --> pdb=" O THR A1837 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER A1842 " --> pdb=" O THR A1838 " (cutoff:3.500A) Processing helix chain 'A' and resid 1853 through 1868 removed outlier: 3.843A pdb=" N ARG A1863 " --> pdb=" O VAL A1859 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET A1864 " --> pdb=" O PHE A1860 " (cutoff:3.500A) Processing helix chain 'A' and resid 1965 through 1977 removed outlier: 3.505A pdb=" N ILE A1969 " --> pdb=" O ILE A1965 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS A1977 " --> pdb=" O LEU A1973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1982 through 1988 removed outlier: 3.805A pdb=" N LEU A1988 " --> pdb=" O LEU A1984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1999 through 2011 Processing helix chain 'A' and resid 2030 through 2042 removed outlier: 3.690A pdb=" N GLN A2035 " --> pdb=" O ALA A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2053 through 2056 No H-bonds generated for 'chain 'A' and resid 2053 through 2056' Processing helix chain 'A' and resid 2063 through 2066 No H-bonds generated for 'chain 'A' and resid 2063 through 2066' Processing helix chain 'A' and resid 2068 through 2071 No H-bonds generated for 'chain 'A' and resid 2068 through 2071' Processing helix chain 'A' and resid 2082 through 2099 removed outlier: 3.972A pdb=" N LEU A2086 " --> pdb=" O MET A2082 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLU A2087 " --> pdb=" O ASP A2083 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU A2088 " --> pdb=" O LEU A2084 " (cutoff:3.500A) Processing helix chain 'A' and resid 2106 through 2113 Processing helix chain 'A' and resid 2118 through 2133 removed outlier: 3.841A pdb=" N GLU A2133 " --> pdb=" O MET A2130 " (cutoff:3.500A) Processing helix chain 'A' and resid 2151 through 2165 removed outlier: 4.261A pdb=" N ARG A2165 " --> pdb=" O HIS A2161 " (cutoff:3.500A) Processing helix chain 'A' and resid 2170 through 2172 No H-bonds generated for 'chain 'A' and resid 2170 through 2172' Processing helix chain 'A' and resid 2183 through 2191 Processing helix chain 'A' and resid 2221 through 2230 Processing helix chain 'A' and resid 2240 through 2263 removed outlier: 3.612A pdb=" N LEU A2245 " --> pdb=" O ASN A2241 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA A2262 " --> pdb=" O LYS A2258 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN A2263 " --> pdb=" O LYS A2259 " (cutoff:3.500A) Processing helix chain 'A' and resid 2265 through 2271 Processing helix chain 'A' and resid 2273 through 2293 Processing helix chain 'A' and resid 2306 through 2327 Processing helix chain 'A' and resid 2333 through 2347 removed outlier: 3.960A pdb=" N ILE A2337 " --> pdb=" O ILE A2333 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A2346 " --> pdb=" O LEU A2342 " (cutoff:3.500A) Processing helix chain 'A' and resid 2350 through 2374 removed outlier: 3.783A pdb=" N MET A2370 " --> pdb=" O ILE A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2383 through 2388 Processing helix chain 'A' and resid 2390 through 2407 Processing helix chain 'A' and resid 2413 through 2423 removed outlier: 4.365A pdb=" N ARG A2423 " --> pdb=" O ASP A2419 " (cutoff:3.500A) Processing helix chain 'A' and resid 2425 through 2435 Processing helix chain 'A' and resid 2438 through 2461 Processing helix chain 'A' and resid 2464 through 2466 No H-bonds generated for 'chain 'A' and resid 2464 through 2466' Processing helix chain 'A' and resid 2534 through 2541 Processing helix chain 'A' and resid 2563 through 2608 removed outlier: 4.105A pdb=" N LEU A2582 " --> pdb=" O ILE A2578 " (cutoff:3.500A) Processing helix chain 'A' and resid 2628 through 2634 removed outlier: 3.808A pdb=" N LYS A2633 " --> pdb=" O GLU A2629 " (cutoff:3.500A) Processing helix chain 'A' and resid 2638 through 2650 Processing helix chain 'A' and resid 2658 through 2668 Processing helix chain 'A' and resid 2688 through 2735 removed outlier: 3.513A pdb=" N ASN A2693 " --> pdb=" O GLU A2689 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A2713 " --> pdb=" O VAL A2709 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 75 Processing helix chain 'D' and resid 88 through 107 removed outlier: 3.776A pdb=" N GLU D 106 " --> pdb=" O GLN D 102 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN D 107 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 462 removed outlier: 3.576A pdb=" N ASP D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS D 462 " --> pdb=" O GLY D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 485 removed outlier: 3.780A pdb=" N THR D 474 " --> pdb=" O ARG D 470 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 476 " --> pdb=" O SER D 472 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL D 481 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR D 482 " --> pdb=" O GLU D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 512 Processing helix chain 'D' and resid 516 through 531 Proline residue: D 526 - end of helix Processing helix chain 'D' and resid 537 through 543 Processing helix chain 'D' and resid 547 through 562 removed outlier: 3.618A pdb=" N ILE D 552 " --> pdb=" O PRO D 548 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU D 555 " --> pdb=" O HIS D 551 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N CYS D 556 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR D 557 " --> pdb=" O CYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 577 removed outlier: 3.814A pdb=" N GLN D 577 " --> pdb=" O TYR D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 598 Processing helix chain 'D' and resid 603 through 608 Processing helix chain 'D' and resid 612 through 620 Processing helix chain 'D' and resid 629 through 636 Processing helix chain 'D' and resid 646 through 656 removed outlier: 3.758A pdb=" N GLU D 650 " --> pdb=" O PRO D 646 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU D 651 " --> pdb=" O VAL D 647 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS D 653 " --> pdb=" O GLN D 649 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 659 through 661 No H-bonds generated for 'chain 'D' and resid 659 through 661' Processing helix chain 'D' and resid 713 through 719 removed outlier: 3.539A pdb=" N GLN D 717 " --> pdb=" O ARG D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 741 Processing helix chain 'D' and resid 754 through 757 No H-bonds generated for 'chain 'D' and resid 754 through 757' Processing helix chain 'D' and resid 762 through 767 Processing helix chain 'D' and resid 776 through 787 removed outlier: 3.613A pdb=" N CYS D 782 " --> pdb=" O ARG D 778 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS D 787 " --> pdb=" O ARG D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 850 removed outlier: 4.564A pdb=" N GLN D 835 " --> pdb=" O GLU D 831 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N THR D 836 " --> pdb=" O ARG D 832 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU D 838 " --> pdb=" O ALA D 834 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE D 839 " --> pdb=" O GLN D 835 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL D 840 " --> pdb=" O THR D 836 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU D 841 " --> pdb=" O MET D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 860 through 875 removed outlier: 5.085A pdb=" N GLU D 865 " --> pdb=" O LYS D 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 881 through 894 removed outlier: 3.630A pdb=" N LEU D 885 " --> pdb=" O PHE D 881 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG D 886 " --> pdb=" O SER D 882 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE D 890 " --> pdb=" O ARG D 886 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ALA D 893 " --> pdb=" O LYS D 889 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE D 894 " --> pdb=" O ILE D 890 " (cutoff:3.500A) Processing helix chain 'D' and resid 965 through 1003 removed outlier: 3.776A pdb=" N LEU D 982 " --> pdb=" O LEU D 978 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN D 983 " --> pdb=" O GLN D 979 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU D 986 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP D 987 " --> pdb=" O ASN D 983 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1040 removed outlier: 3.747A pdb=" N GLU D1031 " --> pdb=" O ALA D1027 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N HIS D1032 " --> pdb=" O LEU D1028 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D1033 " --> pdb=" O ASP D1029 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU D1034 " --> pdb=" O PHE D1030 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU D1035 " --> pdb=" O GLU D1031 " (cutoff:3.500A) Processing helix chain 'D' and resid 1059 through 1068 removed outlier: 3.541A pdb=" N VAL D1063 " --> pdb=" O THR D1059 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D1064 " --> pdb=" O PHE D1060 " (cutoff:3.500A) Processing helix chain 'D' and resid 1075 through 1086 Processing helix chain 'D' and resid 1089 through 1100 Processing helix chain 'D' and resid 1113 through 1124 removed outlier: 3.817A pdb=" N SER D1124 " --> pdb=" O ASP D1120 " (cutoff:3.500A) Processing helix chain 'D' and resid 1173 through 1188 removed outlier: 4.144A pdb=" N LYS D1177 " --> pdb=" O TYR D1173 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU D1178 " --> pdb=" O ARG D1174 " (cutoff:3.500A) Processing helix chain 'D' and resid 1199 through 1206 removed outlier: 4.279A pdb=" N LEU D1204 " --> pdb=" O GLN D1200 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU D1205 " --> pdb=" O GLN D1201 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG D1206 " --> pdb=" O GLN D1202 " (cutoff:3.500A) Processing helix chain 'D' and resid 1212 through 1218 Processing helix chain 'D' and resid 1231 through 1244 removed outlier: 4.062A pdb=" N ARG D1235 " --> pdb=" O GLN D1231 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU D1236 " --> pdb=" O GLU D1232 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1258 removed outlier: 3.674A pdb=" N LEU D1254 " --> pdb=" O GLN D1250 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS D1257 " --> pdb=" O ALA D1253 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N HIS D1258 " --> pdb=" O LEU D1254 " (cutoff:3.500A) Processing helix chain 'D' and resid 1270 through 1276 Processing helix chain 'D' and resid 1292 through 1294 No H-bonds generated for 'chain 'D' and resid 1292 through 1294' Processing helix chain 'D' and resid 1296 through 1299 No H-bonds generated for 'chain 'D' and resid 1296 through 1299' Processing helix chain 'D' and resid 1306 through 1309 No H-bonds generated for 'chain 'D' and resid 1306 through 1309' Processing helix chain 'D' and resid 1312 through 1315 No H-bonds generated for 'chain 'D' and resid 1312 through 1315' Processing helix chain 'D' and resid 1327 through 1336 removed outlier: 3.626A pdb=" N ALA D1332 " --> pdb=" O ASP D1328 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLU D1333 " --> pdb=" O MET D1329 