Starting phenix.real_space_refine on Thu Mar 21 00:40:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8set_40428/03_2024/8set_40428_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8set_40428/03_2024/8set_40428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8set_40428/03_2024/8set_40428.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8set_40428/03_2024/8set_40428.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8set_40428/03_2024/8set_40428_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8set_40428/03_2024/8set_40428_updated.pdb" } resolution = 3.42 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= -0.001 sd= 0.026 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 4 5.49 5 S 960 5.16 5 C 90980 2.51 5 N 24692 2.21 5 O 26408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 5032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 5032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 5032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 5032": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.45s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 143048 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 34921 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4378, 34858 Classifications: {'peptide': 4378} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4161} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 4378, 34858 Classifications: {'peptide': 4378} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4161} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 35570 Chain: "B" Number of atoms: 34921 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4378, 34858 Classifications: {'peptide': 4378} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4161} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 4378, 34858 Classifications: {'peptide': 4378} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4161} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 35570 Chain: "C" Number of atoms: 34921 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4378, 34858 Classifications: {'peptide': 4378} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4161} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 4378, 34858 Classifications: {'peptide': 4378} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4161} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 35570 Chain: "D" Number of atoms: 34921 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4378, 34858 Classifications: {'peptide': 4378} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4161} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 4378, 34858 Classifications: {'peptide': 4378} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4161} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 35570 Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 34247 SG CYS A4958 175.741 201.808 88.318 1.00138.18 S ATOM 34272 SG CYS A4961 178.033 201.953 91.102 1.00139.25 S ATOM 69168 SG CYS B4958 179.325 175.769 88.313 1.00138.18 S ATOM 69193 SG CYS B4961 179.184 178.060 91.098 1.00139.25 S ATOM A035L SG CYS C4958 205.479 179.325 88.312 1.00138.18 S ATOM A036A SG CYS C4961 203.188 179.184 91.097 1.00139.25 S ATOM A0U3M SG CYS D4958 201.923 205.479 88.313 1.00138.18 S ATOM A0U4B SG CYS D4961 202.064 203.188 91.098 1.00139.25 S Time building chain proxies: 100.18, per 1000 atoms: 0.70 Number of scatterers: 143048 At special positions: 0 Unit cell: (382.536, 382.536, 211.232, 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 960 16.00 P 4 15.00 O 26408 8.00 N 24692 7.00 C 90980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A3170 " - pdb=" SG CYS A3240 " distance=2.03 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.03 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B3170 " - pdb=" SG CYS B3240 " distance=2.03 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " distance=2.03 Simple disulfide: pdb=" SG CYS C 230 " - pdb=" SG CYS C 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C3170 " - pdb=" SG CYS C3240 " distance=2.03 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " distance=2.03 Simple disulfide: pdb=" SG CYS D 230 " - pdb=" SG CYS D 253 " distance=2.03 Simple disulfide: pdb=" SG CYS D3170 " - pdb=" SG CYS D3240 " distance=2.03 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 44.17 Conformation dependent library (CDL) restraints added in 37.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5102 " pdb="ZN ZN A5102 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5102 " - pdb=" ND1 HIS A4983 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4958 " pdb=" ZN B5102 " pdb="ZN ZN B5102 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5102 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4958 " pdb=" ZN C5102 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5102 " - pdb=" ND1 HIS C4983 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4958 " pdb=" ZN D5102 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5102 " - pdb=" ND1 HIS D4983 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4958 " Number of angles added : 4 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 33688 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 700 helices and 80 sheets defined 58.3% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 42.71 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 4.531A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N CYS A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 66' Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 308 through 313 removed outlier: 6.396A pdb=" N THR A 312 " --> pdb=" O HIS A 308 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 313 " --> pdb=" O THR A 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 308 through 313' Processing helix chain 'A' and resid 364 through 370 Processing helix chain 'A' and resid 394 through 422 removed outlier: 3.554A pdb=" N HIS A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 453 Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.973A pdb=" N GLN A 465 " --> pdb=" O HIS A 461 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 removed outlier: 3.668A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN A 489 " --> pdb=" O SER A 485 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 491 " --> pdb=" O VAL A 487 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.871A pdb=" N TYR A 506 " --> pdb=" O HIS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 531 removed outlier: 3.562A pdb=" N GLU A 513 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 544 removed outlier: 3.579A pdb=" N LEU A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE A 540 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER A 541 " --> pdb=" O CYS A 537 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR A 542 " --> pdb=" O ALA A 538 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 551 Processing helix chain 'A' and resid 556 through 571 removed outlier: 3.625A pdb=" N ILE A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 570 " --> pdb=" O CYS A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 removed outlier: 4.083A pdb=" N ASN A 576 " --> pdb=" O PRO A 572 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLN A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 593 removed outlier: 3.724A pdb=" N LEU A 590 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 609 removed outlier: 3.759A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N CYS A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 629 removed outlier: 3.673A pdb=" N ASP A 619 " --> pdb=" O ARG A 615 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Proline residue: A 627 - end of helix Processing helix chain 'A' and resid 810 through 815 removed outlier: 4.790A pdb=" N ALA A 814 " --> pdb=" O PRO A 810 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL A 815 " --> pdb=" O CYS A 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 810 through 815' Processing helix chain 'A' and resid 847 through 853 removed outlier: 3.756A pdb=" N PHE A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 852 " --> pdb=" O HIS A 848 " (cutoff:3.500A) Proline residue: A 853 - end of helix No H-bonds generated for 'chain 'A' and resid 847 through 853' Processing helix chain 'A' and resid 864 through 885 removed outlier: 3.529A pdb=" N ILE A 870 " --> pdb=" O HIS A 866 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLU A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS A 873 " --> pdb=" O ARG A 869 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 874 " --> pdb=" O ILE A 870 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA A 875 " --> pdb=" O ARG A 871 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE A 878 " --> pdb=" O LEU A 874 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLU A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU A 881 " --> pdb=" O ASN A 877 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TRP A 882 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ALA A 883 " --> pdb=" O HIS A 879 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.786A pdb=" N LEU A 913 " --> pdb=" O ASN A 909 " (cutoff:3.500A) Proline residue: A 914 - end of helix No H-bonds generated for 'chain 'A' and resid 909 through 914' Processing helix chain 'A' and resid 915 through 936 Processing helix chain 'A' and resid 945 through 950 removed outlier: 3.970A pdb=" N ASN A 949 " --> pdb=" O LYS A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1004 removed outlier: 3.556A pdb=" N VAL A 995 " --> pdb=" O ASN A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1048 removed outlier: 4.066A pdb=" N SER A1038 " --> pdb=" O SER A1034 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A1039 " --> pdb=" O ASN A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1073 removed outlier: 4.593A pdb=" N ARG A1071 " --> pdb=" O SER A1067 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL A1072 " --> pdb=" O ARG A1068 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ARG A1073 " --> pdb=" O TRP A1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1067 through 1073' Processing helix chain 'A' and resid 1217 through 1222 removed outlier: 7.229A pdb=" N GLU A1221 " --> pdb=" O CYS A1217 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY A1222 " --> pdb=" O GLY A1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1217 through 1222' Processing helix chain 'A' and resid 1423 through 1430 removed outlier: 3.620A pdb=" N LEU A1428 " --> pdb=" O PRO A1424 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN A1429 " --> pdb=" O GLU A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1444 through 1449 removed outlier: 4.356A pdb=" N VAL A1448 " --> pdb=" O GLU A1444 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TRP A1449 " --> pdb=" O PRO A1445 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1444 through 1449' Processing helix chain 'A' and resid 1496 through 1501 removed outlier: 4.114A pdb=" N PHE A1500 " --> pdb=" O TRP A1496 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A1501 " --> pdb=" O GLY A1497 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1496 through 1501' Processing helix chain 'A' and resid 1574 through 1580 removed outlier: 4.189A pdb=" N ALA A1578 " --> pdb=" O PRO A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1657 removed outlier: 4.257A pdb=" N LEU A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER A1654 " --> pdb=" O ILE A1650 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLU A1655 " --> pdb=" O LEU A1651 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A1657 " --> pdb=" O LEU A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1675 removed outlier: 3.879A pdb=" N PHE A1662 " --> pdb=" O ASP A1658 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS A1674 " --> pdb=" O TYR A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1689 removed outlier: 3.666A pdb=" N ALA A1684 " --> pdb=" O ARG A1680 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N CYS A1686 " --> pdb=" O ALA A1682 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER A1687 " --> pdb=" O HIS A1683 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N HIS A1688 " --> pdb=" O ALA A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1690 through 1700 removed outlier: 3.538A pdb=" N LEU A1694 " --> pdb=" O ASP A1690 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A1699 " --> pdb=" O LEU A1695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1719 Processing helix chain 'A' and resid 1720 through 1734 removed outlier: 3.502A pdb=" N MET A1730 " --> pdb=" O SER A1726 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER A1732 " --> pdb=" O ARG A1728 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLU A1733 " --> pdb=" O SER A1729 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N TYR A1734 " --> pdb=" O MET A1730 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1745 removed outlier: 3.692A pdb=" N ILE A1745 " --> pdb=" O GLU A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1825 removed outlier: 3.637A pdb=" N ASP A1809 " --> pdb=" O GLU A1805 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS A1825 " --> pdb=" O ASP A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1833 through 1852 Proline residue: A1840 - end of helix Processing helix chain 'A' and resid 1855 through 1867 Processing helix chain 'A' and resid 1934 through 1987 removed outlier: 3.865A pdb=" N GLN A1938 " --> pdb=" O SER A1934 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP A1967 " --> pdb=" O GLU A1963 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A1968 " --> pdb=" O ARG A1964 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE A1984 " --> pdb=" O LEU A1980 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N THR A1985 " --> pdb=" O MET A1981 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N MET A1986 " --> pdb=" O ARG A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1990 through 2001 removed outlier: 4.594A pdb=" N ARG A1994 " --> pdb=" O GLU A1990 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLU A1997 " --> pdb=" O ARG A1993 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N PHE A1998 " --> pdb=" O ARG A1994 " (cutoff:3.500A) Proline residue: A2001 - end of helix Processing helix chain 'A' and resid 2002 through 2011 removed outlier: 3.556A pdb=" N ASN A2007 " --> pdb=" O GLN A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2017 through 2022 removed outlier: 4.188A pdb=" N CYS A2021 " --> pdb=" O ASP A2017 " (cutoff:3.500A) Proline residue: A2022 - end of helix No H-bonds generated for 'chain 'A' and resid 2017 through 2022' Processing helix chain 'A' and resid 2024 through 2043 Processing helix chain 'A' and resid 2093 through 2109 removed outlier: 3.666A pdb=" N ASP A2109 " --> pdb=" O TRP A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2130 removed outlier: 3.972A pdb=" N GLY A2130 " --> pdb=" O ARG A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2131 through 2141 Proline residue: A2139 - end of helix Processing helix chain 'A' and resid 2145 through 2169 removed outlier: 4.184A pdb=" N VAL A2149 " --> pdb=" O SER A2145 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU A2150 " --> pdb=" O PRO A2146 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP A2151 " --> pdb=" O SER A2147 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A2154 " --> pdb=" O GLU A2150 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A2166 " --> pdb=" O ILE A2162 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE A2167 " --> pdb=" O ARG A2163 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL A2168 " --> pdb=" O SER A2164 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLN A2169 " --> pdb=" O LEU A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2171 through 2188 removed outlier: 3.578A pdb=" N LEU A2177 " --> pdb=" O GLN A2173 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET A2178 " --> pdb=" O GLU A2174 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A2179 " --> pdb=" O GLU A2175 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2194 Processing helix chain 'A' and resid 2195 through 2219 removed outlier: 5.358A pdb=" N MET A2203 " --> pdb=" O ARG A2199 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N HIS A2204 " --> pdb=" O ALA A2200 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU A2205 " --> pdb=" O LEU A2201 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A2206 " --> pdb=" O GLY A2202 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY A2218 " --> pdb=" O VAL A2214 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A2219 " --> pdb=" O LEU A2215 " (cutoff:3.500A) Processing helix chain 'A' and resid 2225 through 2244 removed outlier: 3.649A pdb=" N VAL A2229 " --> pdb=" O PHE A2225 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A2241 " --> pdb=" O CYS A2237 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A2242 " --> pdb=" O TYR A2238 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER A2243 " --> pdb=" O PHE A2239 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ARG A2244 " --> pdb=" O CYS A2240 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2255 removed outlier: 3.803A pdb=" N ASP A2252 " --> pdb=" O ARG A2248 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS A2253 " --> pdb=" O SER A2249 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU A2254 " --> pdb=" O MET A2250 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N SER A2255 " --> pdb=" O PHE A2251 " (cutoff:3.500A) Processing helix chain 'A' and resid 2256 through 2262 removed outlier: 3.598A pdb=" N ASN A2260 " --> pdb=" O TYR A2256 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A2262 " --> pdb=" O LEU A2258 " (cutoff:3.500A) Processing helix chain 'A' and resid 2271 through 2281 removed outlier: 3.543A pdb=" N VAL A2275 " --> pdb=" O THR A2271 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A2280 " --> pdb=" O ALA A2276 " (cutoff:3.500A) Processing helix chain 'A' and resid 2283 through 2290 Processing helix chain 'A' and resid 2291 through 2308 removed outlier: 3.808A pdb=" N LEU A2295 " --> pdb=" O GLN A2291 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2317 removed outlier: 3.545A pdb=" N LYS A2316 " --> pdb=" O MET A2312 " (cutoff:3.500A) Processing helix chain 'A' and resid 2324 through 2340 removed outlier: 3.608A pdb=" N PHE A2334 " --> pdb=" O ARG A2330 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2361 removed outlier: 3.713A pdb=" N VAL A2352 " --> pdb=" O GLU A2348 " (cutoff:3.500A) Proline residue: A2361 - end of helix Processing helix chain 'A' and resid 2375 through 2390 removed outlier: 3.824A pdb=" N ILE A2380 " --> pdb=" O LEU A2376 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A2381 " --> pdb=" O LEU A2377 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU A2382 " --> pdb=" O ALA A2378 " (cutoff:3.500A) Proline residue: A2390 - end of helix Processing helix chain 'A' and resid 2417 through 2437 removed outlier: 3.714A pdb=" N TYR A2426 " --> pdb=" O ILE A2422 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA A2427 " --> pdb=" O MET A2423 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A2437 " --> pdb=" O LEU A2433 " (cutoff:3.500A) Processing helix chain 'A' and resid 2439 through 2446 Processing helix chain 'A' and resid 2447 through 2462 Proline residue: A2462 - end of helix Processing helix chain 'A' and resid 2463 through 2472 Processing helix chain 'A' and resid 2495 through 2509 removed outlier: 4.347A pdb=" N LYS A2499 " --> pdb=" O VAL A2495 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A2501 " --> pdb=" O ASP A2497 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET A2502 " --> pdb=" O HIS A2498 " (cutoff:3.500A) Processing helix chain 'A' and resid 2514 through 2525 removed outlier: 4.435A pdb=" N VAL A2524 " --> pdb=" O HIS A2520 " (cutoff:3.500A) Processing helix chain 'A' and resid 2526 through 2537 Processing helix chain 'A' and resid 2539 through 2545 removed outlier: 5.531A pdb=" N THR A2543 " --> pdb=" O ALA A2539 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR A2544 " --> pdb=" O THR A2540 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLU A2545 " --> pdb=" O PHE A2541 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2539 through 2545' Processing helix chain 'A' and resid 2546 through 2566 removed outlier: 3.887A pdb=" N CYS A2555 " --> pdb=" O ASN A2551 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU A2559 " --> pdb=" O CYS A2555 " (cutoff:3.500A) Proline residue: A2560 - end of helix Processing helix chain 'A' and resid 2568 through 2573 removed outlier: 5.411A pdb=" N THR A2572 " --> pdb=" O LEU A2568 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLU A2573 " --> pdb=" O PHE A2569 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2568 through 2573' Processing helix chain 'A' and resid 2575 through 2593 removed outlier: 3.799A pdb=" N GLY A2592 " --> pdb=" O ARG A2588 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ARG A2593 " --> pdb=" O LEU A2589 " (cutoff:3.500A) Processing helix chain 'A' and resid 2596 through 2614 removed outlier: 3.730A pdb=" N TYR A2613 " --> pdb=" O ALA A2609 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A2614 " --> pdb=" O LEU A2610 " (cutoff:3.500A) Processing helix chain 'A' and resid 2615 through 2630 removed outlier: 4.064A pdb=" N LEU A2619 " --> pdb=" O ARG A2615 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN A2620 " --> pdb=" O PRO A2616 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N HIS A2621 " --> pdb=" O SER A2617 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LEU A2622 " --> pdb=" O MET A2618 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A2628 " --> pdb=" O ARG A2624 " (cutoff:3.500A) Processing helix chain 'A' and resid 2636 through 2652 Proline residue: A2640 - end of helix Processing helix chain 'A' and resid 2668 through 2689 removed outlier: 6.919A pdb=" N LEU A2672 " --> pdb=" O SER A2668 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N HIS A2673 " --> pdb=" O GLU A2669 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP A2680 " --> pdb=" O ARG A2676 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A2688 " --> pdb=" O ASP A2684 " (cutoff:3.500A) Processing helix chain 'A' and resid 2693 through 2711 removed outlier: 3.797A pdb=" N MET A2698 " --> pdb=" O GLU A2694 " (cutoff:3.500A) Proline residue: A2701 - end of helix Proline residue: A2711 - end of helix Processing helix chain 'A' and resid 2741 through 2746 removed outlier: 4.599A pdb=" N VAL A2745 " --> pdb=" O GLU A2741 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE A2746 " --> pdb=" O THR A2742 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2741 through 2746' Processing helix chain 'A' and resid 2751 through 2774 removed outlier: 3.874A pdb=" N LYS A2757 " --> pdb=" O SER A2753 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN A2774 " --> pdb=" O LYS A2770 " (cutoff:3.500A) Processing helix chain 'A' and resid 2799 through 2820 removed outlier: 3.537A pdb=" N GLU A2803 " --> pdb=" O GLU A2799 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE A2804 " --> pdb=" O LYS A2800 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG A2806 " --> pdb=" O LYS A2802 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TRP A2807 " --> pdb=" O GLU A2803 " (cutoff:3.500A) Proline residue: A2808 - end of helix removed outlier: 5.286A pdb=" N GLU A2820 " --> pdb=" O MET A2816 " (cutoff:3.500A) Processing helix chain 'A' and resid 2868 through 2895 removed outlier: 4.209A pdb=" N GLU A2893 " --> pdb=" O LYS A2889 " (cutoff:3.500A) Processing helix chain 'A' and resid 2907 through 2912 removed outlier: 6.080A pdb=" N THR A2912 " --> pdb=" O TYR A2908 " (cutoff:3.500A) Processing helix chain 'A' and resid 2913 through 2934 removed outlier: 3.738A pdb=" N ALA A2917 " --> pdb=" O ALA A2913 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ARG