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU D1334 " --> pdb=" O VAL D1330 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL D1335 " --> pdb=" O MET D1331 " (cutoff:3.500A) Processing helix chain 'D' and resid 1363 through 1367 removed outlier: 3.827A pdb=" N ASP D1366 " --> pdb=" O ASP D1363 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D1367 " --> pdb=" O ARG D1364 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1363 through 1367' Processing helix chain 'D' and resid 1374 through 1377 No H-bonds generated for 'chain 'D' and resid 1374 through 1377' Processing helix chain 'D' and resid 1380 through 1383 No H-bonds generated for 'chain 'D' and resid 1380 through 1383' Processing helix chain 'D' and resid 1395 through 1399 Processing helix chain 'D' and resid 1404 through 1413 removed outlier: 4.474A pdb=" N VAL D1409 " --> pdb=" O ASP D1405 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL D1410 " --> pdb=" O ILE D1406 " (cutoff:3.500A) Processing helix chain 'D' and resid 1417 through 1431 Processing helix chain 'D' and resid 1441 through 1462 removed outlier: 3.883A pdb=" N HIS D1446 " --> pdb=" O TYR D1442 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET D1447 " --> pdb=" O THR D1443 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP D1448 " --> pdb=" O SER D1444 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS D1449 " --> pdb=" O ASN D1445 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D1450 " --> pdb=" O HIS D1446 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP D1457 " --> pdb=" O ASN D1453 " (cutoff:3.500A) Processing helix chain 'D' and resid 1600 through 1629 removed outlier: 3.534A pdb=" N GLN D1605 " --> pdb=" O ILE D1601 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG D1614 " --> pdb=" O ALA D1610 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LEU D1615 " --> pdb=" O LEU D1611 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ARG D1616 " --> pdb=" O GLU D1612 " (cutoff:3.500A) Proline residue: D1617 - end of helix removed outlier: 3.797A pdb=" N GLN D1620 " --> pdb=" O ARG D1616 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER D1624 " --> pdb=" O GLN D1620 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL D1625 " --> pdb=" O ALA D1621 " (cutoff:3.500A) Processing helix chain 'D' and resid 1652 through 1660 Processing helix chain 'D' and resid 1670 through 1683 Processing helix chain 'D' and resid 1726 through 1744 removed outlier: 3.679A pdb=" N HIS D1730 " --> pdb=" O GLN D1726 " (cutoff:3.500A) Processing helix chain 'D' and resid 1792 through 1802 removed outlier: 3.742A pdb=" N GLN D1796 " --> pdb=" O LEU D1792 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N CYS D1797 " --> pdb=" O ALA D1793 " (cutoff:3.500A) Processing helix chain 'D' and resid 1804 through 1811 removed outlier: 3.578A pdb=" N VAL D1808 " --> pdb=" O ALA D1804 " (cutoff:3.500A) Processing helix chain 'D' and resid 1818 through 1832 Processing helix chain 'D' and resid 1837 through 1847 removed outlier: 3.505A pdb=" N HIS D1841 " --> pdb=" O THR D1837 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER D1842 " --> pdb=" O THR D1838 " (cutoff:3.500A) Processing helix chain 'D' and resid 1853 through 1868 removed outlier: 3.843A pdb=" N ARG D1863 " --> pdb=" O VAL D1859 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET D1864 " --> pdb=" O PHE D1860 " (cutoff:3.500A) Processing helix chain 'D' and resid 1965 through 1977 removed outlier: 3.505A pdb=" N ILE D1969 " --> pdb=" O ILE D1965 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS D1977 " --> pdb=" O LEU D1973 " (cutoff:3.500A) Processing helix chain 'D' and resid 1982 through 1988 removed outlier: 3.804A pdb=" N LEU D1988 " --> pdb=" O LEU D1984 " (cutoff:3.500A) Processing helix chain 'D' and resid 1999 through 2011 Processing helix chain 'D' and resid 2030 through 2042 removed outlier: 3.691A pdb=" N GLN D2035 " --> pdb=" O ALA D2031 " (cutoff:3.500A) Processing helix chain 'D' and resid 2053 through 2056 No H-bonds generated for 'chain 'D' and resid 2053 through 2056' Processing helix chain 'D' and resid 2063 through 2066 No H-bonds generated for 'chain 'D' and resid 2063 through 2066' Processing helix chain 'D' and resid 2068 through 2071 No H-bonds generated for 'chain 'D' and resid 2068 through 2071' Processing helix chain 'D' and resid 2082 through 2099 removed outlier: 3.972A pdb=" N LEU D2086 " --> pdb=" O MET D2082 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLU D2087 " --> pdb=" O ASP D2083 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU D2088 " --> pdb=" O LEU D2084 " (cutoff:3.500A) Processing helix chain 'D' and resid 2106 through 2113 Processing helix chain 'D' and resid 2118 through 2133 removed outlier: 3.841A pdb=" N GLU D2133 " --> pdb=" O MET D2130 " (cutoff:3.500A) Processing helix chain 'D' and resid 2151 through 2165 removed outlier: 4.261A pdb=" N ARG D2165 " --> pdb=" O HIS D2161 " (cutoff:3.500A) Processing helix chain 'D' and resid 2170 through 2172 No H-bonds generated for 'chain 'D' and resid 2170 through 2172' Processing helix chain 'D' and resid 2183 through 2191 Processing helix chain 'D' and resid 2221 through 2230 Processing helix chain 'D' and resid 2240 through 2263 removed outlier: 3.612A pdb=" N LEU D2245 " --> pdb=" O ASN D2241 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA D2262 " --> pdb=" O LYS D2258 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN D2263 " --> pdb=" O LYS D2259 " (cutoff:3.500A) Processing helix chain 'D' and resid 2265 through 2271 Processing helix chain 'D' and resid 2273 through 2293 Processing helix chain 'D' and resid 2306 through 2327 Processing helix chain 'D' and resid 2333 through 2347 removed outlier: 3.960A pdb=" N ILE D2337 " --> pdb=" O ILE D2333 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE D2346 " --> pdb=" O LEU D2342 " (cutoff:3.500A) Processing helix chain 'D' and resid 2350 through 2374 removed outlier: 3.784A pdb=" N MET D2370 " --> pdb=" O ILE D2366 " (cutoff:3.500A) Processing helix chain 'D' and resid 2383 through 2388 Processing helix chain 'D' and resid 2390 through 2407 Processing helix chain 'D' and resid 2413 through 2423 removed outlier: 4.365A pdb=" N ARG D2423 " --> pdb=" O ASP D2419 " (cutoff:3.500A) Processing helix chain 'D' and resid 2425 through 2435 Processing helix chain 'D' and resid 2438 through 2461 Processing helix chain 'D' and resid 2464 through 2466 No H-bonds generated for 'chain 'D' and resid 2464 through 2466' Processing helix chain 'D' and resid 2534 through 2541 Processing helix chain 'D' and resid 2563 through 2608 removed outlier: 4.105A pdb=" N LEU D2582 " --> pdb=" O ILE D2578 " (cutoff:3.500A) Processing helix chain 'D' and resid 2628 through 2634 removed outlier: 3.809A pdb=" N LYS D2633 " --> pdb=" O GLU D2629 " (cutoff:3.500A) Processing helix chain 'D' and resid 2638 through 2650 Processing helix chain 'D' and resid 2658 through 2668 Processing helix chain 'D' and resid 2688 through 2735 removed outlier: 3.513A pdb=" N ASN D2693 " --> pdb=" O GLU D2689 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER D2713 " --> pdb=" O VAL D2709 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 75 Processing helix chain 'C' and resid 88 through 107 removed outlier: 3.777A pdb=" N GLU C 106 " --> pdb=" O GLN C 102 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN C 107 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 462 removed outlier: 3.576A pdb=" N ASP C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS C 462 " --> pdb=" O GLY C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 485 removed outlier: 3.780A pdb=" N THR C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 476 " --> pdb=" O SER C 472 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR C 482 " --> pdb=" O GLU C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 512 Processing helix chain 'C' and resid 516 through 531 Proline residue: C 526 - end of helix Processing helix chain 'C' and resid 537 through 543 Processing helix chain 'C' and resid 547 through 562 removed outlier: 3.618A pdb=" N ILE C 552 " --> pdb=" O PRO C 548 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU C 555 " --> pdb=" O HIS C 551 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N CYS C 556 " --> pdb=" O ILE C 552 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR C 557 " --> pdb=" O CYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 577 removed outlier: 3.813A pdb=" N GLN C 577 " --> pdb=" O TYR C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 598 Processing helix chain 'C' and resid 603 through 608 Processing helix chain 'C' and resid 612 through 620 Processing helix chain 'C' and resid 629 through 636 Processing helix chain 'C' and resid 646 through 656 removed outlier: 3.758A pdb=" N GLU C 650 " --> pdb=" O PRO C 646 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU C 651 " --> pdb=" O VAL C 647 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS C 653 " --> pdb=" O GLN C 649 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LYS C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 661 No H-bonds generated for 'chain 'C' and resid 659 through 661' Processing helix chain 'C' and resid 713 through 719 removed outlier: 3.539A pdb=" N GLN C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 741 Processing helix chain 'C' and resid 754 through 757 No H-bonds generated for 'chain 'C' and resid 754 through 757' Processing helix chain 'C' and resid 762 through 767 Processing helix chain 'C' and resid 776 through 787 removed outlier: 3.613A pdb=" N CYS C 782 " --> pdb=" O ARG C 778 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS C 787 " --> pdb=" O ARG C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 850 removed outlier: 4.562A pdb=" N GLN C 835 " --> pdb=" O GLU C 831 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N THR C 836 " --> pdb=" O ARG C 832 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU C 838 " --> pdb=" O ALA C 834 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE C 839 " --> pdb=" O GLN C 835 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 840 " --> pdb=" O THR C 836 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU C 841 " --> pdb=" O MET C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 875 removed outlier: 5.084A pdb=" N GLU C 865 " --> pdb=" O LYS C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 894 removed outlier: 3.631A pdb=" N LEU C 885 " --> pdb=" O PHE C 881 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG C 886 " --> pdb=" O SER C 882 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE C 890 " --> pdb=" O ARG C 886 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ALA C 893 " --> pdb=" O LYS C 889 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE C 894 " --> pdb=" O ILE C 890 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 1003 removed outlier: 3.777A pdb=" N LEU C 982 " --> pdb=" O LEU C 978 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN C 983 " --> pdb=" O GLN C 979 