A2918 " --> pdb=" O LYS A2914 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ASP A2919 " --> pdb=" O GLU A2915 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A2922 " --> pdb=" O ARG A2918 " (cutoff:3.500A) Processing helix chain 'A' and resid 2949 through 2982 removed outlier: 5.717A pdb=" N PHE A2955 " --> pdb=" O ILE A2951 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA A2956 " --> pdb=" O GLU A2952 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE A2957 " --> pdb=" O LYS A2953 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A2969 " --> pdb=" O ARG A2965 " (cutoff:3.500A) Processing helix chain 'A' and resid 2991 through 3014 removed outlier: 3.611A pdb=" N LEU A3002 " --> pdb=" O PHE A2998 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU A3003 " --> pdb=" O ALA A2999 " (cutoff:3.500A) Proline residue: A3004 - end of helix removed outlier: 3.806A pdb=" N THR A3011 " --> pdb=" O ASN A3007 " (cutoff:3.500A) Processing helix chain 'A' and resid 3032 through 3051 removed outlier: 3.812A pdb=" N LEU A3042 " --> pdb=" O MET A3038 " (cutoff:3.500A) Processing helix chain 'A' and resid 3053 through 3058 removed outlier: 4.086A pdb=" N PHE A3057 " --> pdb=" O ARG A3053 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY A3058 " --> pdb=" O VAL A3054 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3053 through 3058' Processing helix chain 'A' and resid 3060 through 3075 Processing helix chain 'A' and resid 3076 through 3083 removed outlier: 3.778A pdb=" N VAL A3080 " --> pdb=" O ASP A3076 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET A3081 " --> pdb=" O ALA A3077 " (cutoff:3.500A) Processing helix chain 'A' and resid 3085 through 3112 removed outlier: 3.537A pdb=" N PHE A3095 " --> pdb=" O GLY A3091 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A3096 " --> pdb=" O LEU A3092 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A3108 " --> pdb=" O GLU A3104 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU A3112 " --> pdb=" O GLU A3108 " (cutoff:3.500A) Processing helix chain 'A' and resid 3123 through 3151 removed outlier: 3.632A pdb=" N VAL A3134 " --> pdb=" O THR A3130 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU A3137 " --> pdb=" O THR A3133 " (cutoff:3.500A) Proline residue: A3138 - end of helix removed outlier: 3.707A pdb=" N GLN A3149 " --> pdb=" O GLN A3145 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS A3150 " --> pdb=" O HIS A3146 " (cutoff:3.500A) Processing helix chain 'A' and resid 3159 through 3175 removed outlier: 5.330A pdb=" N VAL A3163 " --> pdb=" O ASP A3159 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU A3175 " --> pdb=" O SER A3171 " (cutoff:3.500A) Processing helix chain 'A' and resid 3180 through 3201 Proline residue: A3188 - end of helix Processing helix chain 'A' and resid 3217 through 3222 Processing helix chain 'A' and resid 3226 through 3231 removed outlier: 6.672A pdb=" N LEU A3230 " --> pdb=" O GLU A3226 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLY A3231 " --> pdb=" O ARG A3227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3226 through 3231' Processing helix chain 'A' and resid 3235 through 3241 removed outlier: 3.540A pdb=" N MET A3239 " --> pdb=" O SER A3235 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N CYS A3240 " --> pdb=" O VAL A3236 " (cutoff:3.500A) Proline residue: A3241 - end of helix No H-bonds generated for 'chain 'A' and resid 3235 through 3241' Processing helix chain 'A' and resid 3245 through 3260 Processing helix chain 'A' and resid 3262 through 3267 Proline residue: A3267 - end of helix Processing helix chain 'A' and resid 3268 through 3288 removed outlier: 4.359A pdb=" N LEU A3274 " --> pdb=" O ILE A3270 " (cutoff:3.500A) Proline residue: A3275 - end of helix Proline residue: A3282 - end of helix removed outlier: 4.343A pdb=" N GLU A3286 " --> pdb=" O PRO A3282 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG A3287 " --> pdb=" O ARG A3283 " (cutoff:3.500A) Processing helix chain 'A' and resid 3308 through 3327 removed outlier: 3.770A pdb=" N LEU A3312 " --> pdb=" O THR A3308 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A3319 " --> pdb=" O LEU A3315 " (cutoff:3.500A) Processing helix chain 'A' and resid 3332 through 3343 removed outlier: 5.756A pdb=" N LYS A3336 " --> pdb=" O ALA A3332 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG A3337 " --> pdb=" O THR A3333 " (cutoff:3.500A) Processing helix chain 'A' and resid 3344 through 3350 removed outlier: 4.729A pdb=" N ARG A3348 " --> pdb=" O PRO A3344 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ALA A3349 " --> pdb=" O ILE A3345 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG A3350 " --> pdb=" O VAL A3346 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3344 through 3350' Processing helix chain 'A' and resid 3351 through 3381 removed outlier: 4.699A pdb=" N HIS A3355 " --> pdb=" O PRO A3351 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A3358 " --> pdb=" O LEU A3354 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ILE A3359 " --> pdb=" O HIS A3355 " (cutoff:3.500A) Proline residue: A3360 - end of helix removed outlier: 3.611A pdb=" N GLN A3378 " --> pdb=" O ALA A3374 " (cutoff:3.500A) Processing helix chain 'A' and resid 3389 through 3413 removed outlier: 6.543A pdb=" N LEU A3393 " --> pdb=" O GLU A3389 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A3407 " --> pdb=" O ARG A3403 " (cutoff:3.500A) Proline residue: A3410 - end of helix Processing helix chain 'A' and resid 3419 through 3426 Processing helix chain 'A' and resid 3428 through 3448 Processing helix chain 'A' and resid 3449 through 3463 removed outlier: 3.755A pdb=" N GLN A3456 " --> pdb=" O LYS A3452 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN A3457 " --> pdb=" O ARG A3453 " (cutoff:3.500A) Processing helix chain 'A' and resid 3466 through 3478 removed outlier: 4.631A pdb=" N LEU A3470 " --> pdb=" O ASN A3466 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP A3473 " --> pdb=" O PHE A3469 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N SER A3474 " --> pdb=" O LEU A3470 " (cutoff:3.500A) Processing helix chain 'A' and resid 3508 through 3526 removed outlier: 3.941A pdb=" N LYS A3516 " --> pdb=" O ALA A3512 " (cutoff:3.500A) Proline residue: A3519 - end of helix removed outlier: 3.951A pdb=" N MET A3524 " --> pdb=" O ILE A3520 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N CYS A3525 " --> pdb=" O GLY A3521 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ALA A3526 " --> pdb=" O LEU A3522 " (cutoff:3.500A) Processing helix chain 'A' and resid 3529 through 3543 removed outlier: 3.572A pdb=" N LEU A3535 " --> pdb=" O ASP A3531 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A3543 " --> pdb=" O ARG A3539 " (cutoff:3.500A) Processing helix chain 'A' and resid 3545 through 3557 Processing helix chain 'A' and resid 3566 through 3579 removed outlier: 3.604A pdb=" N ARG A3570 " --> pdb=" O SER A3566 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TRP A3571 " --> pdb=" O PRO A3567 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN A3572 " --> pdb=" O SER A3568 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU A3579 " --> pdb=" O LEU A3575 " (cutoff:3.500A) Processing helix chain 'A' and resid 3588 through 3612 removed outlier: 3.757A pdb=" N HIS A3605 " --> pdb=" O ALA A3601 " (cutoff:3.500A) Proline residue: A3612 - end of helix Processing helix chain 'A' and resid 3628 through 3638 removed outlier: 4.032A pdb=" N VAL A3632 " --> pdb=" O ARG A3628 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A3633 " --> pdb=" O ARG A3629 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3665 removed outlier: 3.711A pdb=" N GLU A3655 " --> pdb=" O ASN A3651 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU A3663 " --> pdb=" O ALA A3659 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR A3664 " --> pdb=" O ALA A3660 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A3665 " --> pdb=" O TRP A3661 " (cutoff:3.500A) Processing helix chain 'A' and resid 3669 through 3679 Processing helix chain 'A' and resid 3696 through 3711 Processing helix chain 'A' and resid 3719 through 3735 removed outlier: 3.831A pdb=" N CYS A3733 " --> pdb=" O MET A3729 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N HIS A3734 " --> pdb=" O ALA A3730 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU A3735 " --> pdb=" O LYS A3731 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3772 removed outlier: 3.632A pdb=" N TYR A3765 " --> pdb=" O GLN A3761 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A3770 " --> pdb=" O GLN A3766 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A3772 " --> pdb=" O SER A3768 " (cutoff:3.500A) Processing helix chain 'A' and resid 3774 through 3787 removed outlier: 4.018A pdb=" N LYS A3787 " --> pdb=" O ILE A3783 " (cutoff:3.500A) Processing helix chain 'A' and resid 3791 through 3806 Processing helix chain 'A' and resid 3809 through 3824 Processing helix chain 'A' and resid 3825 through 3839 removed outlier: 4.989A pdb=" N PHE A3829 " --> pdb=" O GLU A3825 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3857 Processing helix chain 'A' and resid 3877 through 3893 removed outlier: 3.562A pdb=" N CYS A3892 " --> pdb=" O LEU A3888 " (cutoff:3.500A) Processing helix chain 'A' and resid 3896 through 3905 Processing helix chain 'A' and resid 3914 through 3939 removed outlier: 3.638A pdb=" N TYR A3937 " --> pdb=" O PHE A3933 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY A3939 " --> pdb=" O TRP A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3944 through 3970 removed outlier: 3.556A pdb=" N ILE A3969 " --> pdb=" O LEU A3965 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3983 Processing helix chain 'A' and resid 3984 through 4007 removed outlier: 3.932A pdb=" N ALA A3988 " --> pdb=" O ARG A3984 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS A3998 " --> pdb=" O HIS A3994 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A4005 " --> pdb=" O MET A4001 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASP A4006 " --> pdb=" O LYS A4002 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N SER A4007 " --> pdb=" O LEU A4003 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4032 removed outlier: 3.528A pdb=" N GLU A4015 " --> pdb=" O GLU A4011 " (cutoff:3.500A) Processing helix chain 'A' and resid 4038 through 4052 Processing helix chain 'A' and resid 4053 through 4072 removed outlier: 3.646A pdb=" N MET A4064 " --> pdb=" O LYS A4060 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A4070 " --> pdb=" O LEU A4066 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4082 removed outlier: 4.908A pdb=" N THR A4082 " --> pdb=" O GLN A4078 " (cutoff:3.500A) Processing helix chain 'A' and resid 4089 through 4101 removed outlier: 3.630A pdb=" N MET A4097 " --> pdb=" O PHE A4093 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP A4098 " --> pdb=" O GLN A4094 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER A4099 " --> pdb=" O LYS A4095 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLN A4100 " --> pdb=" O ALA A4096 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LYS A4101 " --> pdb=" O MET A4097 " (cutoff:3.500A) Processing helix chain 'A' and resid 4104 through 4116 removed outlier: 5.443A pdb=" N GLU A4116 " --> pdb=" O LEU A4112 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4133 removed outlier: 3.705A pdb=" N ALA A4129 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN A4130 " --> pdb=" O GLU A4126 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N PHE A4132 " --> pdb=" O PHE A4128 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLN A4133 " --> pdb=" O ALA A4129 " (cutoff:3.500A) Processing helix chain 'A' and resid 4134 through 4155 removed outlier: 4.330A pdb=" N ASP A4138 " --> pdb=" O GLU A4134 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Proline residue: A4155 - end of helix Processing helix chain 'A' and resid 4157 through 4168 removed outlier: 3.551A pdb=" N GLU A4168 " --> pdb=" O LEU A4164 " (cutoff:3.500A) Processing helix chain 'A' and resid 4169 through 4175 removed outlier: 3.695A pdb=" N TYR A4173 " --> pdb=" O SER A4169 " (cutoff:3.500A) Processing helix chain 'A' and resid 4198 through 4207 Processing helix chain 'A' and resid 4208 through 4224 Processing helix chain 'A' and resid 4226 through 4252 removed outlier: 4.465A pdb=" N MET A4231 " --> pdb=" O GLU A4227 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLU A4232 " --> pdb=" O ALA A4228 " (cutoff:3.500A) Processing helix chain 'A' and resid 4540 through 4559 Processing helix chain 'A' and resid 4560 through 4580 removed outlier: 4.609A pdb=" N PHE A4579 " --> pdb=" O PHE A4575 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR A4580 " --> pdb=" O ILE A4576 " (cutoff:3.500A) Processing helix chain 'A' and resid 4640 through 4683 removed outlier: 3.541A pdb=" N TRP A4644 " --> pdb=" O GLU A4640 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL A4666 " --> pdb=" O ASN A4662 " (cutoff:3.500A) Proline residue: A4667 - end of helix Processing helix chain 'A' and resid 4696 through 4707 removed outlier: 3.549A pdb=" N ARG A4703 " --> pdb=" O GLY A4699 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEU A4704 " --> pdb=" O GLN A4700 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL A4705 " --> pdb=" O TRP A4701 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASN A4707 " --> pdb=" O ARG A4703 " (cutoff:3.500A) Processing helix chain 'A' and resid 4719 through 4728 Processing helix chain 'A' and resid 4733 through 4742 Processing helix chain 'A' and resid 4744 through 4750 removed outlier: 3.811A pdb=" N LEU A4748 " --> pdb=" O ASP A4744 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU A4749 " --> pdb=" O LEU A4745 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE A4750 " --> pdb=" O ALA A4746 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4744 through 4750' Processing helix chain 'A' and resid 4772 through 4787 removed outlier: 3.865A pdb=" N THR A4785 " --> pdb=" O GLY A4781 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP A4786 " --> pdb=" O VAL A4782 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ASN A4787 " --> pdb=" O ILE A4783 " (cutoff:3.500A) Processing helix chain 'A' and resid 4788 through 4805 removed outlier: 4.033A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4820 removed outlier: 4.855A pdb=" N ALA A4810 " --> pdb=" O ASN A4806 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ALA A4811 " --> pdb=" O PHE A4807 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N HIS A4812 " --> pdb=" O PHE A4808 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N LEU A4813 " --> pdb=" O PHE A4809 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU A4814 " --> pdb=" O ALA A4810 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASP A4815 " --> pdb=" O ALA A4811 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE A4816 " --> pdb=" O HIS A4812 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ALA A4817 " --> pdb=" O LEU A4813 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) Processing helix chain 'A' and resid 4821 through 4832 removed outlier: 3.788A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) Processing helix chain 'A' and resid 4833 through 4858 Processing helix chain 'A' and resid 4859 through 4864 removed outlier: 4.354A pdb=" N TYR A4863 " --> pdb=" O PHE A4859 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ASN A4864 " --> pdb=" O ARG A4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4859 through 4864' Processing helix chain 'A' and resid 4878 through 4893 removed outlier: 3.959A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A4892 " --> pdb=" O TYR A4888 " (cutoff:3.500A) Processing helix chain 'A' and resid 4896 through 4901 removed outlier: 3.997A pdb=" N GLU A4900 " --> pdb=" O GLY A4896 " (cutoff:3.500A) Processing helix chain 'A' and resid 4909 through 4924 Processing helix chain 'A' and resid 4928 through 4957 Processing helix chain 'A' and resid 4964 through 4970 removed outlier: 3.762A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR A4970 " --> pdb=" O ASP A4966 " (cutoff:3.500A) Processing helix chain 'A' and resid 4973 through 4981 Processing helix chain 'A' and resid 4984 through 4998 Processing helix chain 'A' and resid 4999 through 5004 removed outlier: 3.837A pdb=" N HIS A5003 " --> pdb=" O ASP A4999 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR A5004 " --> pdb=" O GLU A5000 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4999 through 5004' Processing helix chain 'A' and resid 5005 through 5017 Processing helix chain 'A' and resid 5027 through 5033 Processing helix chain 'A' and resid 250 through 256 removed outlier: 4.152A pdb=" N CYS A 253 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A 254 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS A 255 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ALA A 256 " --> pdb=" O CYS A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 256' Processing helix chain 'A' and resid 3682 through 3687 removed outlier: 5.483A pdb=" N GLU A3685 " --> pdb=" O GLU A3682 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU A3686 " --> pdb=" O GLN A3683 " (cutoff:3.500A) Processing helix chain 'A' and resid 3152 through 3157 removed outlier: 3.984A pdb=" N ILE A3157 " --> pdb=" O PHE A3152 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3152 through 3157' Processing helix chain 'A' and resid 4685 through 4690 Processing helix chain 'B' and resid 61 through 66 removed outlier: 4.530A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N CYS B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 66' Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 308 through 313 removed outlier: 6.396A pdb=" N THR B 312 " --> pdb=" O HIS B 308 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B 313 " --> pdb=" O THR B 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 313' Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 394 through 422 removed outlier: 3.554A pdb=" N HIS B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 453 Processing helix chain 'B' and resid 460 through 482 removed outlier: 3.973A pdb=" N GLN B 465 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 removed outlier: 3.668A pdb=" N LEU B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN B 489 " --> pdb=" O SER B 485 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 491 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.871A pdb=" N TYR B 506 " --> pdb=" O HIS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 531 removed outlier: 3.561A pdb=" N GLU B 513 " --> pdb=" O GLU B 509 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLU B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 524 " --> pdb=" O ASN B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 544 removed outlier: 3.580A pdb=" N LEU B 539 " --> pdb=" O ALA B 535 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE B 540 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER B 541 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR B 542 " --> pdb=" O ALA B 538 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 551 Processing helix chain 'B' and resid 556 through 571 removed outlier: 3.625A pdb=" N ILE B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 570 " --> pdb=" O CYS B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 579 removed outlier: 4.083A pdb=" N ASN B 576 " --> pdb=" O PRO B 572 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 593 removed outlier: 3.725A pdb=" N LEU B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP B 591 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 609 removed outlier: 3.759A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N CYS B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 629 removed outlier: 3.673A pdb=" N ASP B 619 " --> pdb=" O ARG B 615 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 626 " --> pdb=" O THR B 622 " (cutoff:3.500A) Proline residue: B 627 - end of helix Processing helix chain 'B' and resid 810 through 815 removed outlier: 4.790A pdb=" N ALA B 814 " --> pdb=" O PRO B 810 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL B 815 " --> pdb=" O CYS B 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 810 through 815' Processing helix chain 'B' and resid 847 through 853 removed outlier: 3.757A pdb=" N PHE B 851 " --> pdb=" O SER B 847 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 852 " --> pdb=" O HIS B 848 " (cutoff:3.500A) Proline residue: B 853 - end of helix No H-bonds generated for 'chain 'B' and resid 847 through 853' Processing helix chain 'B' and resid 864 through 885 removed outlier: 3.530A pdb=" N ILE B 870 " --> pdb=" O HIS B 866 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLU B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LYS B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 874 " --> pdb=" O ILE B 870 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA B 875 " --> pdb=" O ARG B 871 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE B 878 " --> pdb=" O LEU B 874 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLU B 880 " --> pdb=" O GLU B 876 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU B 881 " --> pdb=" O ASN B 877 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TRP B 882 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ALA B 883 " --> pdb=" O HIS B 879 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR B 885 " --> pdb=" O LEU B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 914 removed outlier: 3.787A pdb=" N LEU B 913 " --> pdb=" O ASN B 909 " (cutoff:3.500A) Proline residue: B 914 - end of helix No H-bonds generated for 'chain 'B' and resid 909 through 914' Processing helix chain 'B' and resid 915 through 936 Processing helix chain 'B' and resid 945 through 950 removed outlier: 3.970A pdb=" N ASN B 949 " --> pdb=" O LYS B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 1004 removed outlier: 3.555A pdb=" N VAL B 995 " --> pdb=" O ASN B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1048 removed outlier: 4.066A pdb=" N SER B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B1039 " --> pdb=" O ASN B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1073 removed outlier: 4.594A pdb=" N ARG B1071 " --> pdb=" O SER B1067 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL B1072 " --> pdb=" O ARG B1068 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ARG B1073 " --> pdb=" O TRP B1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1067 through 1073' Processing helix chain 'B' and resid 1217 through 1222 removed outlier: 7.230A pdb=" N GLU B1221 " --> pdb=" O CYS B1217 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY B1222 " --> pdb=" O GLY B1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1217 through 1222' Processing helix chain 'B' and resid 1423 through 1430 removed outlier: 3.620A pdb=" N LEU B1428 " --> pdb=" O PRO B1424 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN B1429 " --> pdb=" O GLU B1425 " (cutoff:3.500A) Processing helix chain 'B' and resid 1444 through 1449 removed outlier: 4.356A pdb=" N VAL B1448 " --> pdb=" O GLU B1444 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TRP B1449 " --> pdb=" O PRO B1445 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1444 through 1449' Processing helix chain 'B' and resid 1496 through 1501 removed outlier: 4.115A pdb=" N PHE B1500 " --> pdb=" O TRP B1496 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL B1501 " --> pdb=" O GLY B1497 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1496 through 1501' Processing helix chain 'B' and resid 1574 through 1580 removed outlier: 4.189A pdb=" N ALA B1578 " --> pdb=" O PRO B1574 " (cutoff:3.500A) Processing helix chain 'B' and resid 1649 through 1657 removed outlier: 4.257A pdb=" N LEU B1653 " --> pdb=" O ASP B1649 