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 986 " --> pdb=" O LEU C 982 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP C 987 " --> pdb=" O ASN C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1027 through 1040 removed outlier: 3.746A pdb=" N GLU C1031 " --> pdb=" O ALA C1027 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N HIS C1032 " --> pdb=" O LEU C1028 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C1033 " --> pdb=" O ASP C1029 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU C1034 " --> pdb=" O PHE C1030 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU C1035 " --> pdb=" O GLU C1031 " (cutoff:3.500A) Processing helix chain 'C' and resid 1059 through 1068 removed outlier: 3.541A pdb=" N VAL C1063 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C1064 " --> pdb=" O PHE C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1086 Processing helix chain 'C' and resid 1089 through 1100 Processing helix chain 'C' and resid 1113 through 1124 removed outlier: 3.817A pdb=" N SER C1124 " --> pdb=" O ASP C1120 " (cutoff:3.500A) Processing helix chain 'C' and resid 1173 through 1188 removed outlier: 4.144A pdb=" N LYS C1177 " --> pdb=" O TYR C1173 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU C1178 " --> pdb=" O ARG C1174 " (cutoff:3.500A) Processing helix chain 'C' and resid 1199 through 1206 removed outlier: 4.279A pdb=" N LEU C1204 " --> pdb=" O GLN C1200 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU C1205 " --> pdb=" O GLN C1201 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG C1206 " --> pdb=" O GLN C1202 " (cutoff:3.500A) Processing helix chain 'C' and resid 1212 through 1218 Processing helix chain 'C' and resid 1231 through 1244 removed outlier: 4.062A pdb=" N ARG C1235 " --> pdb=" O GLN C1231 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU C1236 " --> pdb=" O GLU C1232 " (cutoff:3.500A) Processing helix chain 'C' and resid 1249 through 1258 removed outlier: 3.674A pdb=" N LEU C1254 " --> pdb=" O GLN C1250 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS C1257 " --> pdb=" O ALA C1253 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N HIS C1258 " --> pdb=" O LEU C1254 " (cutoff:3.500A) Processing helix chain 'C' and resid 1270 through 1276 Processing helix chain 'C' and resid 1292 through 1294 No H-bonds generated for 'chain 'C' and resid 1292 through 1294' Processing helix chain 'C' and resid 1296 through 1299 No H-bonds generated for 'chain 'C' and resid 1296 through 1299' Processing helix chain 'C' and resid 1306 through 1309 No H-bonds generated for 'chain 'C' and resid 1306 through 1309' Processing helix chain 'C' and resid 1312 through 1315 No H-bonds generated for 'chain 'C' and resid 1312 through 1315' Processing helix chain 'C' and resid 1327 through 1336 removed outlier: 3.626A pdb=" N ALA C1332 " --> pdb=" O ASP C1328 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLU C1333 " --> pdb=" O MET C1329 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU C1334 " --> pdb=" O VAL C1330 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL C1335 " --> pdb=" O MET C1331 " (cutoff:3.500A) Processing helix chain 'C' and resid 1363 through 1367 removed outlier: 3.826A pdb=" N ASP C1366 " --> pdb=" O ASP C1363 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU C1367 " --> pdb=" O ARG C1364 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1363 through 1367' Processing helix chain 'C' and resid 1374 through 1377 No H-bonds generated for 'chain 'C' and resid 1374 through 1377' Processing helix chain 'C' and resid 1380 through 1383 No H-bonds generated for 'chain 'C' and resid 1380 through 1383' Processing helix chain 'C' and resid 1395 through 1399 Processing helix chain 'C' and resid 1404 through 1413 removed outlier: 4.474A pdb=" N VAL C1409 " --> pdb=" O ASP C1405 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL C1410 " --> pdb=" O ILE C1406 " (cutoff:3.500A) Processing helix chain 'C' and resid 1417 through 1431 Processing helix chain 'C' and resid 1441 through 1462 removed outlier: 3.884A pdb=" N HIS C1446 " --> pdb=" O TYR C1442 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET C1447 " --> pdb=" O THR C1443 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP C1448 " --> pdb=" O SER C1444 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS C1449 " --> pdb=" O ASN C1445 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C1450 " --> pdb=" O HIS C1446 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP C1457 " --> pdb=" O ASN C1453 " (cutoff:3.500A) Processing helix chain 'C' and resid 1600 through 1629 removed outlier: 3.534A pdb=" N GLN C1605 " --> pdb=" O ILE C1601 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG C1614 " --> pdb=" O ALA C1610 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LEU C1615 " --> pdb=" O LEU C1611 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ARG C1616 " --> pdb=" O GLU C1612 " (cutoff:3.500A) Proline residue: C1617 - end of helix removed outlier: 3.798A pdb=" N GLN C1620 " --> pdb=" O ARG C1616 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER C1624 " --> pdb=" O GLN C1620 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL C1625 " --> pdb=" O ALA C1621 " (cutoff:3.500A) Processing helix chain 'C' and resid 1652 through 1660 Processing helix chain 'C' and resid 1670 through 1683 Processing helix chain 'C' and resid 1726 through 1744 removed outlier: 3.680A pdb=" N HIS C1730 " --> pdb=" O GLN C1726 " (cutoff:3.500A) Processing helix chain 'C' and resid 1792 through 1802 removed outlier: 3.741A pdb=" N GLN C1796 " --> pdb=" O LEU C1792 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N CYS C1797 " --> pdb=" O ALA C1793 " (cutoff:3.500A) Processing helix chain 'C' and resid 1804 through 1811 removed outlier: 3.579A pdb=" N VAL C1808 " --> pdb=" O ALA C1804 " (cutoff:3.500A) Processing helix chain 'C' and resid 1818 through 1832 Processing helix chain 'C' and resid 1837 through 1847 removed outlier: 3.505A pdb=" N HIS C1841 " --> pdb=" O THR C1837 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER C1842 " --> pdb=" O THR C1838 " (cutoff:3.500A) Processing helix chain 'C' and resid 1853 through 1868 removed outlier: 3.843A pdb=" N ARG C1863 " --> pdb=" O VAL C1859 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET C1864 " --> pdb=" O PHE C1860 " (cutoff:3.500A) Processing helix chain 'C' and resid 1965 through 1977 removed outlier: 3.506A pdb=" N ILE C1969 " --> pdb=" O ILE C1965 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS C1977 " --> pdb=" O LEU C1973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1982 through 1988 removed outlier: 3.805A pdb=" N LEU C1988 " --> pdb=" O LEU C1984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1999 through 2011 Processing helix chain 'C' and resid 2030 through 2042 removed outlier: 3.690A pdb=" N GLN C2035 " --> pdb=" O ALA C2031 " (cutoff:3.500A) Processing helix chain 'C' and resid 2053 through 2056 No H-bonds generated for 'chain 'C' and resid 2053 through 2056' Processing helix chain 'C' and resid 2063 through 2066 No H-bonds generated for 'chain 'C' and resid 2063 through 2066' Processing helix chain 'C' and resid 2068 through 2071 No H-bonds generated for 'chain 'C' and resid 2068 through 2071' Processing helix chain 'C' and resid 2082 through 2099 removed outlier: 3.973A pdb=" N LEU C2086 " --> pdb=" O MET C2082 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLU C2087 " --> pdb=" O ASP C2083 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C2088 " --> pdb=" O LEU C2084 " (cutoff:3.500A) Processing helix chain 'C' and resid 2106 through 2113 Processing helix chain 'C' and resid 2118 through 2133 removed outlier: 3.841A pdb=" N GLU C2133 " --> pdb=" O MET C2130 " (cutoff:3.500A) Processing helix chain 'C' and resid 2151 through 2165 removed outlier: 4.260A pdb=" N ARG C2165 " --> pdb=" O HIS C2161 " (cutoff:3.500A) Processing helix chain 'C' and resid 2170 through 2172 No H-bonds generated for 'chain 'C' and resid 2170 through 2172' Processing helix chain 'C' and resid 2183 through 2191 Processing helix chain 'C' and resid 2221 through 2230 Processing helix chain 'C' and resid 2240 through 2263 removed outlier: 3.612A pdb=" N LEU C2245 " --> pdb=" O ASN C2241 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA C2262 " --> pdb=" O LYS C2258 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN C2263 " --> pdb=" O LYS C2259 " (cutoff:3.500A) Processing helix chain 'C' and resid 2265 through 2271 Processing helix chain 'C' and resid 2273 through 2293 Processing helix chain 'C' and resid 2306 through 2327 Processing helix chain 'C' and resid 2333 through 2347 removed outlier: 3.960A pdb=" N ILE C2337 " --> pdb=" O ILE C2333 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE C2346 " --> pdb=" O LEU C2342 " (cutoff:3.500A) Processing helix chain 'C' and resid 2350 through 2374 removed outlier: 3.783A pdb=" N MET C2370 " --> pdb=" O ILE C2366 " (cutoff:3.500A) Processing helix chain 'C' and resid 2383 through 2388 Processing helix chain 'C' and resid 2390 through 2407 Processing helix chain 'C' and resid 2413 through 2423 removed outlier: 4.365A pdb=" N ARG C2423 " --> pdb=" O ASP C2419 " (cutoff:3.500A) Processing helix chain 'C' and resid 2425 through 2435 Processing helix chain 'C' and resid 2438 through 2461 Processing helix chain 'C' and resid 2464 through 2466 No H-bonds generated for 'chain 'C' and resid 2464 through 2466' Processing helix chain 'C' and resid 2534 through 2541 Processing helix chain 'C' and resid 2563 through 2608 removed outlier: 4.105A pdb=" N LEU C2582 " --> pdb=" O ILE C2578 " (cutoff:3.500A) Processing helix chain 'C' and resid 2628 through 2634 removed outlier: 3.809A pdb=" N LYS C2633 " --> pdb=" O GLU C2629 " (cutoff:3.500A) Processing helix chain 'C' and resid 2638 through 2650 Processing helix chain 'C' and resid 2658 through 2668 Processing helix chain 'C' and resid 2688 through 2735 removed outlier: 3.513A pdb=" N ASN C2693 " --> pdb=" O GLU C2689 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER C2713 " --> pdb=" O VAL C2709 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 75 Processing helix chain 'B' and resid 88 through 107 removed outlier: 3.776A pdb=" N GLU B 106 " --> pdb=" O GLN B 102 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 462 removed outlier: 3.576A pdb=" N ASP B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS B 462 " --> pdb=" O GLY B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 485 removed outlier: 3.780A pdb=" N THR B 474 " --> pdb=" O ARG B 470 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR B 482 " --> pdb=" O GLU B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 512 Processing helix chain 'B' and resid 516 through 531 Proline residue: B 526 - end of helix Processing helix chain 'B' and resid 537 through 543 Processing helix chain 'B' and resid 547 through 562 removed outlier: 3.618A pdb=" N ILE B 552 " --> pdb=" O PRO B 548 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 555 " --> pdb=" O HIS B 551 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N CYS B 556 " --> pdb=" O ILE B 552 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR B 557 " --> pdb=" O CYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 577 removed outlier: 3.813A pdb=" N GLN B 577 " --> pdb=" O TYR B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 598 Processing helix chain 'B' and resid 603 through 608 Processing helix chain 'B' and resid 612 through 620 Processing helix chain 'B' and resid 629 through 636 Processing helix chain 'B' and resid 646 through 656 removed outlier: 3.758A pdb=" N GLU B 650 " --> pdb=" O PRO B 646 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B 651 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS B 653 " --> pdb=" O GLN B 649 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LYS B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 661 No H-bonds generated for 'chain 'B' and resid 659 through 661' Processing helix chain 'B' and resid 713 through 719 removed outlier: 3.540A pdb=" N GLN B 717 " --> pdb=" O ARG B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 741 Processing helix chain 'B' and resid 754 through 757 No H-bonds generated for 'chain 'B' and resid 754 through 757' Processing helix chain 'B' and resid 762 through 767 Processing helix chain 'B' and resid 776 through 787 removed outlier: 3.613A pdb=" N CYS B 782 " --> pdb=" O ARG B 778 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS B 787 " --> pdb=" O ARG B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 850 removed outlier: 4.563A pdb=" N GLN B 835 " --> pdb=" O GLU B 831 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N THR B 836 " --> pdb=" O ARG B 832 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU B 838 " --> pdb=" O ALA B 834 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE B 839 " --> pdb=" O GLN B 835 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 840 " --> pdb=" O THR B 836 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU B 841 " --> pdb=" O MET B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 875 removed outlier: 5.084A pdb=" N GLU B 865 " --> pdb=" O LYS B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 894 removed outlier: 3.630A pdb=" N LEU B 885 " --> pdb=" O PHE B 881 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG B 886 " --> pdb=" O SER B 882 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 890 " --> pdb=" O ARG B 886 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ALA B 893 " --> pdb=" O LYS B 889 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE B 894 " --> pdb=" O ILE B 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 1003 removed outlier: 3.777A pdb=" N LEU B 982 " --> pdb=" O LEU B 978 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN B 983 " --> pdb=" O GLN B 979 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 986 " --> pdb=" O LEU B 982 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP B 987 " --> pdb=" O ASN B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1040 removed outlier: 3.745A pdb=" N GLU B1031 " --> pdb=" O ALA B1027 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N HIS B1032 " --> pdb=" O LEU B1028 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B1033 " --> pdb=" O ASP B1029 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU B1034 " --> pdb=" O PHE B1030 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU B1035 " --> pdb=" O GLU B1031 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1068 removed outlier: 3.541A pdb=" N VAL B1063 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B1064 " --> pdb=" O PHE B1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1086 Processing helix chain 'B' and resid 1089 through 1100 Processing helix chain 'B' and resid 1113 through 1124 removed outlier: 3.817A pdb=" N SER B1124 " --> pdb=" O ASP B1120 " (cutoff:3.500A) Processing helix chain 'B' and resid 1173 through 1188 removed outlier: 4.145A pdb=" N LYS B1177 " --> pdb=" O TYR B1173 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU B1178 " --> pdb=" O ARG B1174 " (cutoff:3.500A) Processing helix chain 'B' and resid 1199 through 1206 removed outlier: 4.279A pdb=" N LEU B1204 " --> pdb=" O GLN B1200 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LEU B1205 " --> pdb=" O GLN B1201 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG B1206 " --> pdb=" O GLN B1202 " (cutoff:3.500A) Processing helix chain 'B' and resid 1212 through 1218 Processing helix chain 'B' and resid 1231 through 1244 removed outlier: 4.063A pdb=" N ARG B1235 " --> pdb=" O GLN B1231 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU B1236 " --> pdb=" O GLU B1232 " (cutoff:3.500A) Processing helix chain 'B' and resid 1249 through 1258 removed outlier: 3.674A pdb=" N LEU B1254 " --> pdb=" O GLN B1250 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N HIS B1258 " --> pdb=" O LEU B1254 " (cutoff:3.500A) Processing helix chain 'B' and resid 1270 through 1276 Processing helix chain 'B' and resid 1292 through 1294 No H-bonds generated for 'chain 'B' and resid 1292 through 1294' Processing helix chain 'B' and resid 1296 through 1299 No H-bonds generated for 'chain 'B' and resid 1296 through 1299' Processing helix chain 'B' and resid 1306 through 1309 No H-bonds generated for 'chain 'B' and resid 1306 through 1309' Processing helix chain 'B' and resid 1312 through 1315 No H-bonds generated for 'chain 'B' and resid 1312 through 1315' Processing helix chain 'B' and resid 1327 through 1336 removed outlier: 3.626A pdb=" N ALA B1332 " --> pdb=" O ASP B1328 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU B1333 " --> pdb=" O MET B1329 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU B1334 " --> pdb=" O VAL B1330 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL B1335 " --> pdb=" O MET B1331 " (cutoff:3.500A) Processing helix chain 'B' and resid 1363 through 1367 removed outlier: 3.827A pdb=" N ASP B1366 " --> pdb=" O ASP B1363 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B1367 " --> pdb=" O ARG B1364 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1363 through 1367' Processing helix chain 'B' and resid 1374 through 1377 No H-bonds generated for 'chain 'B' and resid 1374 through 1377' Processing helix chain 'B' and resid 1380 through 1383 No H-bonds generated for 'chain 'B' and resid 1380 through 1383' Processing helix chain 'B' and resid 1395 through 1399 Processing helix chain 'B' and resid 1404 through 1413 removed outlier: 4.475A pdb=" N VAL B1409 " --> pdb=" O ASP B1405 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL B1410 " --> pdb=" O ILE B1406 " (cutoff:3.500A) Processing helix chain 'B' and resid 1417 through 1431 Processing helix chain 'B' and resid 1441 through 1462 removed outlier: 3.884A pdb=" N HIS B1446 " --> pdb=" O TYR B1442 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET B1447 " --> pdb=" O THR B1443 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP B1448 " --> pdb=" O SER B1444 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS B1449 " --> pdb=" O ASN B1445 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B1450 " --> pdb=" O HIS B1446 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP B1457 " --> pdb=" O ASN B1453 " (cutoff:3.500A) Processing helix chain 'B' and resid 1600 through 1629 removed outlier: 3.533A pdb=" N GLN B1605 " --> pdb=" O ILE B1601 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG B1614 " --> pdb=" O ALA B1610 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LEU B1615 " --> pdb=" O LEU B1611 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ARG B1616 " --> pdb=" O GLU B1612 " (cutoff:3.500A) Proline residue: B1617 - end of helix removed outlier: 3.798A pdb=" N GLN B1620 " --> pdb=" O ARG B1616 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B1624 " --> pdb=" O GLN B1620 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL B1625 " --> pdb=" O ALA B1621 " (cutoff:3.500A) Processing helix chain 'B' and resid 1652 through 1660 Processing helix chain 'B' and resid 1670 through 1683 Processing helix chain 'B' and resid 1726 through 1744 removed outlier: 3.679A pdb=" N HIS B1730 " --> pdb=" O GLN B1726 " (cutoff:3.500A) Processing helix chain 'B' and resid 1792 through 1802 removed outlier: 3.742A pdb=" N GLN B1796 " --> pdb=" O LEU B1792 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N CYS B1797 " --> pdb=" O ALA B1793 " (cutoff:3.500A) Processing helix chain 'B' and resid 1804 through 1811 removed outlier: 3.577A pdb=" N VAL B1808 " --> pdb=" O ALA B1804 " (cutoff:3.500A) Processing helix chain 'B' and resid 1818 through 1832 Processing helix chain 'B' and resid 1837 through 1847 removed outlier: 3.505A pdb=" N HIS B1841 " --> pdb=" O THR B1837 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER B1842 " --> pdb=" O THR B1838 " (cutoff:3.500A) Processing helix chain 'B' and resid 1853 through 1868 removed outlier: 3.843A pdb=" N ARG B1863 " --> pdb=" O VAL B1859 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET B1864 " --> pdb=" O PHE B1860 " (cutoff:3.500A) Processing helix chain 'B' and resid 1965 through 1977 removed outlier: 3.505A pdb=" N ILE B1969 " --> pdb=" O ILE B1965 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS B1977 " --> pdb=" O LEU B1973 " (cutoff:3.500A) Processing helix chain 'B' and resid 1982 through 1988 removed outlier: 3.805A pdb=" N LEU B1988 " --> pdb=" O LEU B1984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1999 through 2011 Processing helix chain 'B' and resid 2030 through 2042 removed outlier: 3.690A pdb=" N GLN B2035 " --> pdb=" O ALA B2031 " (cutoff:3.500A) Processing helix chain 'B' and resid 2053 through 2056 No H-bonds generated for 'chain 'B' and resid 2053 through 2056' Processing helix chain 'B' and resid 2063 through 2066 No H-bonds generated for 'chain 'B' and resid 2063 through 2066' Processing helix chain 'B' and resid 2068 through 2071 No H-bonds generated for 'chain 'B' and resid 2068 through 2071' Processing helix chain 'B' and resid 2082 through 2099 removed outlier: 3.972A pdb=" N LEU B2086 " --> pdb=" O MET B2082 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLU B2087 " --> pdb=" O ASP B2083 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B2088 " --> pdb=" O LEU B2084 " (cutoff:3.500A) Processing helix chain 'B' and resid 2106 through 2113 Processing helix chain 'B' and resid 2118 through 2133 removed outlier: 3.841A pdb=" N GLU B2133 " --> pdb=" O MET B2130 " (cutoff:3.500A) Processing helix chain 'B' and resid 2151 through 2165 removed outlier: 4.260A pdb=" N ARG B2165 " --> pdb=" O HIS B2161 " (cutoff:3.500A) Processing helix chain 'B' and resid 2170 through 2172 No H-bonds generated for 'chain 'B' and resid 2170 through 2172' Processing helix chain 'B' and resid 2183 through 2191 Processing helix chain 'B' and resid 2221 through 2230 Processing helix chain 'B' and resid 2240 through 2263 removed outlier: 3.612A pdb=" N LEU B2245 " --> pdb=" O ASN B2241 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA B2262 " --> pdb=" O LYS B2258 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN B2263 " --> pdb=" O LYS B2259 " (cutoff:3.500A) Processing helix chain 'B' and resid 2265 through 2271 Processing helix chain 'B' and resid 2273 through 2293 Processing helix chain 'B' and resid 2306 through 2327 Processing helix chain 'B' and resid 2333 through 2347 removed outlier: 3.959A pdb=" N ILE B2337 " --> pdb=" O ILE B2333 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE B2346 " --> pdb=" O LEU B2342 " (cutoff:3.500A) Processing helix chain 'B' and resid 2350 through 2374 removed outlier: 3.782A pdb=" N MET B2370 " --> pdb=" O ILE B2366 " (cutoff:3.500A) Processing helix chain 'B' and resid 2383 through 2388 Processing helix chain 'B' and resid 2390 through 2407 Processing helix chain 'B' and resid 2413 through 2423 removed outlier: 4.364A pdb=" N ARG B2423 " --> pdb=" O ASP B2419 " (cutoff:3.500A) Processing helix chain 'B' and resid 2425 through 2435 Processing helix chain 'B' and resid 2438 through 2461 Processing helix chain 'B' and resid 2464 through 2466 No H-bonds generated for 'chain 'B' and resid 2464 through 2466' Processing helix chain 'B' and resid 2534 through 2541 Processing helix chain 'B' and resid 2563 through 2608 removed outlier: 4.105A pdb=" N LEU B2582 " --> pdb=" O ILE B2578 " (cutoff:3.500A) Processing helix chain 'B' and resid 2628 through 2634 removed outlier: 3.808A pdb=" N LYS B2633 " --> pdb=" O GLU B2629 " (cutoff:3.500A) Processing helix chain 'B' and resid 2638 through 2650 Processing helix chain 'B' and resid 2658 through 2668 Processing helix chain 'B' and resid 2688 through 2735 removed outlier: 3.513A pdb=" N ASN B2693 " --> pdb=" O GLU B2689 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B2713 " --> pdb=" O VAL B2709 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 131 through 134 Processing sheet with id= B, first strand: chain 'A' and resid 161 through 165 Processing sheet with id= C, first strand: chain 'A' and resid 193 through 195 Processing sheet with id= D, first strand: chain 'A' and resid 282 through 286 Processing sheet with id= E, first strand: chain 'A' and resid 313 through 316 Processing sheet with id= F, first strand: chain 'A' and resid 369 through 372 removed outlier: 4.019A pdb=" N GLU A 369 " --> pdb=" O ARG A 391 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 398 through 400 removed outlier: 3.532A pdb=" N HIS A 400 " --> pdb=" O GLY A 419 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A 419 " --> pdb=" O HIS A 400 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 2193 through 2199 removed outlier: 3.693A pdb=" N PHE A2210 " --> pdb=" O ALA A2194 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A2198 " --> pdb=" O GLU A2206 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 14 through 20 removed outlier: 5.698A pdb=" N SER A 16 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU A 222 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N TYR A 18 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE A 220 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLU A 20 " --> pdb=" O TRP A 218 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TRP A 218 " --> pdb=" O GLU A 20 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 131 through 134 Processing sheet with id= K, first strand: chain 'D' and resid 161 through 165 Processing sheet with id= L, first strand: chain 'D' and resid 193 through 195 Processing sheet with id= M, first strand: chain 'D' and resid 282 through 286 Processing sheet with id= N, first strand: chain 'D' and resid 313 through 316 Processing sheet with id= O, first strand: chain 'D' and resid 369 through 372 removed outlier: 4.019A pdb=" N GLU D 369 " --> pdb=" O ARG D 391 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 398 through 400 removed outlier: 3.532A pdb=" N HIS D 400 " --> pdb=" O GLY D 419 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY D 419 " --> pdb=" O HIS D 400 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 2193 through 2199 removed outlier: 3.693A pdb=" N PHE D2210 " --> pdb=" O ALA D2194 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE D2198 " --> pdb=" O GLU D2206 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 14 through 20 removed outlier: 5.698A pdb=" N SER D 16 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU D 222 " --> pdb=" O SER D 16 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TYR D 18 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE D 220 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLU D 20 " --> pdb=" O TRP D 218 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TRP D 218 " --> pdb=" O GLU D 20 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 131 through 134 Processing sheet with id= T, first strand: chain 'C' and resid 161 through 165 Processing sheet with id= U, first strand: chain 'C' and resid 193 through 195 Processing sheet with id= V, first strand: chain 'C' and resid 282 through 286 Processing sheet with id= W, first strand: chain 'C' and resid 313 through 316 Processing sheet with id= X, first strand: chain 'C' and resid 369 through 372 removed outlier: 4.019A pdb=" N GLU C 369 " --> pdb=" O ARG C 391 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 398 through 400 removed outlier: 3.532A pdb=" N HIS C 400 " --> pdb=" O GLY C 419 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY C 419 " --> pdb=" O HIS C 400 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 2193 through 2199 removed outlier: 3.693A pdb=" N PHE C2210 " --> pdb=" O ALA C2194 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE C2198 " --> pdb=" O GLU C2206 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 14 through 20 removed outlier: 5.698A pdb=" N SER C 16 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU C 222 " --> pdb=" O SER C 16 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TYR C 18 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE C 220 " --> pdb=" O TYR C 18 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLU C 20 " --> pdb=" O TRP C 218 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TRP C 218 " --> pdb=" O GLU C 20 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 131 through 134 Processing sheet with id= AC, first strand: chain 'B' and resid 161 through 165 Processing sheet with id= AD, first strand: chain 'B' and resid 193 through 195 Processing sheet with id= AE, first strand: chain 'B' and resid 282 through 286 Processing sheet with id= AF, first strand: chain 'B' and resid 313 through 316 Processing sheet with id= AG, first strand: chain 'B' and resid 369 through 372 removed outlier: 4.019A pdb=" N GLU B 369 " --> pdb=" O ARG B 391 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'B' and resid 398 through 400 removed outlier: 3.533A pdb=" N HIS B 400 " --> pdb=" O GLY B 419 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY B 419 " --> pdb=" O HIS B 400 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'B' and resid 2193 through 2199 removed outlier: 3.693A pdb=" N PHE B2210 " --> pdb=" O ALA B2194 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B2198 " --> pdb=" O GLU B2206 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'B' and resid 14 through 20 removed outlier: 5.698A pdb=" N SER B 16 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU B 222 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TYR B 18 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE B 220 " --> pdb=" O TYR B 18 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLU B 20 " --> pdb=" O TRP B 218 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TRP B 218 " --> pdb=" O GLU B 20 " (cutoff:3.500A) 2732 hydrogen bonds defined for protein. 8004 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: 24.78 Time building geometry restraints manager: 23.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 12156 1.31 - 1.44: 18828 1.44 - 1.57: 43203 1.57 - 1.69: 60 1.69 - 1.82: 660 Bond restraints: 74907 Sorted by residual: bond pdb=" C24 PLX A2806 " pdb=" O9 PLX A2806 " ideal model delta sigma weight residual 1.384 1.186 0.198 2.00e-02 2.50e+03 9.82e+01 bond pdb=" C24 PLX D2804 " pdb=" O9 PLX D2804 " ideal model delta sigma weight residual 1.384 1.187 0.197 2.00e-02 2.50e+03 9.71e+01 bond pdb=" C24 PLX A2804 " pdb=" O9 PLX A2804 " ideal model delta sigma weight residual 1.384 1.187 0.197 2.00e-02 2.50e+03 9.71e+01 bond pdb=" C24 PLX B2808 " pdb=" O9 PLX B2808 " ideal model delta sigma weight residual 1.384 1.187 0.197 2.00e-02 2.50e+03 9.71e+01 bond pdb=" C24 PLX A2802 " pdb=" O9 PLX A2802 " ideal model delta sigma weight residual 1.384 1.187 0.197 2.00e-02 2.50e+03 9.70e+01 ... (remaining 74902 not shown) Histogram of bond angle deviations from ideal: 97.95 - 105.68: 1059 105.68 - 113.41: 41456 113.41 - 121.14: 39178 121.14 - 128.87: 18595 128.87 - 136.59: 503 Bond angle restraints: 100791 Sorted by residual: angle pdb=" C TYR D2129 " pdb=" N MET D2130 " pdb=" CA MET D2130 " ideal model delta sigma weight residual 122.38 111.17 11.21 1.81e+00 3.05e-01 3.83e+01 angle pdb=" C TYR B2129 " pdb=" N MET B2130 " pdb=" CA MET B2130 " ideal model delta sigma weight residual 122.38 111.21 11.17 1.81e+00 3.05e-01 3.81e+01 angle pdb=" C TYR A2129 " pdb=" N MET A2130 " pdb=" CA MET A2130 " ideal model delta sigma weight residual 122.38 111.21 11.17 1.81e+00 3.05e-01 3.81e+01 angle pdb=" C TYR C2129 " pdb=" N MET C2130 " pdb=" CA MET C2130 " ideal model delta sigma weight residual 122.38 111.22 11.16 1.81e+00 3.05e-01 3.80e+01 angle pdb=" CA LEU B1403 " pdb=" CB LEU B1403 " pdb=" CG LEU B1403 " ideal model delta sigma weight residual 116.30 136.59 -20.29 3.50e+00 8.16e-02 3.36e+01 ... (remaining 100786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.51: 44839 33.51 - 67.01: 1392 67.01 - 100.52: 88 100.52 - 134.02: 36 134.02 - 167.53: 12 Dihedral angle restraints: 46367 sinusoidal: 19403 harmonic: 26964 Sorted by residual: dihedral pdb=" CA GLN A2263 " pdb=" C GLN A2263 " pdb=" N PRO A2264 " pdb=" CA PRO A2264 " ideal model delta harmonic sigma weight residual -180.00 -122.41 -57.59 0 5.00e+00 4.00e-02 1.33e+02 dihedral pdb=" CA GLN D2263 " pdb=" C GLN D2263 " pdb=" N PRO D2264 " pdb=" CA PRO D2264 " ideal model delta harmonic sigma weight residual -180.00 -122.41 -57.59 0 5.00e+00 4.00e-02 1.33e+02 dihedral pdb=" CA GLN B2263 " pdb=" C GLN B2263 " pdb=" N PRO B2264 " pdb=" CA PRO B2264 " ideal model delta harmonic sigma weight residual 180.00 -122.42 -57.58 0 5.00e+00 4.00e-02 1.33e+02 ... (remaining 46364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 9544 0.069 - 0.138: 1579 0.138 - 0.207: 215 0.207 - 0.275: 54 0.275 - 0.344: 12 Chirality restraints: 11404 Sorted by residual: chirality pdb=" CB ILE C 163 " pdb=" CA ILE C 163 " pdb=" CG1 ILE C 163 " pdb=" CG2 ILE C 163 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CB ILE D 163 " pdb=" CA ILE D 163 " pdb=" CG1 ILE D 163 " pdb=" CG2 ILE D 163 " 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 B 163 " pdb=" CA ILE B 163 " pdb=" CG1 