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N SER B1654 " --> pdb=" O ILE B1650 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLU B1655 " --> pdb=" O LEU B1651 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU B1657 " --> pdb=" O LEU B1653 " (cutoff:3.500A) Processing helix chain 'B' and resid 1658 through 1675 removed outlier: 3.878A pdb=" N PHE B1662 " --> pdb=" O ASP B1658 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS B1674 " --> pdb=" O TYR B1670 " (cutoff:3.500A) Processing helix chain 'B' and resid 1678 through 1689 removed outlier: 3.666A pdb=" N ALA B1684 " --> pdb=" O ARG B1680 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N CYS B1686 " --> pdb=" O ALA B1682 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER B1687 " --> pdb=" O HIS B1683 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N HIS B1688 " --> pdb=" O ALA B1684 " (cutoff:3.500A) Processing helix chain 'B' and resid 1690 through 1700 removed outlier: 3.538A pdb=" N LEU B1694 " --> pdb=" O ASP B1690 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU B1699 " --> pdb=" O LEU B1695 " (cutoff:3.500A) Processing helix chain 'B' and resid 1704 through 1719 Processing helix chain 'B' and resid 1720 through 1734 removed outlier: 3.501A pdb=" N MET B1730 " --> pdb=" O SER B1726 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER B1732 " --> pdb=" O ARG B1728 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLU B1733 " --> pdb=" O SER B1729 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N TYR B1734 " --> pdb=" O MET B1730 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1745 removed outlier: 3.691A pdb=" N ILE B1745 " --> pdb=" O GLU B1741 " (cutoff:3.500A) Processing helix chain 'B' and resid 1803 through 1825 removed outlier: 3.637A pdb=" N ASP B1809 " --> pdb=" O GLU B1805 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS B1825 " --> pdb=" O ASP B1821 " (cutoff:3.500A) Processing helix chain 'B' and resid 1833 through 1852 Proline residue: B1840 - end of helix Processing helix chain 'B' and resid 1855 through 1867 Processing helix chain 'B' and resid 1934 through 1987 removed outlier: 3.864A pdb=" N GLN B1938 " --> pdb=" O SER B1934 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP B1967 " --> pdb=" O GLU B1963 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS B1968 " --> pdb=" O ARG B1964 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE B1984 " --> pdb=" O LEU B1980 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N THR B1985 " --> pdb=" O MET B1981 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N MET B1986 " --> pdb=" O ARG B1982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1990 through 2001 removed outlier: 4.594A pdb=" N ARG B1994 " --> pdb=" O GLU B1990 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLU B1997 " --> pdb=" O ARG B1993 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE B1998 " --> pdb=" O ARG B1994 " (cutoff:3.500A) Proline residue: B2001 - end of helix Processing helix chain 'B' and resid 2002 through 2011 removed outlier: 3.556A pdb=" N ASN B2007 " --> pdb=" O GLN B2003 " (cutoff:3.500A) Processing helix chain 'B' and resid 2017 through 2022 removed outlier: 4.188A pdb=" N CYS B2021 " --> pdb=" O ASP B2017 " (cutoff:3.500A) Proline residue: B2022 - end of helix No H-bonds generated for 'chain 'B' and resid 2017 through 2022' Processing helix chain 'B' and resid 2024 through 2043 Processing helix chain 'B' and resid 2093 through 2109 removed outlier: 3.667A pdb=" N ASP B2109 " --> pdb=" O TRP B2105 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2130 removed outlier: 3.971A pdb=" N GLY B2130 " --> pdb=" O ARG B2126 " (cutoff:3.500A) Processing helix chain 'B' and resid 2131 through 2141 Proline residue: B2139 - end of helix Processing helix chain 'B' and resid 2145 through 2169 removed outlier: 4.184A pdb=" N VAL B2149 " --> pdb=" O SER B2145 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU B2150 " --> pdb=" O PRO B2146 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP B2151 " --> pdb=" O SER B2147 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B2154 " --> pdb=" O GLU B2150 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B2166 " --> pdb=" O ILE B2162 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE B2167 " --> pdb=" O ARG B2163 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL B2168 " --> pdb=" O SER B2164 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N GLN B2169 " --> pdb=" O LEU B2165 " (cutoff:3.500A) Processing helix chain 'B' and resid 2171 through 2188 removed outlier: 3.578A pdb=" N LEU B2177 " --> pdb=" O GLN B2173 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET B2178 " --> pdb=" O GLU B2174 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B2179 " --> pdb=" O GLU B2175 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2194 Processing helix chain 'B' and resid 2195 through 2219 removed outlier: 5.357A pdb=" N MET B2203 " --> pdb=" O ARG B2199 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N HIS B2204 " --> pdb=" O ALA B2200 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLU B2205 " --> pdb=" O LEU B2201 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR B2206 " --> pdb=" O GLY B2202 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY B2218 " --> pdb=" O VAL B2214 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B2219 " --> pdb=" O LEU B2215 " (cutoff:3.500A) Processing helix chain 'B' and resid 2225 through 2244 removed outlier: 3.650A pdb=" N VAL B2229 " --> pdb=" O PHE B2225 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B2241 " --> pdb=" O CYS B2237 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE B2242 " --> pdb=" O TYR B2238 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER B2243 " --> pdb=" O PHE B2239 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG B2244 " --> pdb=" O CYS B2240 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2255 removed outlier: 3.803A pdb=" N ASP B2252 " --> pdb=" O ARG B2248 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS B2253 " --> pdb=" O SER B2249 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU B2254 " --> pdb=" O MET B2250 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N SER B2255 " --> pdb=" O PHE B2251 " (cutoff:3.500A) Processing helix chain 'B' and resid 2256 through 2262 removed outlier: 3.599A pdb=" N ASN B2260 " --> pdb=" O TYR B2256 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY B2262 " --> pdb=" O LEU B2258 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2281 removed outlier: 3.544A pdb=" N VAL B2275 " --> pdb=" O THR B2271 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B2280 " --> pdb=" O ALA B2276 " (cutoff:3.500A) Processing helix chain 'B' and resid 2283 through 2290 Processing helix chain 'B' and resid 2291 through 2308 removed outlier: 3.807A pdb=" N LEU B2295 " --> pdb=" O GLN B2291 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2317 removed outlier: 3.545A pdb=" N LYS B2316 " --> pdb=" O MET B2312 " (cutoff:3.500A) Processing helix chain 'B' and resid 2324 through 2340 removed outlier: 3.609A pdb=" N PHE B2334 " --> pdb=" O ARG B2330 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2361 removed outlier: 3.713A pdb=" N VAL B2352 " --> pdb=" O GLU B2348 " (cutoff:3.500A) Proline residue: B2361 - end of helix Processing helix chain 'B' and resid 2375 through 2390 removed outlier: 3.823A pdb=" N ILE B2380 " --> pdb=" O LEU B2376 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU B2381 " --> pdb=" O LEU B2377 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B2382 " --> pdb=" O ALA B2378 " (cutoff:3.500A) Proline residue: B2390 - end of helix Processing helix chain 'B' and resid 2417 through 2437 removed outlier: 3.714A pdb=" N TYR B2426 " --> pdb=" O ILE B2422 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA B2427 " --> pdb=" O MET B2423 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B2437 " --> pdb=" O LEU B2433 " (cutoff:3.500A) Processing helix chain 'B' and resid 2439 through 2446 Processing helix chain 'B' and resid 2447 through 2462 Proline residue: B2462 - end of helix Processing helix chain 'B' and resid 2463 through 2472 Processing helix chain 'B' and resid 2495 through 2509 removed outlier: 4.347A pdb=" N LYS B2499 " --> pdb=" O VAL B2495 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER B2501 " --> pdb=" O ASP B2497 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET B2502 " --> pdb=" O HIS B2498 " (cutoff:3.500A) Processing helix chain 'B' and resid 2514 through 2525 removed outlier: 4.435A pdb=" N VAL B2524 " --> pdb=" O HIS B2520 " (cutoff:3.500A) Processing helix chain 'B' and resid 2526 through 2537 Processing helix chain 'B' and resid 2539 through 2545 removed outlier: 5.531A pdb=" N THR B2543 " --> pdb=" O ALA B2539 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR B2544 " --> pdb=" O THR B2540 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLU B2545 " --> pdb=" O PHE B2541 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2539 through 2545' Processing helix chain 'B' and resid 2546 through 2566 removed outlier: 3.887A pdb=" N CYS B2555 " --> pdb=" O ASN B2551 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU B2559 " --> pdb=" O CYS B2555 " (cutoff:3.500A) Proline residue: B2560 - end of helix Processing helix chain 'B' and resid 2568 through 2573 removed outlier: 5.410A pdb=" N THR B2572 " --> pdb=" O LEU B2568 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLU B2573 " --> pdb=" O PHE B2569 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2568 through 2573' Processing helix chain 'B' and resid 2575 through 2593 removed outlier: 3.798A pdb=" N GLY B2592 " --> pdb=" O ARG B2588 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ARG B2593 " --> pdb=" O LEU B2589 " (cutoff:3.500A) Processing helix chain 'B' and resid 2596 through 2614 removed outlier: 3.730A pdb=" N TYR B2613 " --> pdb=" O ALA B2609 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B2614 " --> pdb=" O LEU B2610 " (cutoff:3.500A) Processing helix chain 'B' and resid 2615 through 2630 removed outlier: 4.063A pdb=" N LEU B2619 " --> pdb=" O ARG B2615 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN B2620 " --> pdb=" O PRO B2616 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N HIS B2621 " --> pdb=" O SER B2617 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LEU B2622 " --> pdb=" O MET B2618 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE B2628 " --> pdb=" O ARG B2624 " (cutoff:3.500A) Processing helix chain 'B' and resid 2636 through 2652 Proline residue: B2640 - end of helix Processing helix chain 'B' and resid 2668 through 2689 removed outlier: 6.919A pdb=" N LEU B2672 " --> pdb=" O SER B2668 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N HIS B2673 " --> pdb=" O GLU B2669 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP B2680 " --> pdb=" O ARG B2676 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS B2688 " --> pdb=" O ASP B2684 " (cutoff:3.500A) Processing helix chain 'B' and resid 2693 through 2711 removed outlier: 3.795A pdb=" N MET B2698 " --> pdb=" O GLU B2694 " (cutoff:3.500A) Proline residue: B2701 - end of helix Proline residue: B2711 - end of helix Processing helix chain 'B' and resid 2741 through 2746 removed outlier: 4.599A pdb=" N VAL B2745 " --> pdb=" O GLU B2741 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE B2746 " --> pdb=" O THR B2742 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2741 through 2746' Processing helix chain 'B' and resid 2751 through 2774 removed outlier: 3.875A pdb=" N LYS B2757 " --> pdb=" O SER B2753 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN B2774 " --> pdb=" O LYS B2770 " (cutoff:3.500A) Processing helix chain 'B' and resid 2799 through 2820 removed outlier: 3.538A pdb=" N GLU B2803 " --> pdb=" O GLU B2799 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE B2804 " --> pdb=" O LYS B2800 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG B2806 " --> pdb=" O LYS B2802 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TRP B2807 " --> pdb=" O GLU B2803 " (cutoff:3.500A) Proline residue: B2808 - end of helix removed outlier: 5.286A pdb=" N GLU B2820 " --> pdb=" O MET B2816 " (cutoff:3.500A) Processing helix chain 'B' and resid 2868 through 2895 removed outlier: 4.209A pdb=" N GLU B2893 " --> pdb=" O LYS B2889 " (cutoff:3.500A) Processing helix chain 'B' and resid 2907 through 2912 removed outlier: 6.080A pdb=" N THR B2912 " --> pdb=" O TYR B2908 " (cutoff:3.500A) Processing helix chain 'B' and resid 2913 through 2934 removed outlier: 3.737A pdb=" N ALA B2917 " --> pdb=" O ALA B2913 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ARG B2918 " --> pdb=" O LYS B2914 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ASP B2919 " --> pdb=" O GLU B2915 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B2922 " --> pdb=" O ARG B2918 " (cutoff:3.500A) Processing helix chain 'B' and resid 2949 through 2982 removed outlier: 5.718A pdb=" N PHE B2955 " --> pdb=" O ILE B2951 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA B2956 " --> pdb=" O GLU B2952 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE B2957 " --> pdb=" O LYS B2953 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B2969 " --> pdb=" O ARG B2965 " (cutoff:3.500A) Processing helix chain 'B' and resid 2991 through 3014 removed outlier: 3.611A pdb=" N LEU B3002 " --> pdb=" O PHE B2998 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU B3003 " --> pdb=" O ALA B2999 " (cutoff:3.500A) Proline residue: B3004 - end of helix removed outlier: 3.806A pdb=" N THR B3011 " --> pdb=" O ASN B3007 " (cutoff:3.500A) Processing helix chain 'B' and resid 3032 through 3051 removed outlier: 3.812A pdb=" N LEU B3042 " --> pdb=" O MET B3038 " (cutoff:3.500A) Processing helix chain 'B' and resid 3053 through 3058 removed outlier: 4.086A pdb=" N PHE B3057 " --> pdb=" O ARG B3053 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY B3058 " --> pdb=" O VAL B3054 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3053 through 3058' Processing helix chain 'B' and resid 3060 through 3075 Processing helix chain 'B' and resid 3076 through 3083 removed outlier: 3.777A pdb=" N VAL B3080 " --> pdb=" O ASP B3076 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET B3081 " --> pdb=" O ALA B3077 " (cutoff:3.500A) Processing helix chain 'B' and resid 3085 through 3112 removed outlier: 3.537A pdb=" N PHE B3095 " --> pdb=" O GLY B3091 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE B3096 " --> pdb=" O LEU B3092 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B3108 " --> pdb=" O GLU B3104 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU B3112 " --> pdb=" O GLU B3108 " (cutoff:3.500A) Processing helix chain 'B' and resid 3123 through 3151 removed outlier: 3.631A pdb=" N VAL B3134 " --> pdb=" O THR B3130 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU B3137 " --> pdb=" O THR B3133 " (cutoff:3.500A) Proline residue: B3138 - end of helix removed outlier: 3.708A pdb=" N GLN B3149 " --> pdb=" O GLN B3145 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS B3150 " --> pdb=" O HIS B3146 " (cutoff:3.500A) Processing helix chain 'B' and resid 3159 through 3175 removed outlier: 5.330A pdb=" N VAL B3163 " --> pdb=" O ASP B3159 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU B3175 " --> pdb=" O SER B3171 " (cutoff:3.500A) Processing helix chain 'B' and resid 3180 through 3201 Proline residue: B3188 - end of helix Processing helix chain 'B' and resid 3217 through 3222 Processing helix chain 'B' and resid 3226 through 3231 removed outlier: 6.672A pdb=" N LEU B3230 " --> pdb=" O GLU B3226 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLY B3231 " --> pdb=" O ARG B3227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3226 through 3231' Processing helix chain 'B' and resid 3235 through 3241 removed outlier: 3.539A pdb=" N MET B3239 " --> pdb=" O SER B3235 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N CYS B3240 " --> pdb=" O VAL B3236 " (cutoff:3.500A) Proline residue: B3241 - end of helix No H-bonds generated for 'chain 'B' and resid 3235 through 3241' Processing helix chain 'B' and resid 3245 through 3260 Processing helix chain 'B' and resid 3262 through 3267 Proline residue: B3267 - end of helix Processing helix chain 'B' and resid 3268 through 3288 removed outlier: 4.358A pdb=" N LEU B3274 " --> pdb=" O ILE B3270 " (cutoff:3.500A) Proline residue: B3275 - end of helix Proline residue: B3282 - end of helix removed outlier: 4.343A pdb=" N GLU B3286 " --> pdb=" O PRO B3282 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG B3287 " --> pdb=" O ARG B3283 " (cutoff:3.500A) Processing helix chain 'B' and resid 3308 through 3327 removed outlier: 3.770A pdb=" N LEU B3312 " --> pdb=" O THR B3308 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B3319 " --> pdb=" O LEU B3315 " (cutoff:3.500A) Processing helix chain 'B' and resid 3332 through 3343 removed outlier: 5.755A pdb=" N LYS B3336 " --> pdb=" O ALA B3332 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG B3337 " --> pdb=" O THR B3333 " (cutoff:3.500A) Processing helix chain 'B' and resid 3344 through 3350 removed outlier: 4.728A pdb=" N ARG B3348 " --> pdb=" O PRO B3344 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ALA B3349 " --> pdb=" O ILE B3345 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG B3350 " --> pdb=" O VAL B3346 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3344 through 3350' Processing helix chain 'B' and resid 3351 through 3381 removed outlier: 4.698A pdb=" N HIS B3355 " --> pdb=" O PRO B3351 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE B3358 " --> pdb=" O LEU B3354 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE B3359 " --> pdb=" O HIS B3355 " (cutoff:3.500A) Proline residue: B3360 - end of helix removed outlier: 3.611A pdb=" N GLN B3378 " --> pdb=" O ALA B3374 " (cutoff:3.500A) Processing helix chain 'B' and resid 3389 through 3413 removed outlier: 6.543A pdb=" N LEU B3393 " --> pdb=" O GLU B3389 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B3407 " --> pdb=" O ARG B3403 " (cutoff:3.500A) Proline residue: B3410 - end of helix Processing helix chain 'B' and resid 3419 through 3426 Processing helix chain 'B' and resid 3428 through 3448 Processing helix chain 'B' and resid 3449 through 3463 removed outlier: 3.755A pdb=" N GLN B3456 " --> pdb=" O LYS B3452 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN B3457 " --> pdb=" O ARG B3453 " (cutoff:3.500A) Processing helix chain 'B' and resid 3466 through 3478 removed outlier: 4.631A pdb=" N LEU B3470 " --> pdb=" O ASN B3466 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP B3473 " --> pdb=" O PHE B3469 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N SER B3474 " --> pdb=" O LEU B3470 " (cutoff:3.500A) Processing helix chain 'B' and resid 3508 through 3526 removed outlier: 3.941A pdb=" N LYS B3516 " --> pdb=" O ALA B3512 " (cutoff:3.500A) Proline residue: B3519 - end of helix removed outlier: 3.951A pdb=" N MET B3524 " --> pdb=" O ILE B3520 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N CYS B3525 " --> pdb=" O GLY B3521 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ALA B3526 " --> pdb=" O LEU B3522 " (cutoff:3.500A) Processing helix chain 'B' and resid 3529 through 3543 removed outlier: 3.571A pdb=" N LEU B3535 " --> pdb=" O ASP B3531 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS B3543 " --> pdb=" O ARG B3539 " (cutoff:3.500A) Processing helix chain 'B' and resid 3545 through 3557 Processing helix chain 'B' and resid 3566 through 3579 removed outlier: 3.604A pdb=" N ARG B3570 " --> pdb=" O SER B3566 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TRP B3571 " --> pdb=" O PRO B3567 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN B3572 " --> pdb=" O SER B3568 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU B3579 " --> pdb=" O LEU B3575 " (cutoff:3.500A) Processing helix chain 'B' and resid 3588 through 3612 removed outlier: 3.757A pdb=" N HIS B3605 " --> pdb=" O ALA B3601 " (cutoff:3.500A) Proline residue: B3612 - end of helix Processing helix chain 'B' and resid 3628 through 3638 removed outlier: 4.034A pdb=" N VAL B3632 " --> pdb=" O ARG B3628 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B3633 " --> pdb=" O ARG B3629 " (cutoff:3.500A) Processing helix chain 'B' and resid 3645 through 3665 removed outlier: 3.710A pdb=" N GLU B3655 " --> pdb=" O ASN B3651 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU B3663 " --> pdb=" O ALA B3659 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR B3664 " --> pdb=" O ALA B3660 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B3665 " --> pdb=" O TRP B3661 " (cutoff:3.500A) Processing helix chain 'B' and resid 3669 through 3679 Processing helix chain 'B' and resid 3696 through 3711 Processing helix chain 'B' and resid 3719 through 3735 removed outlier: 3.832A pdb=" N CYS B3733 " --> pdb=" O MET B3729 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N HIS B3734 " --> pdb=" O ALA B3730 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU B3735 " --> pdb=" O LYS B3731 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3772 removed outlier: 3.632A pdb=" N TYR B3765 " --> pdb=" O GLN B3761 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU B3770 " --> pdb=" O GLN B3766 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR B3772 " --> pdb=" O SER B3768 " (cutoff:3.500A) Processing helix chain 'B' and resid 3774 through 3787 removed outlier: 4.018A pdb=" N LYS B3787 " --> pdb=" O ILE B3783 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3806 Processing helix chain 'B' and resid 3809 through 3824 Processing helix chain 'B' and resid 3825 through 3839 removed outlier: 4.989A pdb=" N PHE B3829 " --> pdb=" O GLU B3825 " (cutoff:3.500A) Processing helix chain 'B' and resid 3843 through 3857 Processing helix chain 'B' and resid 3877 through 3893 removed outlier: 3.562A pdb=" N CYS B3892 " --> pdb=" O LEU B3888 " (cutoff:3.500A) Processing helix chain 'B' and resid 3896 through 3905 Processing helix chain 'B' and resid 3914 through 3939 removed outlier: 3.637A pdb=" N TYR B3937 " --> pdb=" O PHE B3933 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY B3939 " --> pdb=" O TRP B3935 " (cutoff:3.500A) Processing helix chain 'B' and resid 3944 through 3970 removed outlier: 3.557A pdb=" N ILE B3969 " --> pdb=" O LEU B3965 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3983 Processing helix chain 'B' and resid 3984 through 4007 removed outlier: 3.934A pdb=" N ALA B3988 " --> pdb=" O ARG B3984 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS B3998 " --> pdb=" O HIS B3994 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET B4001 " --> pdb=" O ALA B3997 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN B4005 " --> pdb=" O MET B4001 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ASP B4006 " --> pdb=" O LYS B4002 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N SER B4007 " --> pdb=" O LEU B4003 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4032 removed outlier: 3.528A pdb=" N GLU B4015 " --> pdb=" O GLU B4011 " (cutoff:3.500A) Processing helix chain 'B' and resid 4038 through 4052 Processing helix chain 'B' and resid 4053 through 4072 removed outlier: 3.646A pdb=" N MET B4064 " --> pdb=" O LYS B4060 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP B4070 " --> pdb=" O LEU B4066 " (cutoff:3.500A) Processing helix chain 'B' and resid 4074 through 4082 removed outlier: 4.908A pdb=" N THR B4082 " --> pdb=" O GLN B4078 " (cutoff:3.500A) Processing helix chain 'B' and resid 4089 through 4101 removed outlier: 3.631A pdb=" N MET B4097 " --> pdb=" O PHE B4093 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP B4098 " --> pdb=" O GLN B4094 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER B4099 " --> pdb=" O LYS B4095 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN B4100 " --> pdb=" O ALA B4096 