ILE B 163 " pdb=" CG2 ILE B 163 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 11401 not shown) Planarity restraints: 12620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C2263 " 0.060 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO C2264 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO C2264 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO C2264 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D2263 " 0.060 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO D2264 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO D2264 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO D2264 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A2263 " 0.060 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO A2264 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO A2264 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A2264 " 0.049 5.00e-02 4.00e+02 ... (remaining 12617 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 63 2.32 - 2.97: 31305 2.97 - 3.61: 109922 3.61 - 4.26: 156085 4.26 - 4.90: 258065 Nonbonded interactions: 555440 Sorted by model distance: nonbonded pdb=" OD2 ASP D2570 " pdb=" NH2 ARG C2544 " model vdw 1.680 2.520 nonbonded pdb=" NH2 ARG A2544 " pdb=" OD2 ASP B2570 " model vdw 1.680 2.520 nonbonded pdb=" OD2 ASP C2570 " pdb=" NH2 ARG B2544 " model vdw 1.684 2.520 nonbonded pdb=" OD2 ASP A2570 " pdb=" NH2 ARG D2544 " model vdw 1.688 2.520 nonbonded pdb=" CE2 PHE D2462 " pdb=" O9 PLX D2806 " model vdw 1.840 2.672 ... (remaining 555435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 2739 or (resid 2801 through 2802 and (name C1 or \ name C10 or name C11 or name C12 or name C1A or name C1B or name C1C or name C2 \ or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name \ C3 or name C30 or name C31 or name C32 or name C4 or name C5 or name C6 or name \ C7 or name C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 \ or name O6 or name O7 or name O8 or name O9 or name P1 )) or resid 2803 or (res \ id 2804 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C1A \ or name C1B or name C1C or name C2 or name C24 or name C25 or name C26 or name \ C27 or name C28 or name C29 or name C3 or name C30 or name C31 or name C32 or na \ me C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name N1 or name \ O1 or name O2 or name O3 or name O4 or name O6 or name O7 or name O8 or name O9 \ or name P1 )) or (resid 2807 and (name C1 or name C10 or name C11 or name C12 or \ name C13 or name C1A or name C1B or name C1C or name C2 or name C24 or name C25 \ or name C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name \ C31 or name C32 or name C33 or name C4 or name C5 or name C6 or name C7 or name \ C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O6 \ or name O7 or name O8 or name O9 or name P1 )))) selection = (chain 'B' and (resid 6 through 2739 or (resid 2801 through 2802 and (name C1 or \ name C10 or name C11 or name C12 or name C1A or name C1B or name C1C or name C2 \ or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name \ C3 or name C30 or name C31 or name C32 or name C4 or name C5 or name C6 or name \ C7 or name C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 \ or name O6 or name O7 or name O8 or name O9 or name P1 )) or (resid 2803 and (n \ ame C1 or name C10 or name C11 or name C12 or name C13 or name C1A or name C1B o \ r name C1C or name C2 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C30 or name C31 or name C32 or name C33 or name \ C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name N1 or name O1 \ or name O2 or name O3 or name O4 or name O6 or name O7 or name O8 or name O9 or \ name P1 )) or (resid 2804 and (name C1 or name C10 or name C11 or name C12 or n \ ame C13 or name C1A or name C1B or name C1C or name C2 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name C3 \ 1 or name C32 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name N1 or name O1 or name O2 or name O3 or name O4 or name O6 or name O7 or \ name O8 or name O9 or name P1 )) or resid 2807)) selection = (chain 'C' and (resid 6 through 2739 or (resid 2801 through 2802 and (name C1 or \ name C10 or name C11 or name C12 or name C1A or name C1B or name C1C or name C2 \ or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name \ C3 or name C30 or name C31 or name C32 or name C4 or name C5 or name C6 or name \ C7 or name C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 \ or name O6 or name O7 or name O8 or name O9 or name P1 )) or resid 2803 or (res \ id 2804 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C1A \ or name C1B or name C1C or name C2 or name C24 or name C25 or name C26 or name \ C27 or name C28 or name C29 or name C3 or name C30 or name C31 or name C32 or na \ me C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name N1 or name \ O1 or name O2 or name O3 or name O4 or name O6 or name O7 or name O8 or name O9 \ or name P1 )) or (resid 2807 and (name C1 or name C10 or name C11 or name C12 or \ name C13 or name C1A or name C1B or name C1C or name C2 or name C24 or name C25 \ or name C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name \ C31 or name C32 or name C33 or name C4 or name C5 or name C6 or name C7 or name \ C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O6 \ or name O7 or name O8 or name O9 or name P1 )))) selection = (chain 'D' and (resid 6 through 2739 or (resid 2801 through 2802 and (name C1 or \ name C10 or name C11 or name C12 or name C1A or name C1B or name C1C or name C2 \ or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name \ C3 or name C30 or name C31 or name C32 or name C4 or name C5 or name C6 or name \ C7 or name C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 \ or name O6 or name O7 or name O8 or name O9 or name P1 )) or resid 2803 or (res \ id 2804 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C1A \ or name C1B or name C1C or name C2 or name C24 or name C25 or name C26 or name \ C27 or name C28 or name C29 or name C3 or name C30 or name C31 or name C32 or na \ me C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name N1 or name \ O1 or name O2 or name O3 or name O4 or name O6 or name O7 or name O8 or name O9 \ or name P1 )) or (resid 2807 and (name C1 or name C10 or name C11 or name C12 or \ name C13 or name C1A or name C1B or name C1C or name C2 or name C24 or name C25 \ or name C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name \ C31 or name C32 or name C33 or name C4 or name C5 or name C6 or name C7 or name \ C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O6 \ or name O7 or name O8 or name O9 or name P1 )))) } 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: 5.620 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: 0.050 Extract box with map and model: 19.700 Check model and map are aligned: 0.890 Set scattering table: 0.510 Process input model: 152.410 Find NCS groups from input model: 5.930 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 188.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.198 74907 Z= 0.460 Angle : 1.162 20.294 100791 Z= 0.551 Chirality : 0.055 0.344 11404 Planarity : 0.006 0.092 12620 Dihedral : 16.349 167.526 28799 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.84 % Favored : 88.90 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 4.62 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.08), residues: 9080 helix: -1.04 (0.07), residues: 4468 sheet: -1.36 (0.30), residues: 336 loop : -3.01 (0.08), residues: 4276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 807 HIS 0.012 0.001 HIS D 261 PHE 0.043 0.002 PHE D 781 TYR 0.020 0.002 TYR C 633 ARG 0.012 0.001 ARG D1632 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18160 Ramachandran restraints generated. 9080 Oldfield, 0 Emsley, 9080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18160 Ramachandran restraints generated. 9080 Oldfield, 0 Emsley, 9080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 8328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1098 time to evaluate : 6.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET A1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1098 average time/residue: 0.7791 time to fit residues: 1452.2260 Evaluate side-chains 550 residues out of total 8328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 550 time to evaluate : 6.519 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.8735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 916 random chunks: chunk 773 optimal weight: 3.9990 chunk 694 optimal weight: 0.0040 chunk 385 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 chunk 468 optimal weight: 0.9980 chunk 370 optimal weight: 6.9990 chunk 717 optimal weight: 0.8980 chunk 277 optimal weight: 1.9990 chunk 436 optimal weight: 5.9990 chunk 534 optimal weight: 0.0270 chunk 831 optimal weight: 7.9990 overall best weight: 0.7852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 GLN ** A 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1446 HIS ** A1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2171 GLN A2195 GLN ** A2729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 GLN ** D 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2195 GLN ** D2729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 GLN ** C 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1446 HIS ** C1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2195 GLN ** C2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 GLN ** B 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1446 HIS ** B1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2195 GLN ** B2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 74907 Z= 0.176 Angle : 0.704 14.387 100791 Z= 0.349 Chirality : 0.041 0.188 11404 Planarity : 0.005 0.082 12620 Dihedral : 13.777 169.084 11079 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.45 % Favored : 89.37 % Rotamer: Outliers : 1.19 % Allowed : 8.37 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 3.08 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.08), residues: 9080 helix: -0.23 (0.08), residues: 4524 sheet: -1.64 (0.26), residues: 440 loop : -2.89 (0.09), residues: 4116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 807 HIS 0.028 0.001 HIS B2409 PHE 0.030 0.001 PHE B 781 TYR 0.015 0.001 TYR A2656 ARG 0.006 0.000 ARG C 470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18160 Ramachandran restraints generated. 9080 Oldfield, 0 Emsley, 9080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18160 Ramachandran restraints generated. 9080 Oldfield, 0 Emsley, 9080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 8328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 589 time to evaluate : 7.