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LYS B4101 " --> pdb=" O MET B4097 " (cutoff:3.500A) Processing helix chain 'B' and resid 4104 through 4116 removed outlier: 5.445A pdb=" N GLU B4116 " --> pdb=" O LEU B4112 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4133 removed outlier: 3.705A pdb=" N ALA B4129 " --> pdb=" O PHE B4125 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN B4130 " --> pdb=" O GLU B4126 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N PHE B4132 " --> pdb=" O PHE B4128 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLN B4133 " --> pdb=" O ALA B4129 " (cutoff:3.500A) Processing helix chain 'B' and resid 4134 through 4155 removed outlier: 4.330A pdb=" N ASP B4138 " --> pdb=" O GLU B4134 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE B4139 " --> pdb=" O PRO B4135 " (cutoff:3.500A) Proline residue: B4155 - end of helix Processing helix chain 'B' and resid 4157 through 4168 removed outlier: 3.551A pdb=" N GLU B4168 " --> pdb=" O LEU B4164 " (cutoff:3.500A) Processing helix chain 'B' and resid 4169 through 4175 removed outlier: 3.694A pdb=" N TYR B4173 " --> pdb=" O SER B4169 " (cutoff:3.500A) Processing helix chain 'B' and resid 4198 through 4207 Processing helix chain 'B' and resid 4208 through 4224 Processing helix chain 'B' and resid 4226 through 4252 removed outlier: 4.465A pdb=" N MET B4231 " --> pdb=" O GLU B4227 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLU B4232 " --> pdb=" O ALA B4228 " (cutoff:3.500A) Processing helix chain 'B' and resid 4540 through 4559 Processing helix chain 'B' and resid 4560 through 4580 removed outlier: 4.610A pdb=" N PHE B4579 " --> pdb=" O PHE B4575 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TYR B4580 " --> pdb=" O ILE B4576 " (cutoff:3.500A) Processing helix chain 'B' and resid 4640 through 4683 removed outlier: 3.541A pdb=" N TRP B4644 " --> pdb=" O GLU B4640 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL B4666 " --> pdb=" O ASN B4662 " (cutoff:3.500A) Proline residue: B4667 - end of helix Processing helix chain 'B' and resid 4696 through 4707 removed outlier: 3.548A pdb=" N ARG B4703 " --> pdb=" O GLY B4699 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LEU B4704 " --> pdb=" O GLN B4700 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL B4705 " --> pdb=" O TRP B4701 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU B4706 " --> pdb=" O ASP B4702 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN B4707 " --> pdb=" O ARG B4703 " (cutoff:3.500A) Processing helix chain 'B' and resid 4719 through 4728 Processing helix chain 'B' and resid 4733 through 4742 Processing helix chain 'B' and resid 4744 through 4750 removed outlier: 3.811A pdb=" N LEU B4748 " --> pdb=" O ASP B4744 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU B4749 " --> pdb=" O LEU B4745 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE B4750 " --> pdb=" O ALA B4746 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4744 through 4750' Processing helix chain 'B' and resid 4772 through 4787 removed outlier: 3.864A pdb=" N THR B4785 " --> pdb=" O GLY B4781 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP B4786 " --> pdb=" O VAL B4782 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ASN B4787 " --> pdb=" O ILE B4783 " (cutoff:3.500A) Processing helix chain 'B' and resid 4788 through 4805 removed outlier: 4.033A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4806 through 4820 removed outlier: 4.855A pdb=" N ALA B4810 " --> pdb=" O ASN B4806 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ALA B4811 " --> pdb=" O PHE B4807 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N HIS B4812 " --> pdb=" O PHE B4808 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU B4813 " --> pdb=" O PHE B4809 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU B4814 " --> pdb=" O ALA B4810 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASP B4815 " --> pdb=" O ALA B4811 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE B4816 " --> pdb=" O HIS B4812 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ALA B4817 " --> pdb=" O LEU B4813 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) Processing helix chain 'B' and resid 4821 through 4832 removed outlier: 3.788A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4858 Processing helix chain 'B' and resid 4859 through 4864 removed outlier: 4.355A pdb=" N TYR B4863 " --> pdb=" O PHE B4859 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ASN B4864 " --> pdb=" O ARG B4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4859 through 4864' Processing helix chain 'B' and resid 4878 through 4893 removed outlier: 3.959A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B4892 " --> pdb=" O TYR B4888 " (cutoff:3.500A) Processing helix chain 'B' and resid 4896 through 4901 removed outlier: 3.998A pdb=" N GLU B4900 " --> pdb=" O GLY B4896 " (cutoff:3.500A) Processing helix chain 'B' and resid 4909 through 4924 Processing helix chain 'B' and resid 4928 through 4957 Processing helix chain 'B' and resid 4964 through 4970 removed outlier: 3.762A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR B4970 " --> pdb=" O ASP B4966 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4981 Processing helix chain 'B' and resid 4984 through 4998 Processing helix chain 'B' and resid 4999 through 5004 removed outlier: 3.836A pdb=" N HIS B5003 " --> pdb=" O ASP B4999 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR B5004 " --> pdb=" O GLU B5000 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4999 through 5004' Processing helix chain 'B' and resid 5005 through 5017 Processing helix chain 'B' and resid 5027 through 5033 Processing helix chain 'B' and resid 250 through 256 removed outlier: 4.152A pdb=" N CYS B 253 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR B 254 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS B 255 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ALA B 256 " --> pdb=" O CYS B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 250 through 256' Processing helix chain 'B' and resid 3682 through 3687 removed outlier: 5.482A pdb=" N GLU B3685 " --> pdb=" O GLU B3682 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU B3686 " --> pdb=" O GLN B3683 " (cutoff:3.500A) Processing helix chain 'B' and resid 3152 through 3157 removed outlier: 3.984A pdb=" N ILE B3157 " --> pdb=" O PHE B3152 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3152 through 3157' Processing helix chain 'B' and resid 4685 through 4690 Processing helix chain 'C' and resid 61 through 66 removed outlier: 4.531A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N CYS C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 66' Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 308 through 313 removed outlier: 6.396A pdb=" N THR C 312 " --> pdb=" O HIS C 308 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER C 313 " --> pdb=" O THR C 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 308 through 313' Processing helix chain 'C' and resid 364 through 370 Processing helix chain 'C' and resid 394 through 422 removed outlier: 3.554A pdb=" N HIS C 405 " --> pdb=" O ALA C 401 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER C 420 " --> pdb=" O LYS C 416 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 453 Processing helix chain 'C' and resid 460 through 482 removed outlier: 3.973A pdb=" N GLN C 465 " --> pdb=" O HIS C 461 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 496 removed outlier: 3.668A pdb=" N LEU C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN C 489 " --> pdb=" O SER C 485 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE C 491 " --> pdb=" O VAL C 487 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL C 496 " --> pdb=" O ASP C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.871A pdb=" N TYR C 506 " --> pdb=" O HIS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 531 removed outlier: 3.561A pdb=" N GLU C 513 " --> pdb=" O GLU C 509 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLU C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C 523 " --> pdb=" O VAL C 519 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 544 removed outlier: 3.580A pdb=" N LEU C 539 " --> pdb=" O ALA C 535 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE C 540 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER C 541 " --> pdb=" O CYS C 537 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR C 542 " --> pdb=" O ALA C 538 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN C 543 " --> pdb=" O LEU C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 551 Processing helix chain 'C' and resid 556 through 571 removed outlier: 3.624A pdb=" N ILE C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU C 570 " --> pdb=" O CYS C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 579 removed outlier: 4.083A pdb=" N ASN C 576 " --> pdb=" O PRO C 572 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLN C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 593 removed outlier: 3.725A pdb=" N LEU C 590 " --> pdb=" O ILE C 586 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP C 591 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 609 removed outlier: 3.759A pdb=" N LEU C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL C 608 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N CYS C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 629 removed outlier: 3.673A pdb=" N ASP C 619 " --> pdb=" O ARG C 615 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 626 " --> pdb=" O THR C 622 " (cutoff:3.500A) Proline residue: C 627 - end of helix Processing helix chain 'C' and resid 810 through 815 removed outlier: 4.790A pdb=" N ALA C 814 " --> pdb=" O PRO C 810 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL C 815 " --> pdb=" O CYS C 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 810 through 815' Processing helix chain 'C' and resid 847 through 853 removed outlier: 3.757A pdb=" N PHE C 851 " --> pdb=" O SER C 847 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 852 " --> pdb=" O HIS C 848 " (cutoff:3.500A) Proline residue: C 853 - end of helix No H-bonds generated for 'chain 'C' and resid 847 through 853' Processing helix chain 'C' and resid 864 through 885 removed outlier: 3.530A pdb=" N ILE C 870 " --> pdb=" O HIS C 866 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLU C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS C 873 " --> pdb=" O ARG C 869 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 874 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA C 875 " --> pdb=" O ARG C 871 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE C 878 " --> pdb=" O LEU C 874 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLU C 880 " --> pdb=" O GLU C 876 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU C 881 " --> pdb=" O ASN C 877 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TRP C 882 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ALA C 883 " --> pdb=" O HIS C 879 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR C 885 " --> pdb=" O LEU C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 914 removed outlier: 3.787A pdb=" N LEU C 913 " --> pdb=" O ASN C 909 " (cutoff:3.500A) Proline residue: C 914 - end of helix No H-bonds generated for 'chain 'C' and resid 909 through 914' Processing helix chain 'C' and resid 915 through 936 Processing helix chain 'C' and resid 945 through 950 removed outlier: 3.970A pdb=" N ASN C 949 " --> pdb=" O LYS C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 1004 removed outlier: 3.555A pdb=" N VAL C 995 " --> pdb=" O ASN C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1048 removed outlier: 4.066A pdb=" N SER C1038 " --> pdb=" O SER C1034 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C1039 " --> pdb=" O ASN C1035 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1073 removed outlier: 4.594A pdb=" N ARG C1071 " --> pdb=" O SER C1067 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL C1072 " --> pdb=" O ARG C1068 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ARG C1073 " --> pdb=" O TRP C1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1067 through 1073' Processing helix chain 'C' and resid 1217 through 1222 removed outlier: 7.230A pdb=" N GLU C1221 " --> pdb=" O CYS C1217 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY C1222 " --> pdb=" O GLY C1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1217 through 1222' Processing helix chain 'C' and resid 1423 through 1430 removed outlier: 3.620A pdb=" N LEU C1428 " --> pdb=" O PRO C1424 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN C1429 " --> pdb=" O GLU C1425 " (cutoff:3.500A) Processing helix chain 'C' and resid 1444 through 1449 removed outlier: 4.356A pdb=" N VAL C1448 " --> pdb=" O GLU C1444 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TRP C1449 " --> pdb=" O PRO C1445 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1444 through 1449' Processing helix chain 'C' and resid 1496 through 1501 removed outlier: 4.115A pdb=" N PHE C1500 " --> pdb=" O TRP C1496 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL C1501 " --> pdb=" O GLY C1497 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1496 through 1501' Processing helix chain 'C' and resid 1574 through 1580 removed outlier: 4.189A pdb=" N ALA C1578 " --> pdb=" O PRO C1574 " (cutoff:3.500A) Processing helix chain 'C' and resid 1649 through 1657 removed outlier: 4.257A pdb=" N LEU C1653 " --> pdb=" O ASP C1649 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N SER C1654 " --> pdb=" O ILE C1650 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLU C1655 " --> pdb=" O LEU C1651 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU C1657 " --> pdb=" O LEU C1653 " (cutoff:3.500A) Processing helix chain 'C' and resid 1658 through 1675 removed outlier: 3.878A pdb=" N PHE C1662 " --> pdb=" O ASP C1658 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS C1674 " --> pdb=" O TYR C1670 " (cutoff:3.500A) Processing helix chain 'C' and resid 1678 through 1689 removed outlier: 3.666A pdb=" N ALA C1684 " --> pdb=" O ARG C1680 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N CYS C1686 " --> pdb=" O ALA C1682 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER C1687 " --> pdb=" O HIS C1683 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N HIS C1688 " --> pdb=" O ALA C1684 " (cutoff:3.500A) Processing helix chain 'C' and resid 1690 through 1700 removed outlier: 3.537A pdb=" N LEU C1694 " --> pdb=" O ASP C1690 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU C1699 " --> pdb=" O LEU C1695 " (cutoff:3.500A) Processing helix chain 'C' and resid 1704 through 1719 Processing helix chain 'C' and resid 1720 through 1734 removed outlier: 3.501A pdb=" N MET C1730 " --> pdb=" O SER C1726 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER C1732 " --> pdb=" O ARG C1728 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLU C1733 " --> pdb=" O SER C1729 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N TYR C1734 " --> pdb=" O MET C1730 " (cutoff:3.500A) Processing helix chain 'C' and resid 1739 through 1745 removed outlier: 3.691A pdb=" N ILE C1745 " --> pdb=" O GLU C1741 " (cutoff:3.500A) Processing helix chain 'C' and resid 1803 through 1825 removed outlier: 3.636A pdb=" N ASP C1809 " --> pdb=" O GLU C1805 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS C1825 " --> pdb=" O ASP C1821 " (cutoff:3.500A) Processing helix chain 'C' and resid 1833 through 1852 Proline residue: C1840 - end of helix Processing helix chain 'C' and resid 1855 through 1867 Processing helix chain 'C' and resid 1934 through 1987 removed outlier: 3.864A pdb=" N GLN C1938 " --> pdb=" O SER C1934 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP C1967 " --> pdb=" O GLU C1963 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS C1968 " --> pdb=" O ARG C1964 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE C1984 " --> pdb=" O LEU C1980 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N THR C1985 " --> pdb=" O MET C1981 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N MET C1986 " --> pdb=" O ARG C1982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1990 through 2001 removed outlier: 4.594A pdb=" N ARG C1994 " --> pdb=" O GLU C1990 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLU C1997 " --> pdb=" O ARG C1993 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE C1998 " --> pdb=" O ARG C1994 " (cutoff:3.500A) Proline residue: C2001 - end of helix Processing helix chain 'C' and resid 2002 through 2011 removed outlier: 3.556A pdb=" N ASN C2007 " --> pdb=" O GLN C2003 " (cutoff:3.500A) Processing helix chain 'C' and resid 2017 through 2022 removed outlier: 4.188A pdb=" N CYS C2021 " --> pdb=" O ASP C2017 " (cutoff:3.500A) Proline residue: C2022 - end of helix No H-bonds generated for 'chain 'C' and resid 2017 through 2022' Processing helix chain 'C' and resid 2024 through 2043 Processing helix chain 'C' and resid 2093 through 2109 removed outlier: 3.667A pdb=" N ASP C2109 " --> pdb=" O TRP C2105 " (cutoff:3.500A) Processing helix chain 'C' and resid 2113 through 2130 removed outlier: 3.971A pdb=" N GLY C2130 " --> pdb=" O ARG C2126 " (cutoff:3.500A) Processing helix chain 'C' and resid 2131 through 2141 Proline residue: C2139 - end of helix Processing helix chain 'C' and resid 2145 through 2169 removed outlier: 4.184A pdb=" N VAL C2149 " --> pdb=" O SER C2145 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU C2150 " --> pdb=" O PRO C2146 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP C2151 " --> pdb=" O SER C2147 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER C2154 " --> pdb=" O GLU C2150 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C2166 " --> pdb=" O ILE C2162 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE C2167 " --> pdb=" O ARG C2163 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL C2168 " --> pdb=" O SER C2164 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N GLN C2169 " --> pdb=" O LEU C2165 " (cutoff:3.500A) Processing helix chain 'C' and resid 2171 through 2188 removed outlier: 3.578A pdb=" N LEU C2177 " --> pdb=" O GLN C2173 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET C2178 " --> pdb=" O GLU C2174 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C2179 " --> pdb=" O GLU C2175 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2194 Processing helix chain 'C' and resid 2195 through 2219 removed outlier: 5.358A pdb=" N MET C2203 " --> pdb=" O ARG C2199 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N HIS C2204 " --> pdb=" O ALA C2200 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLU C2205 " --> pdb=" O LEU C2201 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR C2206 " --> pdb=" O GLY C2202 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY C2218 " --> pdb=" O VAL C2214 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C2219 " --> pdb=" O LEU C2215 " (cutoff:3.500A) Processing helix chain 'C' and resid 2225 through 2244 removed outlier: 3.650A pdb=" N VAL C2229 " --> pdb=" O PHE C2225 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C2241 " --> pdb=" O CYS C2237 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE C2242 " --> pdb=" O TYR C2238 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER C2243 " --> pdb=" O PHE C2239 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ARG C2244 " --> pdb=" O CYS C2240 " (cutoff:3.500A) Processing helix chain 'C' and resid 2245 through 2255 removed outlier: 3.803A pdb=" N ASP C2252 " --> pdb=" O ARG C2248 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS C2253 " --> pdb=" O SER C2249 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU C2254 " --> pdb=" O MET C2250 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N SER C2255 " --> pdb=" O PHE C2251 " (cutoff:3.500A) Processing helix chain 'C' and resid 2256 through 2262 removed outlier: 3.599A pdb=" N ASN C2260 " --> pdb=" O TYR C2256 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY C2262 " --> pdb=" O LEU C2258 " (cutoff:3.500A) Processing helix chain 'C' and resid 2271 through 2281 removed outlier: 3.544A pdb=" N VAL C2275 " --> pdb=" O THR C2271 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C2280 " --> pdb=" O ALA C2276 " (cutoff:3.500A) Processing helix chain 'C' and resid 2283 through 2290 Processing helix chain 'C' and resid 2291 through 2308 removed outlier: 3.807A pdb=" N LEU C2295 " --> pdb=" O GLN C2291 " (cutoff:3.500A) Processing helix chain 'C' and resid 2310 through 2317 removed outlier: 3.545A pdb=" N LYS C2316 " --> pdb=" O MET C2312 " (cutoff:3.500A) Processing helix chain 'C' and resid 2324 through 2340 removed outlier: 3.609A pdb=" N PHE C2334 " --> pdb=" O ARG C2330 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2361 removed outlier: 3.713A pdb=" N VAL C2352 " --> pdb=" O GLU C2348 " (cutoff:3.500A) Proline residue: C2361 - end of helix Processing helix chain 'C' and resid 2375 through 2390 removed outlier: 3.823A pdb=" N ILE C2380 " --> pdb=" O LEU C2376 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU C2381 " --> pdb=" O LEU C2377 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU C2382 " --> pdb=" O ALA C2378 " (cutoff:3.500A) Proline residue: C2390 - end of helix Processing helix chain 'C' and resid 2417 through 2437 removed outlier: 3.714A pdb=" N TYR C2426 " --> pdb=" O ILE C2422 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA C2427 " --> pdb=" O MET C2423 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C2437 " --> pdb=" O LEU C2433 " (cutoff:3.500A) Processing helix chain 'C' and resid 2439 through 2446 Processing helix chain 'C' and resid 2447 through 2462 Proline residue: C2462 - end of helix Processing helix chain 'C' and resid 2463 through 2472 Processing helix chain 'C' and resid 2495 through 2509 removed outlier: 4.347A pdb=" N LYS C2499 " --> pdb=" O VAL C2495 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER C2501 " --> pdb=" O ASP C2497 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET C2502 " --> pdb=" O HIS C2498 " (cutoff:3.500A) Processing helix chain 'C' and resid 2514 through 2525 removed outlier: 4.434A pdb=" N VAL C2524 " --> pdb=" O HIS C2520 " (cutoff:3.500A) Processing helix chain 'C' and resid 2526 through 2537 Processing helix chain 'C' and resid 2539 through 2545 removed outlier: 5.531A pdb=" N THR C2543 " --> pdb=" O ALA C2539 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR C2544 " --> pdb=" O THR C2540 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLU C2545 " --> pdb=" O PHE C2541 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2539 through 2545' Processing helix chain 'C' and resid 2546 through 2566 removed outlier: 3.887A pdb=" N CYS C2555 " --> pdb=" O ASN C2551 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU C2559 " --> pdb=" O CYS C2555 " (cutoff:3.500A) Proline residue: C2560 - end of helix Processing helix chain 'C' and resid 2568 through 2573 removed outlier: 5.410A pdb=" N THR C2572 " --> pdb=" O LEU C2568 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLU C2573 " --> pdb=" O PHE C2569 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2568 through 2573' Processing helix chain 'C' and resid 2575 through 2593 removed outlier: 3.798A pdb=" N GLY C2592 " --> pdb=" O ARG C2588 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ARG C2593 " --> pdb=" O LEU C2589 " (cutoff:3.500A) Processing helix chain 'C' and resid 2596 through 2614 removed outlier: 3.730A pdb=" N TYR C2613 " --> pdb=" O ALA C2609 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE C2614 " --> pdb=" O LEU C2610 " (cutoff:3.500A) Processing helix chain 'C' and resid 2615 through 2630 removed outlier: 4.063A pdb=" N LEU C2619 " --> pdb=" O ARG C2615 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN C2620 " --> pdb=" O PRO C2616 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N HIS C2621 " --> pdb=" O SER C2617 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LEU C2622 " --> pdb=" O MET C2618 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE C2628 " --> pdb=" O ARG C2624 " (cutoff:3.500A) Processing helix chain 'C' and resid 2636 through 2652 Proline residue: C2640 - end of helix Processing helix chain 'C' and resid 2668 through 2689 removed outlier: 6.919A pdb=" N LEU C2672 " --> pdb=" O SER C2668 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N HIS C2673 " --> pdb=" O GLU C2669 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP C2680 " --> pdb=" O ARG C2676 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS C2688 " --> pdb=" O ASP C2684 " (cutoff:3.500A) Processing helix chain 'C' and resid 2693 through 2711 removed outlier: 3.795A pdb=" N MET C2698 " --> pdb=" O GLU C2694 " (cutoff:3.500A) Proline residue: C2701 - end of helix Proline residue: C2711 - end of helix Processing helix chain 'C' and resid 2741 through 2746 removed outlier: 4.599A pdb=" N VAL C2745 " --> pdb=" O GLU C2741 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE C2746 " --> pdb=" O THR C2742 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2741 through 2746' Processing helix chain 'C' and resid 2751 through 2774 removed outlier: 3.874A pdb=" N LYS C2757 " --> pdb=" O SER C2753 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN C2774 " --> pdb=" O LYS C2770 " (cutoff:3.500A) Processing helix chain 'C' and resid 2799 through 2820 removed outlier: 3.538A pdb=" N GLU C2803 " --> pdb=" O GLU C2799 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE C2804 " --> pdb=" O LYS C2800 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG C2806 " --> pdb=" O LYS C2802 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TRP C2807 " --> pdb=" O GLU C2803 " (cutoff:3.500A) Proline residue: C2808 - end of helix removed outlier: 5.286A pdb=" N GLU C2820 " --> pdb=" O MET C2816 " (cutoff:3.500A) Processing helix chain 'C' and resid 2868 through 2895 removed outlier: 4.209A pdb=" N GLU C2893 " --> pdb=" O LYS C2889 " (cutoff:3.500A) Processing helix chain 'C' and resid 2907 through 2912 removed outlier: 6.081A pdb=" N THR C2912 " --> pdb=" O TYR C2908 " (cutoff:3.500A) Processing helix chain 'C' and resid 2913 through 2934 removed outlier: 3.737A pdb=" N ALA C2917 " --> pdb=" O ALA C2913 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ARG C2918 " --> pdb=" O LYS C2914 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ASP C2919 " --> pdb=" O GLU C2915 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS C2922 " --> pdb=" O ARG C2918 " (cutoff:3.500A) Processing helix chain 'C' and resid 2949 through 2982 removed outlier: 5.718A pdb=" N PHE C2955 " --> pdb=" O ILE C2951 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA C2956 " --> pdb=" O GLU C2952 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE C2957 " --> pdb=" O LYS C2953 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C2969 " --> pdb=" O ARG C2965 " (cutoff:3.500A) Processing helix chain 'C' and resid 2991 through 3014 removed outlier: 3.611A pdb=" N LEU C3002 " --> pdb=" O PHE C2998 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU C3003 " --> pdb=" O ALA C2999 " (cutoff:3.500A) Proline residue: C3004 - end of helix removed outlier: 3.806A pdb=" N THR C3011 " --> pdb=" O ASN C3007 " (cutoff:3.500A) Processing helix chain 'C' and resid 3032 through 3051 removed outlier: 3.812A pdb=" N LEU C3042 " --> pdb=" O MET C3038 " (cutoff:3.500A) Processing helix chain 'C' and resid 3053 through 3058 removed outlier: 4.086A pdb=" N PHE C3057 " --> pdb=" O ARG C3053 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY C3058 " --> pdb=" O VAL C3054 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3053 through 3058' Processing helix chain 'C' and resid 3060 through 3075 Processing helix chain 'C' and resid 3076 through 3083 removed outlier: 3.777A pdb=" N VAL C3080 " --> pdb=" O ASP C3076 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET C3081 " --> pdb=" O ALA C3077 " (cutoff:3.500A) Processing helix chain 'C' and resid 3085 through 3112 removed outlier: 3.537A pdb=" N PHE C3095 " --> pdb=" O GLY C3091 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE C3096 " --> pdb=" O LEU C3092 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C3108 " --> pdb=" O GLU C3104 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU C3112 " --> pdb=" O GLU C3108 " (cutoff:3.500A) Processing helix chain 'C' and resid 3123 through 3151 removed outlier: 3.631A pdb=" N VAL C3134 " --> pdb=" O THR C3130 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU C3137 " --> pdb=" O THR C3133 " (cutoff:3.500A) Proline residue: C3138 - end of helix removed outlier: 3.708A pdb=" N GLN C3149 " --> pdb=" O GLN C3145 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS C3150 " --> pdb=" O HIS C3146 " (cutoff:3.500A) Processing helix chain 'C' and resid 3159 through 3175 removed outlier: 5.330A pdb=" N VAL C3163 " --> pdb=" O ASP C3159 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU C3175 " --> pdb=" O SER C3171 " (cutoff:3.500A) Processing helix chain 'C' and resid 3180 through 3201 Proline residue: C3188 - end of helix Processing helix chain 'C' and resid 3217 through 3222 Processing helix chain 'C' and resid 3226 through 3231 removed outlier: 6.672A pdb=" N LEU C3230 " --> pdb=" O GLU C3226 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLY C3231 " --> pdb=" O ARG C3227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3226 through 3231' Processing helix chain 'C' and resid 3235 through 3241 removed outlier: 3.539A pdb=" N MET C3239 " --> pdb=" O SER C3235 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N CYS C3240 " --> pdb=" O VAL C3236 " (cutoff:3.500A) Proline residue: C3241 - end of helix No H-bonds generated for 'chain 'C' and resid 3235 through 3241' Processing helix chain 'C' and resid 3245 through 3260 Processing helix chain 'C' and resid 3262 through 3267 Proline residue: C3267 - end of helix Processing helix chain 'C' and resid 3268 through 3288 removed outlier: 4.358A pdb=" N LEU C3274 " --> pdb=" O ILE C3270 " (cutoff:3.500A) Proline residue: C3275 - end of helix Proline residue: C3282 - end of helix removed outlier: 4.343A pdb=" N GLU C3286 " --> pdb=" O PRO C3282 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG C3287 " --> pdb=" O ARG C3283 " (cutoff:3.500A) Processing helix chain 'C' and resid 3308 through 3327 removed outlier: 3.770A pdb=" N LEU C3312 " --> pdb=" O THR C3308 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C3319 " --> pdb=" O LEU C3315 " (cutoff:3.500A) Processing helix chain 'C' and resid 3332 through 3343 removed outlier: 5.755A pdb=" N LYS C3336 " --> pdb=" O ALA C3332 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG C3337 " --> pdb=" O THR C3333 " (cutoff:3.500A) Processing helix chain 'C' and resid 3344 through 3350 removed outlier: 4.728A pdb=" N ARG C3348 " --> pdb=" O PRO C3344 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ALA C3349 " --> pdb=" O ILE C3345 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG C3350 " --> pdb=" O VAL C3346 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3344 through 3350' Processing helix chain 'C' and resid 3351 through 3381 removed outlier: 4.698A pdb=" N HIS C3355 " --> pdb=" O PRO C3351 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE C3358 " --> pdb=" O LEU C3354 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE C3359 " --> pdb=" O HIS C3355 " (cutoff:3.500A) Proline residue: C3360 - end of helix removed outlier: 3.611A pdb=" N GLN C3378 " --> pdb=" O ALA C3374 " (cutoff:3.500A) Processing helix chain 'C' and resid 3389 through 3413 removed outlier: 6.543A pdb=" N LEU C3393 " --> pdb=" O GLU C3389 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA C3407 " --> pdb=" O ARG C3403 " (cutoff:3.500A) Proline residue: C3410 - end of helix Processing helix chain 'C' and resid 3419 through 3426 Processing helix chain 'C' and resid 3428 through 3448 Processing helix chain 'C' and resid 3449 through 3463 removed outlier: 3.755A pdb=" N GLN C3456 " --> pdb=" O LYS C3452 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN C3457 " --> pdb=" O ARG C3453 " (cutoff:3.500A) Processing helix chain 'C' and resid 3466 through 3478 removed outlier: 4.631A pdb=" N LEU C3470 " --> pdb=" O ASN C3466 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP C3473 " --> pdb=" O PHE C3469 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N SER C3474 " --> pdb=" O LEU C3470 " (cutoff:3.500A) Processing helix chain 'C' and resid 3508 through 3526 removed outlier: 3.941A pdb=" N LYS C3516 " --> pdb=" O ALA C3512 " (cutoff:3.500A) Proline residue: C3519 - end of helix removed outlier: 3.952A pdb=" N MET C3524 " --> pdb=" O ILE C3520 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N CYS C3525 " --> pdb=" O GLY C3521 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ALA C3526 " --> pdb=" O LEU C3522 " (cutoff:3.500A) Processing helix chain 'C' and resid 3529 through 3543 removed outlier: 3.572A pdb=" N LEU C3535 " --> pdb=" O ASP C3531 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS C3543 " --> pdb=" O ARG C3539 " (cutoff:3.500A) Processing helix chain 'C' and resid 3545 through 3557 Processing helix chain 'C' and resid 3566 through 3579 removed outlier: 3.604A pdb=" N ARG C3570 " --> pdb=" O SER C3566 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TRP C3571 " --> pdb=" O PRO C3567 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C3572 " --> pdb=" O SER C3568 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU C3579 " --> pdb=" O LEU C3575 " (cutoff:3.500A) Processing helix chain 'C' and resid 3588 through 3612 removed outlier: 3.757A pdb=" N HIS C3605 " --> pdb=" O ALA C3601 " (cutoff:3.500A) Proline residue: C3612 - end of helix Processing helix chain 'C' and resid 3628 through 3638 removed outlier: 4.034A pdb=" N VAL C3632 " --> pdb=" O ARG C3628 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL C3633 " --> pdb=" O ARG C3629 " (cutoff:3.500A) Processing helix chain 'C' and resid 3645 through 3665 removed outlier: 3.710A pdb=" N GLU C3655 " --> pdb=" O ASN C3651 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU C3663 " --> pdb=" O ALA C3659 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR C3664 " --> pdb=" O ALA C3660 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU C3665 " --> pdb=" O TRP C3661 " (cutoff:3.500A) Processing helix chain 'C' and resid 3669 through 3679 Processing helix chain 'C' and resid 3696 through 3711 Processing helix chain 'C' and resid 3719 through 3735 removed outlier: 3.832A pdb=" N CYS C3733 " --> pdb=" O MET C3729 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N HIS C3734 " --> pdb=" O ALA C3730 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU C3735 " --> pdb=" O LYS C3731 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3772 removed outlier: 3.632A pdb=" N TYR C3765 " --> pdb=" O GLN C3761 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU C3770 " --> pdb=" O GLN C3766 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR C3772 " --> pdb=" O SER C3768 " (cutoff:3.500A) Processing helix chain 'C' and resid 3774 through 3787 removed outlier: 4.018A pdb=" N LYS C3787 " --> pdb=" O ILE C3783 " (cutoff:3.500A) Processing helix chain 'C' and resid 3791 through 3806 Processing helix chain 'C' and resid 3809 through 3824 Processing helix chain 'C' and resid 3825 through 3839 removed outlier: 4.989A pdb=" N PHE C3829 " --> pdb=" O GLU C3825 " (cutoff:3.500A) Processing helix chain 'C' and resid 3843 through 3857 Processing helix chain 'C' and resid 3877 through 3893 removed outlier: 3.562A pdb=" N CYS C3892 " --> pdb=" O LEU C3888 " (cutoff:3.500A) Processing helix chain 'C' and resid 3896 through 3905 Processing helix chain 'C' and resid 3914 through 3939 removed outlier: 3.637A pdb=" N TYR C3937 " --> pdb=" O PHE C3933 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY C3939 " --> pdb=" O TRP C3935 " (cutoff:3.500A) Processing helix chain 'C' and resid 3944 through 3970 removed outlier: 3.557A pdb=" N ILE C3969 " --> pdb=" O LEU C3965 " (cutoff:3.500A) Processing helix chain 'C' and resid 3973 through 3983 Processing helix chain 'C' and resid 3984 through 4007 removed outlier: 3.934A pdb=" N ALA C3988 " --> pdb=" O ARG C3984 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS C3998 " --> pdb=" O HIS C3994 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN C4005 " --> pdb=" O MET C4001 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASP C4006 " --> pdb=" O LYS C4002 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N SER C4007 " --> pdb=" O LEU C4003 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4032 removed outlier: 3.528A pdb=" N GLU C4015 " --> pdb=" O GLU C4011 " (cutoff:3.500A) Processing helix chain 'C' and resid 4038 through 4052 Processing helix chain 'C' and resid 4053 through 4072 removed outlier: 3.646A pdb=" N MET C4064 " --> pdb=" O LYS C4060 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP C4070 " --> pdb=" O LEU C4066 " (cutoff:3.500A) Processing helix chain 'C' and resid 4074 through 4082 removed outlier: 4.908A pdb=" N THR C4082 " --> pdb=" O GLN C4078 " (cutoff:3.500A) Processing helix chain 'C' and resid 4089 through 4101 removed outlier: 3.631A pdb=" N MET C4097 " --> pdb=" O PHE C4093 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP C4098 " --> pdb=" O GLN C4094 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER C4099 " --> pdb=" O LYS C4095 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN C4100 " --> pdb=" O ALA C4096 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LYS C4101 " --> pdb=" O MET C4097 " (cutoff:3.500A) Processing helix chain 'C' and resid 4104 through 4116 removed outlier: 5.444A pdb=" N GLU C4116 " --> pdb=" O LEU C4112 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4133 removed outlier: 3.705A pdb=" N ALA C4129 " --> pdb=" O PHE C4125 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN C4130 " --> pdb=" O GLU C4126 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N PHE C4132 " --> pdb=" O PHE C4128 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLN C4133 " --> pdb=" O ALA C4129 " (cutoff:3.500A) Processing helix chain 'C' and resid 4134 through 4155 removed outlier: 4.330A pdb=" N ASP C4138 " --> pdb=" O GLU C4134 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE C4139 " --> pdb=" O PRO C4135 " (cutoff:3.500A) Proline residue: C4155 - end of helix Processing helix chain 'C' and resid 4157 through 4168 removed outlier: 3.551A pdb=" N GLU C4168 " --> pdb=" O LEU C4164 " (cutoff:3.500A) Processing helix chain 'C' and resid 4169 through 4175 removed outlier: 3.695A pdb=" N TYR C4173 " --> pdb=" O SER C4169 " (cutoff:3.500A) Processing helix chain 'C' and resid 4198 through 4207 Processing helix chain 'C' and resid 4208 through 4224 Processing helix chain 'C' and resid 4226 through 4252 removed outlier: 4.465A pdb=" N MET C4231 " --> pdb=" O GLU C4227 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLU C4232 " --> pdb=" O ALA C4228 " (cutoff:3.500A) Processing helix chain 'C' and resid 4540 through 4559 Processing helix chain 'C' and resid 4560 through 4580 removed outlier: 4.609A pdb=" N PHE C4579 " --> pdb=" O PHE C4575 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TYR C4580 " --> pdb=" O ILE C4576 " (cutoff:3.500A) Processing helix chain 'C' and resid 4640 through 4683 removed outlier: 3.542A pdb=" N TRP C4644 " --> pdb=" O GLU C4640 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL C4666 " --> pdb=" O ASN C4662 " (cutoff:3.500A) Proline residue: C4667 - end of helix Processing helix chain 'C' and resid 4696 through 4707 removed outlier: 3.548A pdb=" N ARG C4703 " --> pdb=" O GLY C4699 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEU C4704 " --> pdb=" O GLN C4700 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL C4705 " --> pdb=" O TRP C4701 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU C4706 " --> pdb=" O ASP C4702 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN C4707 " --> pdb=" O ARG C4703 " (cutoff:3.500A) Processing helix chain 'C' and resid 4719 through 4728 Processing helix chain 'C' and resid 4733 through 4742 Processing helix chain 'C' and resid 4744 through 4750 removed outlier: 3.810A pdb=" N LEU C4748 " --> pdb=" O ASP C4744 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU C4749 " --> pdb=" O LEU C4745 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE C4750 " --> pdb=" O ALA C4746 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4744 through 4750' Processing helix chain 'C' and resid 4772 through 4787 removed outlier: 3.865A pdb=" N THR C4785 " --> pdb=" O GLY C4781 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP C4786 " --> pdb=" O VAL C4782 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ASN C4787 " --> pdb=" O ILE C4783 " (cutoff:3.500A) Processing helix chain 'C' and resid 4788 through 4805 removed outlier: 4.033A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4806 through 4820 removed outlier: 4.854A pdb=" N ALA C4810 " --> pdb=" O ASN C4806 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ALA C4811 " --> pdb=" O PHE C4807 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N HIS C4812 " --> pdb=" O PHE C4808 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N LEU C4813 " --> pdb=" O PHE C4809 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU C4814 " --> pdb=" O ALA C4810 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASP C4815 " --> pdb=" O ALA C4811 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE C4816 " --> pdb=" O HIS C4812 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ALA C4817 " --> pdb=" O LEU C4813 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N MET C4818 " --> pdb=" O LEU C4814 " (cutoff:3.500A) Processing helix chain 'C' and resid 4821 through 4832 removed outlier: 3.788A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) Processing helix chain 'C' and resid 4833 through 4858 Processing helix chain 'C' and resid 4859 through 4864 removed outlier: 4.354A pdb=" N TYR C4863 " --> pdb=" O PHE C4859 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASN C4864 " --> pdb=" O ARG C4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4859 through 4864' Processing helix chain 'C' and resid 4878 through 4893 removed outlier: 3.959A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C4892 " --> pdb=" O TYR C4888 " (cutoff:3.500A) Processing helix chain 'C' and resid 4896 through 4901 removed outlier: 3.997A pdb=" N GLU C4900 " --> pdb=" O GLY C4896 " (cutoff:3.500A) Processing helix chain 'C' and resid 4909 through 4924 Processing helix chain 'C' and resid 4928 through 4957 Processing helix chain 'C' and resid 4964 through 4970 removed outlier: 3.761A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR C4970 " --> pdb=" O ASP C4966 " (cutoff:3.500A) Processing helix chain 'C' and resid 4973 through 4981 Processing helix chain 'C' and resid 4984 through 4998 Processing helix chain 'C' and resid 4999 through 5004 removed outlier: 3.836A pdb=" N HIS C5003 " --> pdb=" O ASP C4999 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR C5004 " --> pdb=" O GLU C5000 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4999 through 5004' Processing helix chain 'C' and resid 5005 through 5017 Processing helix chain 'C' and resid 5027 through 5033 Processing helix chain 'C' and resid 250 through 256 removed outlier: 4.152A pdb=" N CYS C 253 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR C 254 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS C 255 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ALA C 256 " --> pdb=" O CYS C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 256' Processing helix chain 'C' and resid 3682 through 3687 removed outlier: 5.483A pdb=" N GLU C3685 " --> pdb=" O GLU C3682 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU C3686 " --> pdb=" O GLN C3683 " (cutoff:3.500A) Processing helix chain 'C' and resid 3152 through 3157 removed outlier: 3.984A pdb=" N ILE C3157 " --> pdb=" O PHE C3152 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3152 through 3157' Processing helix chain 'C' and resid 4685 through 4690 Processing helix chain 'D' and resid 61 through 66 removed outlier: 4.530A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N CYS D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 66' Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 308 through 313 removed outlier: 6.396A pdb=" N THR D 312 " --> pdb=" O HIS D 308 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER D 313 " --> pdb=" O THR D 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 313' Processing helix chain 'D' and resid 364 through 370 Processing helix chain 'D' and resid 394 through 422 removed outlier: 3.554A pdb=" N HIS D 405 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 453 Processing helix chain 'D' and resid 460 through 482 removed outlier: 3.973A pdb=" N GLN D 465 " --> pdb=" O HIS D 461 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 496 removed outlier: 3.667A pdb=" N LEU D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN D 489 " --> pdb=" O SER D 485 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS D 490 " --> pdb=" O LEU D 486 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE D 491 " --> pdb=" O VAL D 487 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.871A pdb=" N TYR D 506 " --> pdb=" O HIS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 531 removed outlier: 3.561A pdb=" N GLU D 513 " --> pdb=" O GLU D 509 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER D 514 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLU D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR D 523 " --> pdb=" O VAL D 519 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU D 524 " --> pdb=" O ASN D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 544 removed outlier: 3.580A pdb=" N LEU D 539 " --> pdb=" O ALA D 535 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE D 540 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER D 541 " --> pdb=" O CYS D 537 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR D 542 " --> pdb=" O ALA D 538 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN D 543 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 551 Processing helix chain 'D' and resid 556 through 571 removed outlier: 3.625A pdb=" N ILE D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D 570 " --> pdb=" O CYS D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 579 removed outlier: 4.083A pdb=" N ASN D 576 " --> pdb=" O PRO D 572 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLN D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 593 removed outlier: 3.725A pdb=" N LEU D 590 " --> pdb=" O ILE D 586 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP D 591 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 609 removed outlier: 3.759A pdb=" N LEU D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL D 608 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N CYS D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 629 removed outlier: 3.673A pdb=" N ASP D 619 " --> pdb=" O ARG D 615 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU D 620 " --> pdb=" O SER D 616 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU D 626 " --> pdb=" O THR D 622 " (cutoff:3.500A) Proline residue: D 627 - end of helix Processing helix chain 'D' and resid 810 through 815 removed outlier: 4.790A pdb=" N ALA D 814 " --> pdb=" O PRO D 810 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL D 815 " --> pdb=" O CYS D 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 810 through 815' Processing helix chain 'D' and resid 847 through 853 removed outlier: 3.756A pdb=" N PHE D 851 " --> pdb=" O SER D 847 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL D 852 " --> pdb=" O HIS D 848 " (cutoff:3.500A) Proline residue: D 853 - end