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET A1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 41 residues processed: 648 average time/residue: 0.6736 time to fit residues: 765.8443 Evaluate side-chains 533 residues out of total 8328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 492 time to evaluate : 6.447 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.5376 time to fit residues: 51.7149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 916 random chunks: chunk 462 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 692 optimal weight: 4.9990 chunk 566 optimal weight: 8.9990 chunk 229 optimal weight: 6.9990 chunk 833 optimal weight: 9.9990 chunk 900 optimal weight: 1.9990 chunk 742 optimal weight: 7.9990 chunk 826 optimal weight: 10.0000 chunk 284 optimal weight: 6.9990 chunk 668 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 261 HIS A 467 GLN A 546 HIS A 600 HIS ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 HIS ** A1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1822 HIS ** A1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2722 GLN ** A2729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 HIS D 261 HIS D 467 GLN D 546 HIS D 600 HIS D 753 ASN ** D1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 HIS ** D1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1822 HIS ** D1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2171 GLN ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2726 GLN C 194 HIS C 261 HIS C 467 GLN C 546 HIS C 600 HIS ** C1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1238 HIS ** C1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1822 HIS ** C1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2171 GLN ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2722 GLN ** C2729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 HIS B 261 HIS B 467 GLN B 546 HIS B 600 HIS ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1238 HIS ** B1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1822 HIS ** B1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2171 GLN ** B2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2722 GLN ** B2729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 74907 Z= 0.480 Angle : 0.834 12.365 100791 Z= 0.427 Chirality : 0.047 0.234 11404 Planarity : 0.006 0.087 12620 Dihedral : 13.207 179.000 11079 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.54 % Favored : 88.19 % Rotamer: Outliers : 2.35 % Allowed : 13.74 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 3.08 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.09), residues: 9080 helix: -0.27 (0.08), residues: 4612 sheet: -1.82 (0.26), residues: 452 loop : -2.95 (0.09), residues: 4016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A2256 HIS 0.023 0.002 HIS B2409 PHE 0.030 0.003 PHE A2412 TYR 0.037 0.002 TYR A2656 ARG 0.007 0.001 ARG B 537 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18160 Ramachandran restraints generated. 9080 Oldfield, 0 Emsley, 9080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18160 Ramachandran restraints generated. 9080 Oldfield, 0 Emsley, 9080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 8328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 499 time to evaluate : 7.083 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET A1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 185 outliers final: 96 residues processed: 651 average time/residue: 0.7101 time to fit residues: 810.8886 Evaluate side-chains 526 residues out of total 8328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 430 time to evaluate : 7.367 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 0 residues processed: 96 average time/residue: 0.5974 time to fit residues: 114.0623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 916 random chunks: chunk 823 optimal weight: 9.9990 chunk 626 optimal weight: 5.9990 chunk 432 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 397 optimal weight: 0.0050 chunk 559 optimal weight: 0.3980 chunk 836 optimal weight: 5.9990 chunk 885 optimal weight: 9.9990 chunk 436 optimal weight: 3.9990 chunk 792 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 overall best weight: 1.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2623 ASN ** A2729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1081 GLN ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1189 GLN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2623 ASN D2726 GLN ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1189 GLN ** C1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2623 ASN C2726 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1189 GLN ** B1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2726 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 74907 Z= 0.242 Angle : 0.689 11.795 100791 Z= 0.349 Chirality : 0.042 0.199 11404 Planarity : 0.004 0.080 12620 Dihedral : 12.475 177.810 11079 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.02 % Favored : 88.74 % Rotamer: Outliers : 1.57 % Allowed : 16.65 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 3.08 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.09), residues: 9080 helix: 0.02 (0.08), residues: 4600 sheet: -1.90 (0.26), residues: 428 loop : -2.87 (0.09), residues: 4052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A2256 HIS 0.021 0.001 HIS B2409 PHE 0.026 0.001 PHE A1344 TYR 0.021 0.001 TYR B2656 ARG 0.005 0.000 ARG B1725 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18160 Ramachandran restraints generated. 9080 Oldfield, 0 Emsley, 9080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18160 Ramachandran restraints generated. 9080 Oldfield, 0 Emsley, 9080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 8328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 493 time to evaluate : 6.622 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET A1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 124 outliers final: 57 residues processed: 602 average time/residue: 0.6983 time to fit residues: 742.1910 Evaluate side-chains 524 residues out of total 8328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 467 time to evaluate : 6.411 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.5850 time to fit residues: 70.3995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 916 random chunks: chunk 737 optimal weight: 0.7980 chunk 502 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 659 optimal weight: 0.0980 chunk 365 optimal weight: 9.9990 chunk 755 optimal weight: 6.9990 chunk 612 optimal weight: 6.9990 chunk 1 optimal weight: 0.0670 chunk 452 optimal weight: 0.0570 chunk 794 optimal weight: 10.0000 chunk 223 optimal weight: 0.3980 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 GLN ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1189 GLN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2623 ASN ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN D 736 GLN ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2623 ASN ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN C 736 GLN ** C1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2623 ASN C2726 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2726 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 74907 Z= 0.143 Angle : 0.642 12.497 100791 Z= 0.320 Chirality : 0.040 0.188 11404 Planarity : 0.004 0.080 12620 Dihedral : 11.711 173.314 11079 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.61 % Favored : 89.22 % Rotamer: Outliers : 0.91 % Allowed : 17.51 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 3.08 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.09), residues: 9080 helix: 0.35 (0.08), residues: 4568 sheet: -1.78 (0.26), residues: 428 loop : -2.82 (0.09), residues: 4084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 700 HIS 0.020 0.001 HIS B2409 PHE 0.016 0.001 PHE B 864 TYR 0.033 0.001 TYR D1345 ARG 0.006 0.000 ARG D1348 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18160 Ramachandran restraints generated. 9080 Oldfield, 0 Emsley, 9080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18160 Ramachandran restraints generated. 9080 Oldfield, 0 Emsley, 9080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 8328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 536 time to evaluate : 6.535 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET A1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 19 residues processed: 596 average time/residue: 0.6779 time to fit residues: 713.7589 Evaluate side-chains 483 residues out of total 8328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 464 time to evaluate : 6.473 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.7246 time to fit residues: 32.2166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 916 random chunks: chunk 297 optimal weight: 3.9990 chunk 797 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 chunk 519 optimal weight: 0.8980 chunk 218 optimal weight: 1.9990 chunk 886 optimal weight: 10.0000 chunk 735 optimal weight: 1.9990 chunk 410 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 293 optimal weight: 10.0000 chunk 465 optimal weight: 20.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2167 ASN ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN D 103 ASN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2115 ASN ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2722 GLN B 48 ASN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 74907 Z= 0.251 Angle : 0.687 14.401 100791 Z= 0.345 Chirality : 0.042 0.202 11404 Planarity : 0.004 0.080 12620 Dihedral : 11.816 175.747 11079 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.67 % Favored : 88.09 % Rotamer: Outliers : 1.84 % Allowed : 18.66 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 3.08 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.09), residues: 9080 helix: 0.34 (0.08), residues: 4600 sheet: -1.67 (0.27), residues: 412 loop : -2.82 (0.09), residues: 4068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 700 HIS 0.020 0.001 HIS B2409 PHE 0.028 0.002 PHE D1344 TYR 0.021 0.001 TYR C2656 ARG 0.008 0.000 ARG D2670 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18160 Ramachandran restraints generated. 9080 Oldfield, 0 Emsley, 9080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18160 Ramachandran restraints generated. 