of helix No H-bonds generated for 'chain 'D' and resid 847 through 853' Processing helix chain 'D' and resid 864 through 885 removed outlier: 3.530A pdb=" N ILE D 870 " --> pdb=" O HIS D 866 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLU D 872 " --> pdb=" O GLU D 868 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS D 873 " --> pdb=" O ARG D 869 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU D 874 " --> pdb=" O ILE D 870 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA D 875 " --> pdb=" O ARG D 871 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE D 878 " --> pdb=" O LEU D 874 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLU D 880 " --> pdb=" O GLU D 876 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU D 881 " --> pdb=" O ASN D 877 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TRP D 882 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ALA D 883 " --> pdb=" O HIS D 879 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR D 885 " --> pdb=" O LEU D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 909 through 914 removed outlier: 3.787A pdb=" N LEU D 913 " --> pdb=" O ASN D 909 " (cutoff:3.500A) Proline residue: D 914 - end of helix No H-bonds generated for 'chain 'D' and resid 909 through 914' Processing helix chain 'D' and resid 915 through 936 Processing helix chain 'D' and resid 945 through 950 removed outlier: 3.970A pdb=" N ASN D 949 " --> pdb=" O LYS D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 1004 removed outlier: 3.556A pdb=" N VAL D 995 " --> pdb=" O ASN D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1030 through 1048 removed outlier: 4.066A pdb=" N SER D1038 " --> pdb=" O SER D1034 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU D1039 " --> pdb=" O ASN D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1067 through 1073 removed outlier: 4.594A pdb=" N ARG D1071 " --> pdb=" O SER D1067 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL D1072 " --> pdb=" O ARG D1068 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ARG D1073 " --> pdb=" O TRP D1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1067 through 1073' Processing helix chain 'D' and resid 1217 through 1222 removed outlier: 7.230A pdb=" N GLU D1221 " --> pdb=" O CYS D1217 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY D1222 " --> pdb=" O GLY D1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1217 through 1222' Processing helix chain 'D' and resid 1423 through 1430 removed outlier: 3.619A pdb=" N LEU D1428 " --> pdb=" O PRO D1424 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN D1429 " --> pdb=" O GLU D1425 " (cutoff:3.500A) Processing helix chain 'D' and resid 1444 through 1449 removed outlier: 4.356A pdb=" N VAL D1448 " --> pdb=" O GLU D1444 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TRP D1449 " --> pdb=" O PRO D1445 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1444 through 1449' Processing helix chain 'D' and resid 1496 through 1501 removed outlier: 4.115A pdb=" N PHE D1500 " --> pdb=" O TRP D1496 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL D1501 " --> pdb=" O GLY D1497 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1496 through 1501' Processing helix chain 'D' and resid 1574 through 1580 removed outlier: 4.189A pdb=" N ALA D1578 " --> pdb=" O PRO D1574 " (cutoff:3.500A) Processing helix chain 'D' and resid 1649 through 1657 removed outlier: 4.257A pdb=" N LEU D1653 " --> pdb=" O ASP D1649 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER D1654 " --> pdb=" O ILE D1650 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLU D1655 " --> pdb=" O LEU D1651 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU D1657 " --> pdb=" O LEU D1653 " (cutoff:3.500A) Processing helix chain 'D' and resid 1658 through 1675 removed outlier: 3.878A pdb=" N PHE D1662 " --> pdb=" O ASP D1658 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS D1674 " --> pdb=" O TYR D1670 " (cutoff:3.500A) Processing helix chain 'D' and resid 1678 through 1689 removed outlier: 3.666A pdb=" N ALA D1684 " --> pdb=" O ARG D1680 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N CYS D1686 " --> pdb=" O ALA D1682 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER D1687 " --> pdb=" O HIS D1683 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N HIS D1688 " --> pdb=" O ALA D1684 " (cutoff:3.500A) Processing helix chain 'D' and resid 1690 through 1700 removed outlier: 3.537A pdb=" N LEU D1694 " --> pdb=" O ASP D1690 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU D1699 " --> pdb=" O LEU D1695 " (cutoff:3.500A) Processing helix chain 'D' and resid 1704 through 1719 Processing helix chain 'D' and resid 1720 through 1734 removed outlier: 3.501A pdb=" N MET D1730 " --> pdb=" O SER D1726 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER D1732 " --> pdb=" O ARG D1728 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU D1733 " --> pdb=" O SER D1729 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N TYR D1734 " --> pdb=" O MET D1730 " (cutoff:3.500A) Processing helix chain 'D' and resid 1739 through 1745 removed outlier: 3.691A pdb=" N ILE D1745 " --> pdb=" O GLU D1741 " (cutoff:3.500A) Processing helix chain 'D' and resid 1803 through 1825 removed outlier: 3.636A pdb=" N ASP D1809 " --> pdb=" O GLU D1805 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS D1825 " --> pdb=" O ASP D1821 " (cutoff:3.500A) Processing helix chain 'D' and resid 1833 through 1852 Proline residue: D1840 - end of helix Processing helix chain 'D' and resid 1855 through 1867 Processing helix chain 'D' and resid 1934 through 1987 removed outlier: 3.865A pdb=" N GLN D1938 " --> pdb=" O SER D1934 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP D1967 " --> pdb=" O GLU D1963 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS D1968 " --> pdb=" O ARG D1964 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE D1984 " --> pdb=" O LEU D1980 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N THR D1985 " --> pdb=" O MET D1981 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N MET D1986 " --> pdb=" O ARG D1982 " (cutoff:3.500A) Processing helix chain 'D' and resid 1990 through 2001 removed outlier: 4.594A pdb=" N ARG D1994 " --> pdb=" O GLU D1990 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLU D1997 " --> pdb=" O ARG D1993 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE D1998 " --> pdb=" O ARG D1994 " (cutoff:3.500A) Proline residue: D2001 - end of helix Processing helix chain 'D' and resid 2002 through 2011 removed outlier: 3.556A pdb=" N ASN D2007 " --> pdb=" O GLN D2003 " (cutoff:3.500A) Processing helix chain 'D' and resid 2017 through 2022 removed outlier: 4.188A pdb=" N CYS D2021 " --> pdb=" O ASP D2017 " (cutoff:3.500A) Proline residue: D2022 - end of helix No H-bonds generated for 'chain 'D' and resid 2017 through 2022' Processing helix chain 'D' and resid 2024 through 2043 Processing helix chain 'D' and resid 2093 through 2109 removed outlier: 3.667A pdb=" N ASP D2109 " --> pdb=" O TRP D2105 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2130 removed outlier: 3.971A pdb=" N GLY D2130 " --> pdb=" O ARG D2126 " (cutoff:3.500A) Processing helix chain 'D' and resid 2131 through 2141 Proline residue: D2139 - end of helix Processing helix chain 'D' and resid 2145 through 2169 removed outlier: 4.184A pdb=" N VAL D2149 " --> pdb=" O SER D2145 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU D2150 " --> pdb=" O PRO D2146 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP D2151 " --> pdb=" O SER D2147 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER D2154 " --> pdb=" O GLU D2150 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D2166 " --> pdb=" O ILE D2162 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE D2167 " --> pdb=" O ARG D2163 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL D2168 " --> pdb=" O SER D2164 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLN D2169 " --> pdb=" O LEU D2165 " (cutoff:3.500A) Processing helix chain 'D' and resid 2171 through 2188 removed outlier: 3.578A pdb=" N LEU D2177 " --> pdb=" O GLN D2173 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET D2178 " --> pdb=" O GLU D2174 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D2179 " --> pdb=" O GLU D2175 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2194 Processing helix chain 'D' and resid 2195 through 2219 removed outlier: 5.358A pdb=" N MET D2203 " --> pdb=" O ARG D2199 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N HIS D2204 " --> pdb=" O ALA D2200 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU D2205 " --> pdb=" O LEU D2201 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR D2206 " --> pdb=" O GLY D2202 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY D2218 " --> pdb=" O VAL D2214 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU D2219 " --> pdb=" O LEU D2215 " (cutoff:3.500A) Processing helix chain 'D' and resid 2225 through 2244 removed outlier: 3.650A pdb=" N VAL D2229 " --> pdb=" O PHE D2225 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D2241 " --> pdb=" O CYS D2237 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE D2242 " --> pdb=" O TYR D2238 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER D2243 " --> pdb=" O PHE D2239 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG D2244 " --> pdb=" O CYS D2240 " (cutoff:3.500A) Processing helix chain 'D' and resid 2245 through 2255 removed outlier: 3.803A pdb=" N ASP D2252 " --> pdb=" O ARG D2248 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS D2253 " --> pdb=" O SER D2249 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU D2254 " --> pdb=" O MET D2250 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N SER D2255 " --> pdb=" O PHE D2251 " (cutoff:3.500A) Processing helix chain 'D' and resid 2256 through 2262 removed outlier: 3.599A pdb=" N ASN D2260 " --> pdb=" O TYR D2256 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY D2262 " --> pdb=" O LEU D2258 " (cutoff:3.500A) Processing helix chain 'D' and resid 2271 through 2281 removed outlier: 3.544A pdb=" N VAL D2275 " --> pdb=" O THR D2271 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL D2280 " --> pdb=" O ALA D2276 " (cutoff:3.500A) Processing helix chain 'D' and resid 2283 through 2290 Processing helix chain 'D' and resid 2291 through 2308 removed outlier: 3.807A pdb=" N LEU D2295 " --> pdb=" O GLN D2291 " (cutoff:3.500A) Processing helix chain 'D' and resid 2310 through 2317 removed outlier: 3.545A pdb=" N LYS D2316 " --> pdb=" O MET D2312 " (cutoff:3.500A) Processing helix chain 'D' and resid 2324 through 2340 removed outlier: 3.608A pdb=" N PHE D2334 " --> pdb=" O ARG D2330 " (cutoff:3.500A) Processing helix chain 'D' and resid 2346 through 2361 removed outlier: 3.713A pdb=" N VAL D2352 " --> pdb=" O GLU D2348 " (cutoff:3.500A) Proline residue: D2361 - end of helix Processing helix chain 'D' and resid 2375 through 2390 removed outlier: 3.824A pdb=" N ILE D2380 " --> pdb=" O LEU D2376 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU D2381 " --> pdb=" O LEU D2377 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU D2382 " --> pdb=" O ALA D2378 " (cutoff:3.500A) Proline residue: D2390 - end of helix Processing helix chain 'D' and resid 2417 through 2437 removed outlier: 3.714A pdb=" N TYR D2426 " --> pdb=" O ILE D2422 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA D2427 " --> pdb=" O MET D2423 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D2437 " --> pdb=" O LEU D2433 " (cutoff:3.500A) Processing helix chain 'D' and resid 2439 through 2446 Processing helix chain 'D' and resid 2447 through 2462 Proline residue: D2462 - end of helix Processing helix chain 'D' and resid 2463 through 2472 Processing helix chain 'D' and resid 2495 through 2509 removed outlier: 4.347A pdb=" N LYS D2499 " --> pdb=" O VAL D2495 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER D2501 " --> pdb=" O ASP D2497 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET D2502 " --> pdb=" O HIS D2498 " (cutoff:3.500A) Processing helix chain 'D' and resid 2514 through 2525 removed outlier: 4.434A pdb=" N VAL D2524 " --> pdb=" O HIS D2520 " (cutoff:3.500A) Processing helix chain 'D' and resid 2526 through 2537 Processing helix chain 'D' and resid 2539 through 2545 removed outlier: 5.531A pdb=" N THR D2543 " --> pdb=" O ALA D2539 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR D2544 " --> pdb=" O THR D2540 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLU D2545 " --> pdb=" O PHE D2541 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2539 through 2545' Processing helix chain 'D' and resid 2546 through 2566 removed outlier: 3.887A pdb=" N CYS D2555 " --> pdb=" O ASN D2551 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU D2559 " --> pdb=" O CYS D2555 " (cutoff:3.500A) Proline residue: D2560 - end of helix Processing helix chain 'D' and resid 2568 through 2573 removed outlier: 5.410A pdb=" N THR D2572 " --> pdb=" O LEU D2568 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLU D2573 " --> pdb=" O PHE D2569 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2568 through 2573' Processing helix chain 'D' and resid 2575 through 2593 removed outlier: 3.799A pdb=" N GLY D2592 " --> pdb=" O ARG D2588 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ARG D2593 " --> pdb=" O LEU D2589 " (cutoff:3.500A) Processing helix chain 'D' and resid 2596 through 2614 removed outlier: 3.730A pdb=" N TYR D2613 " --> pdb=" O ALA D2609 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE D2614 " --> pdb=" O LEU D2610 " (cutoff:3.500A) Processing helix chain 'D' and resid 2615 through 2630 removed outlier: 4.063A pdb=" N LEU D2619 " --> pdb=" O ARG D2615 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN D2620 " --> pdb=" O PRO D2616 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N HIS D2621 " --> pdb=" O SER D2617 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LEU D2622 " --> pdb=" O MET D2618 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE D2628 " --> pdb=" O ARG D2624 " (cutoff:3.500A) Processing helix chain 'D' and resid 2636 through 2652 Proline residue: D2640 - end of helix Processing helix chain 'D' and resid 2668 through 2689 removed outlier: 6.919A pdb=" N LEU D2672 " --> pdb=" O SER D2668 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N HIS D2673 " --> pdb=" O GLU D2669 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP D2680 " --> pdb=" O ARG D2676 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS D2688 " --> pdb=" O ASP D2684 " (cutoff:3.500A) Processing helix chain 'D' and resid 2693 through 2711 removed outlier: 3.795A pdb=" N MET D2698 " --> pdb=" O GLU D2694 " (cutoff:3.500A) Proline residue: D2701 - end of helix Proline residue: D2711 - end of helix Processing helix chain 'D' and resid 2741 through 2746 removed outlier: 4.599A pdb=" N VAL D2745 " --> pdb=" O GLU D2741 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE D2746 " --> pdb=" O THR D2742 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2741 through 2746' Processing helix chain 'D' and resid 2751 through 2774 removed outlier: 3.875A pdb=" N LYS D2757 " --> pdb=" O SER D2753 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN D2774 " --> pdb=" O LYS D2770 " (cutoff:3.500A) Processing helix chain 'D' and resid 2799 through 2820 removed outlier: 3.538A pdb=" N GLU D2803 " --> pdb=" O GLU D2799 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE D2804 " --> pdb=" O LYS D2800 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG D2806 " --> pdb=" O LYS D2802 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TRP D2807 " --> pdb=" O GLU D2803 " (cutoff:3.500A) Proline residue: D2808 - end of helix removed outlier: 5.287A pdb=" N GLU D2820 " --> pdb=" O MET D2816 " (cutoff:3.500A) Processing helix chain 'D' and resid 2868 through 2895 removed outlier: 4.209A pdb=" N GLU D2893 " --> pdb=" O LYS D2889 " (cutoff:3.500A) Processing helix chain 'D' and resid 2907 through 2912 removed outlier: 6.081A pdb=" N THR D2912 " --> pdb=" O TYR D2908 " (cutoff:3.500A) Processing helix chain 'D' and resid 2913 through 2934 removed outlier: 3.737A pdb=" N ALA D2917 " --> pdb=" O ALA D2913 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ARG D2918 " --> pdb=" O LYS D2914 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ASP D2919 " --> pdb=" O GLU D2915 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS D2922 " --> pdb=" O ARG D2918 " (cutoff:3.500A) Processing helix chain 'D' and resid 2949 through 2982 removed outlier: 5.717A pdb=" N PHE D2955 " --> pdb=" O ILE D2951 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA D2956 " --> pdb=" O GLU D2952 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE D2957 " --> pdb=" O LYS D2953 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE D2969 " --> pdb=" O ARG D2965 " (cutoff:3.500A) Processing helix chain 'D' and resid 2991 through 3014 removed outlier: 3.611A pdb=" N LEU D3002 " --> pdb=" O PHE D2998 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU D3003 " --> pdb=" O ALA D2999 " (cutoff:3.500A) Proline residue: D3004 - end of helix removed outlier: 3.807A pdb=" N THR D3011 " --> pdb=" O ASN D3007 " (cutoff:3.500A) Processing helix chain 'D' and resid 3032 through 3051 removed outlier: 3.812A pdb=" N LEU D3042 " --> pdb=" O MET D3038 " (cutoff:3.500A) Processing helix chain 'D' and resid 3053 through 3058 removed outlier: 4.086A pdb=" N PHE D3057 " --> pdb=" O ARG D3053 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY D3058 " --> pdb=" O VAL D3054 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3053 through 3058' Processing helix chain 'D' and resid 3060 through 3075 Processing helix chain 'D' and resid 3076 through 3083 removed outlier: 3.777A pdb=" N VAL D3080 " --> pdb=" O ASP D3076 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET D3081 " --> pdb=" O ALA D3077 " (cutoff:3.500A) Processing helix chain 'D' and resid 3085 through 3112 removed outlier: 3.538A pdb=" N PHE D3095 " --> pdb=" O GLY D3091 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE D3096 " --> pdb=" O LEU D3092 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D3108 " --> pdb=" O GLU D3104 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU D3112 " --> pdb=" O GLU D3108 " (cutoff:3.500A) Processing helix chain 'D' and resid 3123 through 3151 removed outlier: 3.631A pdb=" N VAL D3134 " --> pdb=" O THR D3130 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU D3137 " --> pdb=" O THR D3133 " (cutoff:3.500A) Proline residue: D3138 - end of helix removed outlier: 3.708A pdb=" N GLN D3149 " --> pdb=" O GLN D3145 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS D3150 " --> pdb=" O HIS D3146 " (cutoff:3.500A) Processing helix chain 'D' and resid 3159 through 3175 removed outlier: 5.331A pdb=" N VAL D3163 " --> pdb=" O ASP D3159 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU D3175 " --> pdb=" O SER D3171 " (cutoff:3.500A) Processing helix chain 'D' and resid 3180 through 3201 Proline residue: D3188 - end of helix Processing helix chain 'D' and resid 3217 through 3222 Processing helix chain 'D' and resid 3226 through 3231 removed outlier: 6.671A pdb=" N LEU D3230 " --> pdb=" O GLU D3226 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLY D3231 " --> pdb=" O ARG D3227 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3226 through 3231' Processing helix chain 'D' and resid 3235 through 3241 removed outlier: 3.539A pdb=" N MET D3239 " --> pdb=" O SER D3235 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N CYS D3240 " --> pdb=" O VAL D3236 " (cutoff:3.500A) Proline residue: D3241 - end of helix No H-bonds generated for 'chain 'D' and resid 3235 through 3241' Processing helix chain 'D' and resid 3245 through 3260 Processing helix chain 'D' and resid 3262 through 3267 Proline residue: D3267 - end of helix Processing helix chain 'D' and resid 3268 through 3288 removed outlier: 4.358A pdb=" N LEU D3274 " --> pdb=" O ILE D3270 " (cutoff:3.500A) Proline residue: D3275 - end of helix Proline residue: D3282 - end of helix removed outlier: 4.343A pdb=" N GLU D3286 " --> pdb=" O PRO D3282 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG D3287 " --> pdb=" O ARG D3283 " (cutoff:3.500A) Processing helix chain 'D' and resid 3308 through 3327 removed outlier: 3.770A pdb=" N LEU D3312 " --> pdb=" O THR D3308 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D3319 " --> pdb=" O LEU D3315 " (cutoff:3.500A) Processing helix chain 'D' and resid 3332 through 3343 removed outlier: 5.755A pdb=" N LYS D3336 " --> pdb=" O ALA D3332 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG D3337 " --> pdb=" O THR D3333 " (cutoff:3.500A) Processing helix chain 'D' and resid 3344 through 3350 removed outlier: 4.728A pdb=" N ARG D3348 " --> pdb=" O PRO D3344 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ALA D3349 " --> pdb=" O ILE D3345 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG D3350 " --> pdb=" O VAL D3346 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3344 through 3350' Processing helix chain 'D' and resid 3351 through 3381 removed outlier: 4.698A pdb=" N HIS D3355 " --> pdb=" O PRO D3351 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE D3358 " --> pdb=" O LEU D3354 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE D3359 " --> pdb=" O HIS D3355 " (cutoff:3.500A) Proline residue: D3360 - end of helix removed outlier: 3.611A pdb=" N GLN D3378 " --> pdb=" O ALA D3374 " (cutoff:3.500A) Processing helix chain 'D' and resid 3389 through 3413 removed outlier: 6.543A pdb=" N LEU D3393 " --> pdb=" O GLU D3389 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA D3407 " --> pdb=" O ARG D3403 " (cutoff:3.500A) Proline residue: D3410 - end of helix Processing helix chain 'D' and resid 3419 through 3426 Processing helix chain 'D' and resid 3428 through 3448 Processing helix chain 'D' and resid 3449 through 3463 removed outlier: 3.755A pdb=" N GLN D3456 " --> pdb=" O LYS D3452 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN D3457 " --> pdb=" O ARG D3453 " (cutoff:3.500A) Processing helix chain 'D' and resid 3466 through 3478 removed outlier: 4.631A pdb=" N LEU D3470 " --> pdb=" O ASN D3466 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP D3473 " --> pdb=" O PHE D3469 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N SER D3474 " --> pdb=" O LEU D3470 " (cutoff:3.500A) Processing helix chain 'D' and resid 3508 through 3526 removed outlier: 3.941A pdb=" N LYS D3516 " --> pdb=" O ALA D3512 " (cutoff:3.500A) Proline residue: D3519 - end of helix removed outlier: 3.951A pdb=" N MET D3524 " --> pdb=" O ILE D3520 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N CYS D3525 " --> pdb=" O GLY D3521 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ALA D3526 " --> pdb=" O LEU D3522 " (cutoff:3.500A) Processing helix chain 'D' and resid 3529 through 3543 removed outlier: 3.571A pdb=" N LEU D3535 " --> pdb=" O ASP D3531 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS D3543 " --> pdb=" O ARG D3539 " (cutoff:3.500A) Processing helix chain 'D' and resid 3545 through 3557 Processing helix chain 'D' and resid 3566 through 3579 removed outlier: 3.604A pdb=" N ARG D3570 " --> pdb=" O SER D3566 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TRP D3571 " --> pdb=" O PRO D3567 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN D3572 " --> pdb=" O SER D3568 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU D3579 " --> pdb=" O LEU D3575 " (cutoff:3.500A) Processing helix chain 'D' and resid 3588 through 3612 removed outlier: 3.757A pdb=" N HIS D3605 " --> pdb=" O ALA D3601 " (cutoff:3.500A) Proline residue: D3612 - end of helix Processing helix chain 'D' and resid 3628 through 3638 removed outlier: 4.033A pdb=" N VAL D3632 " --> pdb=" O ARG D3628 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL D3633 " --> pdb=" O ARG D3629 " (cutoff:3.500A) Processing helix chain 'D' and resid 3645 through 