9080 Oldfield, 0 Emsley, 9080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 8328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 470 time to evaluate : 6.601 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET A1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 145 outliers final: 63 residues processed: 572 average time/residue: 0.6796 time to fit residues: 692.2941 Evaluate side-chains 515 residues out of total 8328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 452 time to evaluate : 6.552 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.5992 time to fit residues: 79.2620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 916 random chunks: chunk 854 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 504 optimal weight: 3.9990 chunk 647 optimal weight: 2.9990 chunk 501 optimal weight: 0.0770 chunk 746 optimal weight: 0.7980 chunk 494 optimal weight: 0.9990 chunk 882 optimal weight: 0.8980 chunk 552 optimal weight: 5.9990 chunk 538 optimal weight: 0.0980 chunk 407 optimal weight: 0.2980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 GLN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1086 HIS ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2167 ASN ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN ** C1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 74907 Z= 0.147 Angle : 0.653 13.914 100791 Z= 0.320 Chirality : 0.040 0.273 11404 Planarity : 0.004 0.078 12620 Dihedral : 11.454 172.998 11079 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.46 % Favored : 89.36 % Rotamer: Outliers : 0.84 % Allowed : 19.41 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 3.08 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.09), residues: 9080 helix: 0.58 (0.08), residues: 4508 sheet: -1.76 (0.26), residues: 428 loop : -2.73 (0.09), residues: 4144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 700 HIS 0.019 0.001 HIS B2409 PHE 0.030 0.001 PHE D1344 TYR 0.027 0.001 TYR C1345 ARG 0.008 0.000 ARG D2670 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18160 Ramachandran restraints generated. 9080 Oldfield, 0 Emsley, 9080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18160 Ramachandran restraints generated. 9080 Oldfield, 0 Emsley, 9080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 8328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 497 time to evaluate : 6.501 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET A1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1526 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 66 outliers final: 13 residues processed: 543 average time/residue: 0.6911 time to fit residues: 667.1102 Evaluate side-chains 465 residues out of total 8328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 452 time to evaluate : 6.501 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.7528 time to fit residues: 25.2173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 916 random chunks: chunk 546 optimal weight: 5.9990 chunk 352 optimal weight: 10.0000 chunk 527 optimal weight: 0.0970 chunk 265 optimal weight: 5.9990 chunk 173 optimal weight: 0.0870 chunk 171 optimal weight: 1.9990 chunk 561 optimal weight: 8.9990 chunk 601 optimal weight: 0.9990 chunk 436 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 693 optimal weight: 1.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 HIS ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2115 ASN A2167 ASN ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 HIS ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2115 ASN ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 HIS ** C1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2167 ASN ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2115 ASN B2167 ASN ** B2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 74907 Z= 0.175 Angle : 0.663 13.159 100791 Z= 0.324 Chirality : 0.041 0.197 11404 Planarity : 0.004 0.079 12620 Dihedral : 11.398 173.293 11079 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.05 % Favored : 88.72 % Rotamer: Outliers : 1.03 % Allowed : 19.73 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 3.08 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.09), residues: 9080 helix: 0.57 (0.08), residues: 4560 sheet: -1.67 (0.26), residues: 428 loop : -2.74 (0.09), residues: 4092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 700 HIS 0.019 0.001 HIS B2409 PHE 0.034 0.001 PHE A1372 TYR 0.020 0.001 TYR A2656 ARG 0.012 0.000 ARG D2670 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18160 Ramachandran restraints generated. 9080 Oldfield, 0 Emsley, 9080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18160 Ramachandran restraints generated. 9080 Oldfield, 0 Emsley, 9080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 8328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 463 time to evaluate : 7.876 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET A1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1526 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 81 outliers final: 31 residues processed: 533 average time/residue: 0.6864 time to fit residues: 650.3689 Evaluate side-chains 476 residues out of total 8328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 445 time to evaluate : 6.386 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.5793 time to fit residues: 42.5520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 916 random chunks: chunk 803 optimal weight: 0.0770 chunk 845 optimal weight: 0.9980 chunk 771 optimal weight: 6.9990 chunk 822 optimal weight: 0.0770 chunk 495 optimal weight: 0.8980 chunk 358 optimal weight: 50.0000 chunk 646 optimal weight: 3.9990 chunk 252 optimal weight: 6.9990 chunk 743 optimal weight: 7.9990 chunk 778 optimal weight: 20.0000 chunk 819 optimal weight: 50.0000 overall best weight: 1.2098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2167 ASN ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** C1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2167 ASN ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2167 ASN ** B2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 74907 Z= 0.186 Angle : 0.677 13.697 100791 Z= 0.330 Chirality : 0.041 0.203 11404 Planarity : 0.004 0.077 12620 Dihedral : 11.410 179.769 11079 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.85 % Favored : 88.92 % Rotamer: Outliers : 0.49 % Allowed : 20.17 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 3.08 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.09), residues: 9080 helix: 0.65 (0.08), residues: 4536 sheet: -1.71 (0.26), residues: 428 loop : -2.71 (0.09), residues: 4116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 700 HIS 0.019 0.001 HIS B2409 PHE 0.034 0.001 PHE C1344 TYR 0.021 0.001 TYR A2656 ARG 0.013 0.000 ARG D2670 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18160 Ramachandran restraints generated. 9080 Oldfield, 0 Emsley, 9080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18160 Ramachandran restraints generated. 9080 Oldfield, 0 Emsley, 9080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 8328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 460 time to evaluate : 6.710 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET A1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1526 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 39 outliers final: 14 residues processed: 489 average time/residue: 0.6964 time to fit residues: 605.0854 Evaluate side-chains 456 residues out of total 8328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 442 time to evaluate : 6.926 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.5755 time to fit residues: 24.3735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 916 random chunks: chunk 540 optimal weight: 3.9990 chunk 869 optimal weight: 5.9990 chunk 531 optimal weight: 4.9990 chunk 412 optimal weight: 2.9990 chunk 604 optimal weight: 5.9990 chunk 912 optimal weight: 30.0000 chunk 839 optimal weight: 0.8980 chunk 726 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 561 optimal weight: 5.9990 chunk 445 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2167 ASN ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 602 ASN ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1279 ASN ** B1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1993 ASN ** B2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 74907 Z= 0.316 Angle : 0.755 13.670 100791 Z= 0.374 Chirality : 0.044 0.239 11404 Planarity : 0.004 0.081 12620 Dihedral : 11.815 179.132 11079 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.97 % Favored : 87.79 % Rotamer: Outliers : 0.56 % Allowed : 20.35 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 3.08 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.09), residues: 9080 helix: 0.40 (0.08), residues: 4624 sheet: -1.63 (0.27), residues: 412 loop : -2.78 (0.09), residues: 4044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A2639 HIS 0.020 0.001 HIS B2409 PHE 0.031 0.002 PHE B1372 TYR 0.030 0.002 TYR C2656 ARG 0.009 0.001 ARG A2233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18160 Ramachandran restraints generated. 9080 Oldfield, 0 Emsley, 9080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18160 Ramachandran restraints generated. 9080 Oldfield, 0 Emsley, 9080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 8328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 446 time to evaluate : 6.426 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET A1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1526 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET D1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1526 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET C1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1526 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET B1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1526 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 44 outliers final: 14 residues processed: 479 average time/residue: 0.6978 time to fit residues: 594.6082 Evaluate side-chains 446 residues out of total 8328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 432 time to evaluate : 6.548 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.5709 time to fit residues: 24.1925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 916 random chunks: chunk 577 optimal weight: 0.0050 chunk 774 optimal weight: 0.9990 chunk 222 optimal weight: 1.9990 chunk 670 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 727 optimal weight: 0.9990 chunk 304 optimal weight: 0.9990 chunk 747 optimal weight: 1.9990 chunk 92 optimal weight: 0.0980 chunk 134 optimal weight: 0.0870 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 GLN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 GLN ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2167 ASN ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS B 736 GLN ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2167 ASN ** B2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.118226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.082704 restraints weight = 228070.505| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 4.24 r_work: 0.3380 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 74907 Z= 0.154 Angle : 0.685 13.152 100791 Z= 0.332 Chirality : 0.041 0.211 11404 Planarity : 0.004 0.077 12620 Dihedral : 11.180 176.083 11079 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.53 % Favored : 89.30 % Rotamer: Outliers : 0.16 % Allowed : 20.78 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 3.08 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.09), residues: 9080 helix: 0.67 (0.08), residues: 4512 sheet: -1.59 (0.26), residues: 468 loop : -2.65 (0.09), residues: 4100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2256 HIS 0.019 0.001 HIS B2409 PHE 0.021 0.001 PHE A2612 TYR 0.014 0.001 TYR B2656 ARG 0.010 0.000 ARG D1603 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15346.36 seconds wall clock time: 272 minutes 30.36 seconds (16350.36 seconds total)