3665 removed outlier: 3.711A pdb=" N GLU D3655 " --> pdb=" O ASN D3651 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU D3663 " --> pdb=" O ALA D3659 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR D3664 " --> pdb=" O ALA D3660 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU D3665 " --> pdb=" O TRP D3661 " (cutoff:3.500A) Processing helix chain 'D' and resid 3669 through 3679 Processing helix chain 'D' and resid 3696 through 3711 Processing helix chain 'D' and resid 3719 through 3735 removed outlier: 3.832A pdb=" N CYS D3733 " --> pdb=" O MET D3729 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N HIS D3734 " --> pdb=" O ALA D3730 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU D3735 " --> pdb=" O LYS D3731 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3772 removed outlier: 3.632A pdb=" N TYR D3765 " --> pdb=" O GLN D3761 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU D3770 " --> pdb=" O GLN D3766 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR D3772 " --> pdb=" O SER D3768 " (cutoff:3.500A) Processing helix chain 'D' and resid 3774 through 3787 removed outlier: 4.018A pdb=" N LYS D3787 " --> pdb=" O ILE D3783 " (cutoff:3.500A) Processing helix chain 'D' and resid 3791 through 3806 Processing helix chain 'D' and resid 3809 through 3824 Processing helix chain 'D' and resid 3825 through 3839 removed outlier: 4.989A pdb=" N PHE D3829 " --> pdb=" O GLU D3825 " (cutoff:3.500A) Processing helix chain 'D' and resid 3843 through 3857 Processing helix chain 'D' and resid 3877 through 3893 removed outlier: 3.562A pdb=" N CYS D3892 " --> pdb=" O LEU D3888 " (cutoff:3.500A) Processing helix chain 'D' and resid 3896 through 3905 Processing helix chain 'D' and resid 3914 through 3939 removed outlier: 3.637A pdb=" N TYR D3937 " --> pdb=" O PHE D3933 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY D3939 " --> pdb=" O TRP D3935 " (cutoff:3.500A) Processing helix chain 'D' and resid 3944 through 3970 removed outlier: 3.557A pdb=" N ILE D3969 " --> pdb=" O LEU D3965 " (cutoff:3.500A) Processing helix chain 'D' and resid 3973 through 3983 Processing helix chain 'D' and resid 3984 through 4007 removed outlier: 3.933A pdb=" N ALA D3988 " --> pdb=" O ARG D3984 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS D3998 " --> pdb=" O HIS D3994 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN D4005 " --> pdb=" O MET D4001 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ASP D4006 " --> pdb=" O LYS D4002 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N SER D4007 " --> pdb=" O LEU D4003 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4032 removed outlier: 3.528A pdb=" N GLU D4015 " --> pdb=" O GLU D4011 " (cutoff:3.500A) Processing helix chain 'D' and resid 4038 through 4052 Processing helix chain 'D' and resid 4053 through 4072 removed outlier: 3.646A pdb=" N MET D4064 " --> pdb=" O LYS D4060 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP D4070 " --> pdb=" O LEU D4066 " (cutoff:3.500A) Processing helix chain 'D' and resid 4074 through 4082 removed outlier: 4.908A pdb=" N THR D4082 " --> pdb=" O GLN D4078 " (cutoff:3.500A) Processing helix chain 'D' and resid 4089 through 4101 removed outlier: 3.631A pdb=" N MET D4097 " --> pdb=" O PHE D4093 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP D4098 " --> pdb=" O GLN D4094 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER D4099 " --> pdb=" O LYS D4095 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN D4100 " --> pdb=" O ALA D4096 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LYS D4101 " --> pdb=" O MET D4097 " (cutoff:3.500A) Processing helix chain 'D' and resid 4104 through 4116 removed outlier: 5.445A pdb=" N GLU D4116 " --> pdb=" O LEU D4112 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4133 removed outlier: 3.705A pdb=" N ALA D4129 " --> pdb=" O PHE D4125 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN D4130 " --> pdb=" O GLU D4126 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N PHE D4132 " --> pdb=" O PHE D4128 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLN D4133 " --> pdb=" O ALA D4129 " (cutoff:3.500A) Processing helix chain 'D' and resid 4134 through 4155 removed outlier: 4.330A pdb=" N ASP D4138 " --> pdb=" O GLU D4134 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE D4139 " --> pdb=" O PRO D4135 " (cutoff:3.500A) Proline residue: D4155 - end of helix Processing helix chain 'D' and resid 4157 through 4168 removed outlier: 3.551A pdb=" N GLU D4168 " --> pdb=" O LEU D4164 " (cutoff:3.500A) Processing helix chain 'D' and resid 4169 through 4175 removed outlier: 3.694A pdb=" N TYR D4173 " --> pdb=" O SER D4169 " (cutoff:3.500A) Processing helix chain 'D' and resid 4198 through 4207 Processing helix chain 'D' and resid 4208 through 4224 Processing helix chain 'D' and resid 4226 through 4252 removed outlier: 4.465A pdb=" N MET D4231 " --> pdb=" O GLU D4227 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLU D4232 " --> pdb=" O ALA D4228 " (cutoff:3.500A) Processing helix chain 'D' and resid 4540 through 4559 Processing helix chain 'D' and resid 4560 through 4580 removed outlier: 4.610A pdb=" N PHE D4579 " --> pdb=" O PHE D4575 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TYR D4580 " --> pdb=" O ILE D4576 " (cutoff:3.500A) Processing helix chain 'D' and resid 4640 through 4683 removed outlier: 3.541A pdb=" N TRP D4644 " --> pdb=" O GLU D4640 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL D4666 " --> pdb=" O ASN D4662 " (cutoff:3.500A) Proline residue: D4667 - end of helix Processing helix chain 'D' and resid 4696 through 4707 removed outlier: 3.548A pdb=" N ARG D4703 " --> pdb=" O GLY D4699 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LEU D4704 " --> pdb=" O GLN D4700 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL D4705 " --> pdb=" O TRP D4701 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU D4706 " --> pdb=" O ASP D4702 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN D4707 " --> pdb=" O ARG D4703 " (cutoff:3.500A) Processing helix chain 'D' and resid 4719 through 4728 Processing helix chain 'D' and resid 4733 through 4742 Processing helix chain 'D' and resid 4744 through 4750 removed outlier: 3.811A pdb=" N LEU D4748 " --> pdb=" O ASP D4744 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU D4749 " --> pdb=" O LEU D4745 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE D4750 " --> pdb=" O ALA D4746 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4744 through 4750' Processing helix chain 'D' and resid 4772 through 4787 removed outlier: 3.865A pdb=" N THR D4785 " --> pdb=" O GLY D4781 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP D4786 " --> pdb=" O VAL D4782 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ASN D4787 " --> pdb=" O ILE D4783 " (cutoff:3.500A) Processing helix chain 'D' and resid 4788 through 4805 removed outlier: 4.033A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4806 through 4820 removed outlier: 4.855A pdb=" N ALA D4810 " --> pdb=" O ASN D4806 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ALA D4811 " --> pdb=" O PHE D4807 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N HIS D4812 " --> pdb=" O PHE D4808 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU D4813 " --> pdb=" O PHE D4809 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU D4814 " --> pdb=" O ALA D4810 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASP D4815 " --> pdb=" O ALA D4811 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE D4816 " --> pdb=" O HIS D4812 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ALA D4817 " --> pdb=" O LEU D4813 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N MET D4818 " --> pdb=" O LEU D4814 " (cutoff:3.500A) Processing helix chain 'D' and resid 4821 through 4832 removed outlier: 3.788A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) Processing helix chain 'D' and resid 4833 through 4858 Processing helix chain 'D' and resid 4859 through 4864 removed outlier: 4.355A pdb=" N TYR D4863 " --> pdb=" O PHE D4859 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASN D4864 " --> pdb=" O ARG D4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4859 through 4864' Processing helix chain 'D' and resid 4878 through 4893 removed outlier: 3.959A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG D4892 " --> pdb=" O TYR D4888 " (cutoff:3.500A) Processing helix chain 'D' and resid 4896 through 4901 removed outlier: 3.998A pdb=" N GLU D4900 " --> pdb=" O GLY D4896 " (cutoff:3.500A) Processing helix chain 'D' and resid 4909 through 4924 Processing helix chain 'D' and resid 4928 through 4957 Processing helix chain 'D' and resid 4964 through 4970 removed outlier: 3.762A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR D4970 " --> pdb=" O ASP D4966 " (cutoff:3.500A) Processing helix chain 'D' and resid 4973 through 4981 Processing helix chain 'D' and resid 4984 through 4998 Processing helix chain 'D' and resid 4999 through 5004 removed outlier: 3.836A pdb=" N HIS D5003 " --> pdb=" O ASP D4999 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR D5004 " --> pdb=" O GLU D5000 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4999 through 5004' Processing helix chain 'D' and resid 5005 through 5017 Processing helix chain 'D' and resid 5027 through 5033 Processing helix chain 'D' and resid 250 through 256 removed outlier: 4.152A pdb=" N CYS D 253 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR D 254 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS D 255 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ALA D 256 " --> pdb=" O CYS D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 250 through 256' Processing helix chain 'D' and resid 3682 through 3687 removed outlier: 5.482A pdb=" N GLU D3685 " --> pdb=" O GLU D3682 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU D3686 " --> pdb=" O GLN D3683 " (cutoff:3.500A) Processing helix chain 'D' and resid 3152 through 3157 removed outlier: 3.984A pdb=" N ILE D3157 " --> pdb=" O PHE D3152 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3152 through 3157' Processing helix chain 'D' and resid 4685 through 4690 Processing helix chain 'E' and resid 38 through 43 removed outlier: 4.990A pdb=" N ARG E 42 " --> pdb=" O SER E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 66 removed outlier: 4.036A pdb=" N ALA E 64 " --> pdb=" O GLU E 60 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLN E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N MET E 66 " --> pdb=" O GLY E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 82 removed outlier: 4.034A pdb=" N TYR E 82 " --> pdb=" O PRO E 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 43 removed outlier: 4.990A pdb=" N ARG F 42 " --> pdb=" O SER F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 66 removed outlier: 4.036A pdb=" N ALA F 64 " --> pdb=" O GLU F 60 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLN F 65 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N MET F 66 " --> pdb=" O GLY F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 82 removed outlier: 4.034A pdb=" N TYR F 82 " --> pdb=" O PRO F 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 43 removed outlier: 4.990A pdb=" N ARG G 42 " --> pdb=" O SER G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 66 removed outlier: 4.036A pdb=" N ALA G 64 " --> pdb=" O GLU G 60 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLN G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N MET G 66 " --> pdb=" O GLY G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 82 removed outlier: 4.034A pdb=" N TYR G 82 " --> pdb=" O PRO G 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 43 removed outlier: 4.990A pdb=" N ARG H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 66 removed outlier: 4.036A pdb=" N ALA H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLN H 65 " --> pdb=" O GLU H 61 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N MET H 66 " --> pdb=" O GLY H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 82 removed outlier: 4.034A pdb=" N TYR H 82 " --> pdb=" O PRO H 78 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 52 removed outlier: 5.953A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 35 " --> pdb=" O CYS A 24 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 37 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 11.437A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 14.336A pdb=" N VAL A 20 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 109 through 112 removed outlier: 5.284A pdb=" N LEU A 109 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N MET A 116 " --> pdb=" O HIS A 111 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 148 through 153 removed outlier: 3.824A pdb=" N ALA A 153 " --> pdb=" O ASP A 168 " (cutoff:3.500A) removed outlier: 9.137A pdb=" N ASP A 168 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 181 through 184 removed outlier: 3.917A pdb=" N GLN A 190 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 229 through 233 removed outlier: 5.317A pdb=" N VAL A 245 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 299 through 303 removed outlier: 5.573A pdb=" N ILE A 282 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 10.877A pdb=" N LEU A 293 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 14.862A pdb=" N LEU A 280 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 285 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N LEU A 259 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS A 218 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 221 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR A 391 " --> pdb=" O ARG A 221 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 314 through 318 Processing sheet with id= 8, first strand: chain 'A' and resid 754 through 758 removed outlier: 3.645A pdb=" N ASP A 742 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS A 788 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP A1626 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLY A1625 " --> pdb=" O ALA A1620 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 766 through 769 Processing sheet with id= 10, first strand: chain 'A' and resid 780 through 783 Processing sheet with id= 11, first strand: chain 'A' and resid 830 through 833 removed outlier: 3.828A pdb=" N GLY A 836 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU A1202 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLN A1198 " --> pdb=" O GLY A 841 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL A1199 " --> pdb=" O VAL A1095 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLY A1086 " --> pdb=" O LEU A1155 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP A1147 " --> pdb=" O ALA A1094 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE A1161 " --> pdb=" O MET A1152 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 937 through 941 No H-bonds generated for sheet with id= 12 Processing sheet with id= 13, first strand: chain 'A' and resid 1134 through 1138 removed outlier: 3.501A pdb=" N VAL A1102 " --> pdb=" O PHE A1124 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY A1126 " --> pdb=" O MET A1100 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N MET A1100 " --> pdb=" O GLY A1126 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU A1099 " --> pdb=" O GLY A1195 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 1267 through 1273 removed outlier: 3.610A pdb=" N ILE A1562 " --> pdb=" O LEU A1272 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 1294 through 1297 removed outlier: 4.756A pdb=" N THR A1546 " --> pdb=" O PHE A1297 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE A1288 " --> pdb=" O LEU A1600 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A1600 " --> pdb=" O PHE A1288 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLU A1596 " --> pdb=" O SER A1292 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 1516 through 1522 removed outlier: 3.764A pdb=" N LEU A1526 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLY A1525 " --> pdb=" O VAL A1542 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 1776 through 1779 removed outlier: 3.778A pdb=" N SER A1799 " --> pdb=" O HIS A1776 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 4177 through 4184 removed outlier: 5.429A pdb=" N TYR A4177 " --> pdb=" O ILE A4197 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'A' and resid 4581 through 4584 Processing sheet with id= 20, first strand: chain 'B' and resid 47 through 52 removed outlier: 5.952A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 35 " --> pdb=" O CYS B 24 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU B 37 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 11.437A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 14.336A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 109 through 112 removed outlier: 5.284A pdb=" N LEU B 109 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N MET B 116 " --> pdb=" O HIS B 111 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 148 through 153 removed outlier: 3.823A pdb=" N ALA B 153 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N ASP B 168 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 181 through 184 removed outlier: 3.917A pdb=" N GLN B 190 " --> pdb=" O SER B 183 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 229 through 233 removed outlier: 5.317A pdb=" N VAL B 245 " --> pdb=" O ALA B 376 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 299 through 303 removed outlier: 5.573A pdb=" N ILE B 282 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 10.878A pdb=" N LEU B 293 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 14.862A pdb=" N LEU B 280 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 285 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N LEU B 259 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS B 218 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 221 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR B 391 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 314 through 318 Processing sheet with id= 27, first strand: chain 'B' and resid 754 through 758 removed outlier: 3.645A pdb=" N ASP B 742 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS B 788 " --> pdb=" O ASP B 669 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP B1626 " --> pdb=" O PHE B 791 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLY B1625 " --> pdb=" O ALA B1620 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 766 through 769 Processing sheet with id= 29, first strand: chain 'B' and resid 780 through 783 Processing sheet with id= 30, first strand: chain 'B' and resid 830 through 833 removed outlier: 3.827A pdb=" N GLY B 836 " --> pdb=" O GLY B 833 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU B1202 " --> pdb=" O PRO B 837 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLN B1198 " --> pdb=" O GLY B 841 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B1199 " --> pdb=" O VAL B1095 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N GLY B1086 " --> pdb=" O LEU B1155 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP B1147 " --> pdb=" O ALA B1094 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE B1161 " --> pdb=" O MET B1152 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 937 through 941 No H-bonds generated for sheet with id= 31 Processing sheet with id= 32, first strand: chain 'B' and resid 1134 through 1138 removed outlier: 3.502A pdb=" N VAL B1102 " --> pdb=" O PHE B1124 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY B1126 " --> pdb=" O MET B1100 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N MET B1100 " --> pdb=" O GLY B1126 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU B1099 " --> pdb=" O GLY B1195 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 1267 through 1273 removed outlier: 3.610A pdb=" N ILE B1562 " --> pdb=" O LEU B1272 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'B' and resid 1294 through 1297 removed outlier: 4.758A pdb=" N THR B1546 " --> pdb=" O PHE B1297 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE B1288 " --> pdb=" O LEU B1600 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B1600 " --> pdb=" O PHE B1288 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLU B1596 " --> pdb=" O SER B1292 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'B' and resid 1516 through 1522 removed outlier: 3.764A pdb=" N LEU B1526 " --> pdb=" O ASP B1521 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLY B1525 " --> pdb=" O VAL B1542 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 1776 through 1779 removed outlier: 3.779A pdb=" N SER B1799 " --> pdb=" O HIS B1776 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'B' and resid 4177 through 4184 removed outlier: 5.429A pdb=" N TYR B4177 " --> pdb=" O ILE B4197 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'B' and resid 4581 through 4584 Processing sheet with id= 39, first strand: chain 'C' and resid 47 through 52 removed outlier: 5.952A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 35 " --> pdb=" O CYS C 24 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU C 37 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 11.436A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 14.335A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'C' and resid 109 through 112 removed outlier: 5.284A pdb=" N LEU C 109 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N MET C 116 " --> pdb=" O HIS C 111 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'C' and resid 148 through 153 removed outlier: 3.823A pdb=" N ALA C 153 " --> pdb=" O ASP C 168 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N ASP C 168 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'C' and resid 181 through 184 removed outlier: 3.917A pdb=" N GLN C 190 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 229 through 233 removed outlier: 5.316A pdb=" N VAL C 245 " --> pdb=" O ALA C 376 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C' and resid 299 through 303 removed outlier: 5.573A pdb=" N ILE C 282 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 10.878A pdb=" N LEU C 293 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 14.862A pdb=" N LEU C 280 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL C 285 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N LEU C 259 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS C 218 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG C 221 " --> pdb=" O THR C 391 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR C 391 " --> pdb=" O ARG C 221 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'C' and resid 314 through 318 Processing sheet with id= 46, first strand: chain 'C' and resid 754 through 758 removed outlier: 3.644A pdb=" N ASP C 742 " --> pdb=" O VAL C 668 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS C 788 " --> pdb=" O ASP C 669 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP C1626 " --> pdb=" O PHE C 791 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLY C1625 " --> pdb=" O ALA C1620 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'C' and resid 766 through 769 Processing sheet with id= 48, first strand: chain 'C' and resid 780 through 783 Processing sheet with id= 49, first strand: chain 'C' and resid 830 through 833 removed outlier: 3.827A pdb=" N GLY C 836 " --> pdb=" O GLY C 833 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU C1202 " --> pdb=" O PRO C 837 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLN C1198 " --> pdb=" O GLY C 841 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL C1199 " --> pdb=" O VAL C1095 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N GLY C1086 " --> pdb=" O LEU C1155 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP C1147 " --> pdb=" O ALA C1094 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE C1161 " --> pdb=" O MET C1152 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 937 through 941 No H-bonds generated for sheet with id= 50 Processing sheet with id= 51, first strand: chain 'C' and resid 1134 through 1138 removed outlier: 3.503A pdb=" N VAL C1102 " --> pdb=" O PHE C1124 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY C1126 " --> pdb=" O MET C1100 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N MET C1100 " --> pdb=" O GLY C1126 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU C1099 " --> pdb=" O GLY C1195 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 1267 through 1273 removed outlier: 3.610A pdb=" N ILE C1562 " --> pdb=" O LEU C1272 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 1294 through 1297 removed outlier: 4.758A pdb=" N THR C1546 " --> pdb=" O PHE C1297 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE C1288 " --> pdb=" O LEU C1600 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C1600 " --> pdb=" O PHE C1288 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLU C1596 " --> pdb=" O SER C1292 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 1516 through 1522 removed outlier: 3.764A pdb=" N LEU C1526 " --> pdb=" O ASP C1521 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLY C1525 " --> pdb=" O VAL C1542 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'C' and resid 1776 through 1779 removed outlier: 3.779A pdb=" N SER C1799 " --> pdb=" O HIS C1776 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'C' and resid 4177 through 4184 removed outlier: 5.430A pdb=" N TYR C4177 " --> pdb=" O ILE C4197 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'C' and resid 4581 through 4584 Processing sheet with id= 58, first strand: chain 'D' and resid 47 through 52 removed outlier: 5.952A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 35 " --> pdb=" O CYS D 24 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU D 37 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 11.437A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 14.336A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'D' and resid 109 through 112 removed outlier: 5.284A pdb=" N LEU D 109 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N MET D 116 " --> pdb=" O HIS D 111 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'D' and resid 148 through 153 removed outlier: 3.823A pdb=" N ALA D 153 " --> pdb=" O ASP D 168 " (cutoff:3.500A) removed outlier: 9.137A pdb=" N ASP D 168 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'D' and resid 181 through 184 removed outlier: 3.917A pdb=" N GLN D 190 " --> pdb=" O SER D 183 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'D' and resid 229 through 233 removed outlier: 5.316A pdb=" N VAL D 245 " --> pdb=" O ALA D 376 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'D' and resid 299 through 303 removed outlier: 5.573A pdb=" N ILE D 282 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 10.878A pdb=" N LEU D 293 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 14.862A pdb=" N LEU D 280 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL D 285 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N LEU D 259 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS D 218 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG D 221 " --> pdb=" O THR D 391 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR D 391 " --> pdb=" O ARG D 221 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'D' and resid 314 through 318 Processing sheet with id= 65, first strand: chain 'D' and resid 754 through 758 removed outlier: 3.644A pdb=" N ASP D 742 " --> pdb=" O VAL D 668 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS D 788 " --> pdb=" O ASP D 669 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP D1626 " --> pdb=" O PHE D 791 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLY D1625 " --> pdb=" O ALA D1620 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'D' and resid 766 through 769 Processing sheet with id= 67, first strand: chain 'D' and resid 780 through 783 Processing sheet with id= 68, first strand: chain 'D' and resid 830 through 833 removed outlier: 3.828A pdb=" N GLY D 836 " --> pdb=" O GLY D 833 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU D1202 " --> pdb=" O PRO D 837 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLN D1198 " --> pdb=" O GLY D 841 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL D1199 " --> pdb=" O VAL D1095 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLY D1086 " --> pdb=" O LEU D1155 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP D1147 " --> pdb=" O ALA D1094 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE D1161 " --> pdb=" O MET D1152 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'D' and resid 937 through 941 No H-bonds generated for sheet with id= 69 Processing sheet with id= 70, first strand: chain 'D' and resid 1134 through 1138 removed outlier: 3.503A pdb=" N VAL D1102 " --> pdb=" O PHE D1124 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY D1126 " --> pdb=" O MET D1100 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N MET D1100 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU D1099 " --> pdb=" O GLY D1195 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'D' and resid 1267 through 1273 removed outlier: 3.609A pdb=" N ILE D1562 " --> pdb=" O LEU D1272 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'D' and resid 1294 through 1297 removed outlier: 4.758A pdb=" N THR D1546 " --> pdb=" O PHE D1297 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE D1288 " --> pdb=" O LEU D1600 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D1600 " --> pdb=" O PHE D1288 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLU D1596 " --> pdb=" O SER D1292 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'D' and resid 1516 through 1522 removed outlier: 3.764A pdb=" N LEU D1526 " --> pdb=" O ASP D1521 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLY D1525 " --> pdb=" O VAL D1542 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'D' and resid 1776 through 1779 removed outlier: 3.778A pdb=" N SER D1799 " --> pdb=" O HIS D1776 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'D' and resid 4177 through 4184 removed outlier: 5.429A pdb=" N TYR D4177 " --> pdb=" O ILE D4197 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'D' and resid 4581 through 4584 Processing sheet with id= 77, first strand: chain 'E' and resid 2 through 7 removed outlier: 6.853A pdb=" N ARG E 71 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN E 70 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE E 99 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU E 102 " --> pdb=" O HIS E 25 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'F' and resid 2 through 7 removed outlier: 6.853A pdb=" N ARG F 71 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN F 70 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE F 99 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU F 102 " --> pdb=" O HIS F 25 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'G' and resid 2 through 7 removed outlier: 6.853A pdb=" N ARG G 71 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN G 70 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE G 99 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU G 102 " --> pdb=" O HIS G 25 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'H' and resid 2 through 7 removed outlier: 6.854A pdb=" N ARG H 71 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN H 70 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE H 99 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU H 102 " --> pdb=" O HIS H 25 " (cutoff:3.500A) 6832 hydrogen bonds defined for protein. 20372 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: 94.58 Time building geometry restraints manager: 48.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 42369 1.34 - 1.46: 34088 1.46 - 1.58: 68338 1.58 - 1.71: 9 1.71 - 1.83: 1512 Bond restraints: 146316 Sorted by residual: bond pdb=" C ARG C4175 " pdb=" N PRO C4176 " ideal model delta sigma weight residual 1.337 1.393 -0.056 9.80e-03 1.04e+04 3.32e+01 bond pdb=" C ARG A4175 " pdb=" N PRO A4176 " ideal model delta sigma weight residual 1.337 1.392 -0.056 9.80e-03 1.04e+04 3.21e+01 bond pdb=" C ARG D4175 " pdb=" N PRO D4176 " ideal model delta sigma weight residual 1.337 1.392 -0.055 9.80e-03 1.04e+04 3.16e+01 bond pdb=" C ARG B4175 " pdb=" N PRO B4176 " ideal model delta sigma weight residual 1.337 1.392 -0.055 9.80e-03 1.04e+04 3.15e+01 bond pdb=" C HIS B 904 " pdb=" N PRO B 905 " ideal model delta sigma weight residual 1.334 1.428 -0.094 2.34e-02 1.83e+03 1.62e+01 ... (remaining 146311 not shown) Histogram of bond angle deviations from ideal: 95.74 - 103.76: 2259 103.76 - 111.79: 63528 111.79 - 119.82: 64761 119.82 - 127.85: 66166 127.85 - 135.87: 1490 Bond angle restraints: 198204 Sorted by residual: angle pdb=" CA PHE D5028 " pdb=" CB PHE D5028 " pdb=" CG PHE D5028 " ideal model delta sigma weight residual 113.80 119.56 -5.76 1.00e+00 1.00e+00 3.31e+01 angle pdb=" CA PHE B5028 " pdb=" CB PHE B5028 " pdb=" CG PHE B5028 " ideal model delta sigma weight residual 113.80 119.56 -5.76 1.00e+00 1.00e+00 3.31e+01 angle pdb=" CA PHE A5028 " pdb=" CB PHE A5028 " pdb=" CG PHE A5028 " ideal model delta sigma weight residual 113.80 119.54 -5.74 1.00e+00 1.00e+00 3.29e+01 angle pdb=" CA PHE C5028 " pdb=" CB PHE C5028 " pdb=" CG PHE C5028 " ideal model delta sigma weight residual 113.80 119.54 -5.74 1.00e+00 1.00e+00 3.29e+01 angle pdb=" N PRO A 905 " pdb=" CA PRO A 905 " pdb=" C PRO A 905 " ideal model delta sigma weight residual 112.47 122.80 -10.33 2.06e+00 2.36e-01 2.51e+01 ... (remaining 198199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.32: 84359 28.32 - 56.64: 3599 56.64 - 84.96: 354 84.96 - 113.28: 24 113.28 - 141.60: 16 Dihedral angle restraints: 88352 sinusoidal: 36160 harmonic: 52192 Sorted by residual: dihedral pdb=" C8 CMP C5101 " pdb=" C1' CMP C5101 " pdb=" N9 CMP C5101 " pdb=" O4' CMP C5101 " ideal model delta sinusoidal sigma weight residual -28.23 113.37 -141.60 1 2.00e+01 2.50e-03 4.28e+01 dihedral pdb=" C8 CMP B5101 " pdb=" C1' CMP B5101 " pdb=" N9 CMP B5101 " pdb=" O4' CMP B5101 " ideal model delta sinusoidal sigma weight residual -28.22 113.33 -141.55 1 2.00e+01 2.50e-03 4.28e+01 dihedral pdb=" C8 CMP D5101 " pdb=" C1' CMP D5101 " pdb=" N9 CMP D5101 " pdb=" O4' CMP D5101 " ideal model delta sinusoidal sigma weight residual -28.23 113.31 -141.54 1 2.00e+01 2.50e-03 4.28e+01 ... (remaining 88349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 17767 0.072 - 0.144: 3475 0.144 - 0.215: 450 0.215 - 0.287: 68 0.287 - 0.359: 28 Chirality restraints: 21788 Sorted by residual: chirality pdb=" CB ILE A 759 " pdb=" CA ILE A 759 " pdb=" CG1 ILE A 759 " pdb=" CG2 ILE A 759 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CB ILE B 759 " pdb=" CA ILE B 759 " pdb=" CG1 ILE B 759 " pdb=" CG2 ILE B 759 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CB ILE C 759 " pdb=" CA ILE C 759 " pdb=" CG1 ILE C 759 " pdb=" CG2 ILE C 759 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 21785 not shown) Planarity restraints: 25764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR D2553 " 0.023 2.00e-02 2.50e+03 4.75e-02 2.26e+01 pdb=" C TYR D2553 " -0.082 2.00e-02 2.50e+03 pdb=" O TYR D2553 " 0.030 2.00e-02 2.50e+03 pdb=" N LEU D2554 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1143 " -0.023 2.00e-02 2.50e+03 3.00e-02 2.24e+01 pdb=" CG TRP B1143 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP B1143 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP B1143 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B1143 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B1143 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP B1143 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1143 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1143 " -0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP B1143 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B2553 " 0.023 2.00e-02 2.50e+03 4.74e-02 2.24e+01 pdb=" C TYR B2553 " -0.082 2.00e-02 2.50e+03 pdb=" O TYR B2553 " 0.030 2.00e-02 2.50e+03 pdb=" N LEU B2554 " 0.028 2.00e-02 2.50e+03 ... (remaining 25761 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 5419 2.72 - 3.26: 143419 3.26 - 3.81: 241914 3.81 - 4.35: 296706 4.35 - 4.90: 489672 Nonbonded interactions: 1177130 Sorted by model distance: nonbonded pdb=" OG1 THR D 978 " pdb=" OE1 GLN D 981 " model vdw 2.173 2.440 nonbonded pdb=" OG1 THR A 978 " pdb=" OE1 GLN A 981 " model vdw 2.173 2.440 nonbonded pdb=" OG1 THR C 978 " pdb=" OE1 GLN C 981 " model vdw 2.173 2.440 nonbonded pdb=" OG1 THR B 978 " pdb=" OE1 GLN B 981 " model vdw 2.173 2.440 nonbonded pdb=" OG1 THR A 27 " pdb=" OE1 GLN A 32 " model vdw 2.233 2.440 ... (remaining 1177125 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 11 through 1230 or resid 1232 through 1742 or resid 1744 t \ hrough 2099 or resid 2101 through 2267 or resid 2269 through 2368 or resid 2370 \ through 2583 or resid 2585 through 2611 or resid 2613 through 2869 or resid 2871 \ through 3421 or resid 3423 through 5037 or resid 5101 through 5102)) selection = (chain 'B' and (resid 11 through 1230 or resid 1232 through 1742 or resid 1744 t \ hrough 2099 or resid 2101 through 2267 or resid 2269 through 2368 or resid 2370 \ through 2583 or resid 2585 through 2611 or resid 2613 through 2869 or resid 2871 \ through 3421 or resid 3423 through 5037 or resid 5101 through 5102)) selection = (chain 'C' and (resid 11 through 1230 or resid 1232 through 1742 or resid 1744 t \ hrough 2099 or resid 2101 through 2267 or resid 2269 through 2368 or resid 2370 \ through 2583 or resid 2585 through 2611 or resid 2613 through 2869 or resid 2871 \ through 3421 or resid 3423 through 5037 or resid 5101 through 5102)) selection = (chain 'D' and (resid 11 through 1230 or resid 1232 through 1742 or resid 1744 t \ hrough 2099 or resid 2101 through 2267 or resid 2269 through 2368 or resid 2370 \ through 2583 or resid 2585 through 2611 or resid 2613 through 2869 or resid 2871 \ through 3421 or resid 3423 through 5037 or resid 5101 through 5102)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.50 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: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 18.780 Check model and map are aligned: 1.580 Set scattering table: 1.030 Process input model: 456.400 Find NCS groups from input model: 7.440 Set up NCS constraints: 0.920 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: 0.030 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 492.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 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 : 0.006 0.111 146316 Z= 0.369 Angle : 1.034 14.624 198204 Z= 0.558 Chirality : 0.059 0.359 21788 Planarity : 0.007 0.062 25764 Dihedral : 14.781 141.596 54628 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.02 % Favored : 96.89 % Rotamer: Outliers : 2.98 % Allowed : 1.59 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.06), residues: 17840 helix: 0.36 (0.05), residues: 8720 sheet: -0.45 (0.13), residues: 1656 loop : -0.67 (0.07), residues: 7464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP B1143 HIS 0.016 0.002 HIS A3069 PHE 0.046 0.003 PHE D2973 TYR 0.061 0.003 TYR A2553 ARG 0.015 0.001 ARG A3539 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1531 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 440 poor density : 1091 time to evaluate : 12.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 TYR cc_start: 0.7914 (m-80) cc_final: 0.7616 (m-80) REVERT: A 202 MET cc_start: 0.8226 (tpt) cc_final: 0.7907 (tpp) REVERT: A 569 ILE cc_start: 0.9498 (tp) cc_final: 0.9174 (pt) REVERT: A 1152 MET cc_start: 0.7713 (mmp) cc_final: 0.7511 (mmp) REVERT: A 1170 MET cc_start: 0.9045 (mmt) cc_final: 0.8822 (mmm) REVERT: A 1260 MET cc_start: 0.8665 (mtp) cc_final: 0.8439 (mtm) REVERT: A 1462 MET cc_start: 0.8659 (mpp) cc_final: 0.8428 (mpp) REVERT: A 2008 MET cc_start: 0.9387 (mtm) cc_final: 0.8790 (tmm) REVERT: A 2170 MET cc_start: 0.8389 (mmm) cc_final: 0.8160 (mmm) REVERT: A 2440 MET cc_start: 0.8741 (ppp) cc_final: 0.8483 (ppp) REVERT: A 2562 ILE cc_start: 0.9260 (mm) cc_final: 0.8981 (tt) REVERT: A 2700 MET cc_start: 0.8545 (mtt) cc_final: 0.8332 (tpp) REVERT: A 2874 MET cc_start: 0.6880 (mmp) cc_final: 0.5946 (ttp) REVERT: A 3248 ARG cc_start: 0.8815 (tpt-90) cc_final: 0.8232 (ptm160) REVERT: A 3652 MET cc_start: 0.9365 (pmm) cc_final: 0.9076 (pmm) REVERT: A 3968 TYR cc_start: 0.8769 (m-10) cc_final: 0.8540 (m-80) REVERT: A 4039 MET cc_start: 0.8558 (tpp) cc_final: 0.8348 (tpp) REVERT: A 4047 MET cc_start: 0.9038 (tmm) cc_final: 0.8698 (tmm) REVERT: A 4580 TYR cc_start: 0.6945 (OUTLIER) cc_final: 0.6660 (t80) REVERT: A 4639 MET cc_start: 0.8893 (mtm) cc_final: 0.8628 (mtm) REVERT: A 4680 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.9045 (mtmm) REVERT: A 4684 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8430 (t0) REVERT: A 4730 ASP cc_start: 0.9120 (m-30) cc_final: 0.8871 (p0) REVERT: A 4731 ILE cc_start: 0.9524 (tt) cc_final: 0.9120 (mp) REVERT: A 4809 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8350 (m-80) REVERT: A 4874 MET cc_start: 0.9011 (mmm) cc_final: 0.8721 (mmm) REVERT: A 4878 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7815 (t0) REVERT: A 4945 ASP cc_start: 0.9147 (OUTLIER) cc_final: 0.8802 (p0) REVERT: A 4957 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8191 (mtmm) REVERT: A 5016 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8797 (mt-10) REVERT: A 5030 LYS cc_start: 0.9356 (ttmm) cc_final: 0.9129 (ttmm) REVERT: A 5036 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7961 (mm) REVERT: B 81 MET cc_start: 0.9074 (ttp) cc_final: 0.8852 (ptm) REVERT: B 179 TYR cc_start: 0.7970 (m-80) cc_final: 0.7706 (m-80) REVERT: B 202 MET cc_start: 0.8138 (tpt) cc_final: 0.7783 (tpp) REVERT: B 513 GLU cc_start: 0.9303 (mm-30) cc_final: 0.8861 (mp0) REVERT: B 569 ILE cc_start: 0.9540 (tp) cc_final: 0.9214 (pt) REVERT: B 918 ARG cc_start: 0.7670 (tmt170) cc_final: 0.7448 (ttp80) REVERT: B 961 MET cc_start: 0.5679 (pmm) cc_final: 0.5421 (pmm) REVERT: B 1170 MET cc_start: 0.8926 (mmt) cc_final: 0.8683 (mmm) REVERT: B 1260 MET cc_start: 0.8670 (mtp) cc_final: 0.8457 (mtm) REVERT: B 1462 MET cc_start: 0.8580 (mpp) cc_final: 0.8374 (mpp) REVERT: B 2008 MET cc_start: 0.9423 (mtm) cc_final: 0.8814 (tmm) REVERT: B 2186 MET cc_start: 0.8341 (mmt) cc_final: 0.8133 (mmt) REVERT: B 2440 MET cc_start: 0.8748 (ppp) cc_final: 0.8479 (ppp) REVERT: B 2700 MET cc_start: 0.8571 (mtt) cc_final: 0.8280 (tpp) REVERT: B 2874 MET cc_start: 0.6952 (mmp) cc_final: 0.5816 (ttp) REVERT: B 3248 ARG cc_start: 0.8802 (tpt-90) cc_final: 0.8225 (ptm160) REVERT: B 3652 MET cc_start: 0.9362 (pmm) cc_final: 0.9107 (pmm) REVERT: B 3968 TYR cc_start: 0.8762 (m-10) cc_final: 0.8526 (m-80) REVERT: B 4039 MET cc_start: 0.8596 (tpp) cc_final: 0.8366 (tpp) REVERT: B 4047 MET cc_start: 0.9017 (tmm) cc_final: 0.8675 (tmm) REVERT: B 4253 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7861 (tp30) REVERT: B 4577 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7540 (mt) REVERT: B 4580 TYR cc_start: 0.6853 (OUTLIER) cc_final: 0.6173 (t80) REVERT: B 4639 MET cc_start: 0.8726 (mtm) cc_final: 0.8271 (mtm) REVERT: B 4680 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.9145 (mtmm) REVERT: B 4684 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8336 (t0) REVERT: B 4730 ASP cc_start: 0.9110 (m-30) cc_final: 0.8845 (p0) REVERT: B 4731 ILE cc_start: 0.9501 (tt) cc_final: 0.9099 (mp) REVERT: B 4874 MET cc_start: 0.8924 (mmm) cc_final: 0.8711 (mmm) REVERT: B 4879 MET cc_start: 0.8208 (mmm) cc_final: 0.7991 (tpt) REVERT: B 4902 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7998 (mt-10) REVERT: B 5016 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8700 (pt0) REVERT: B 5020 ASP cc_start: 0.8969 (m-30) cc_final: 0.8715 (t0) REVERT: B 5036 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8069 (mm) REVERT: C 81 MET cc_start: 0.9074 (ttp) cc_final: 0.8850 (ptm) REVERT: C 179 TYR cc_start: 0.7969 (m-80) cc_final: 0.7706 (m-80) REVERT: C 202 MET cc_start: 0.8139 (tpt) cc_final: 0.7784 (tpp) REVERT: C 513 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8862 (mp0) REVERT: C 569 ILE cc_start: 0.9540 (tp) cc_final: 0.9213 (pt) REVERT: C 918 ARG cc_start: 0.7673 (tmt170) cc_final: 0.7451 (ttp80) REVERT: C 961 MET cc_start: 0.5681 (pmm) cc_final: 0.5424 (pmm) REVERT: C 1170 MET cc_start: 0.8925 (mmt) cc_final: 0.8680 (mmm) REVERT: C 1260 MET cc_start: 0.8669 (mtp) cc_final: 0.8456 (mtm) REVERT: C 1462 MET cc_start: 0.8578 (mpp) cc_final: 0.8370 (mpp) REVERT: C 2008 MET cc_start: 0.9425 (mtm) cc_final: 0.8816 (tmm) REVERT: C 2186 MET cc_start: 0.8343 (mmt) cc_final: 0.8136 (mmt) REVERT: C 2440 MET cc_start: 0.8744 (ppp) cc_final: 0.8519 (ppp) REVERT: C 2700 MET cc_start: 0.8570 (mtt) cc_final: 0.8279 (tpp) REVERT: C 2874 MET cc_start: 0.6951 (mmp) cc_final: 0.5817 (ttp) REVERT: C 3248 ARG cc_start: 0.8803 (tpt-90) cc_final: 0.8226 (ptm160) REVERT: C 3652 MET cc_start: 0.9361 (pmm) cc_final: 0.9108 (pmm) REVERT: C 3968 TYR cc_start: 0.8761 (m-10) cc_final: 0.8527 (m-80) REVERT: C 4039 MET cc_start: 0.8598 (tpp) cc_final: 0.8367 (tpp) REVERT: C 4047 MET cc_start: 0.9016 (tmm) cc_final: 0.8730 (tmm) REVERT: C 4253 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7862 (tp30) REVERT: C 4577 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7540 (mt) REVERT: C 4580 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.6181 (t80) REVERT: C 4639 MET cc_start: 0.8722 (mtm) cc_final: 0.8269 (mtm) REVERT: C 4680 LYS cc_start: 0.9369 (OUTLIER) cc_final: 0.9144 (mtmm) REVERT: C 4684 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8336 (t0) REVERT: C 4730 ASP cc_start: 0.9113 (m-30) cc_final: 0.8849 (p0) REVERT: C 4731 ILE cc_start: 0.9497 (tt) cc_final: 0.9095 (mp) REVERT: C 4874 MET cc_start: 0.8925 (mmm) cc_final: 0.8709 (mmm) REVERT: C 4878 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.7652 (t70) REVERT: C 4902 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: C 5016 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8700 (pt0) REVERT: C 5020 ASP cc_start: 0.8971 (m-30) cc_final: 0.8716 (t0) REVERT: C 5036 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8068 (mm) REVERT: D 81 MET cc_start: 0.9074 (ttp) cc_final: 0.8850 (ptm) REVERT: D 179 TYR cc_start: 0.7966 (m-80) cc_final: 0.7703 (m-80) REVERT: D 202 MET cc_start: 0.8136 (tpt) cc_final: 0.7784 (tpp) REVERT: D 513 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8861 (mp0) REVERT: D 569 ILE cc_start: 0.9539 (tp) cc_final: 0.9213 (pt) REVERT: D 918 ARG cc_start: 0.7673 (tmt170) cc_final: 0.7450 (ttp80) REVERT: D 961 MET cc_start: 0.5683 (pmm) cc_final: 0.5426 (pmm) REVERT: D 1170 MET cc_start: 0.8911 (mmt) cc_final: 0.8655 (mmm) REVERT: D 1260 MET cc_start: 0.8669 (mtp) cc_final: 0.8456 (mtm) REVERT: D 1462 MET cc_start: 0.8577 (mpp) cc_final: 0.8370 (mpp) REVERT: D 2008 MET cc_start: 0.9426 (mtm) cc_final: 0.8817 (tmm) REVERT: D 2186 MET cc_start: 0.8341 (mmt) cc_final: 0.8135 (mmt) REVERT: D 2440 MET cc_start: 0.8746 (ppp) cc_final: 0.8479 (ppp) REVERT: D 2700 MET cc_start: 0.8571 (mtt) cc_final: 0.8279 (tpp) REVERT: D 2874 MET cc_start: 0.6949 (mmp) cc_final: 0.5816 (ttp) REVERT: D 3248 ARG cc_start: 0.8815 (tpt-90) cc_final: 0.8203 (ptm160) REVERT: D 3652 MET cc_start: 0.9360 (pmm) cc_final: 0.9106 (pmm) REVERT: D 3968 TYR cc_start: 0.8762 (m-10) cc_final: 0.8529 (m-80) REVERT: D 4039 MET cc_start: 0.8599 (tpp) cc_final: 0.8368 (tpp) REVERT: D 4047 MET cc_start: 0.9017 (tmm) cc_final: 0.8730 (tmm) REVERT: D 4253 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7860 (tp30) REVERT: D 4577 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7553 (mt) REVERT: D 4580 TYR cc_start: 0.6836 (OUTLIER) cc_final: 0.6194 (t80) REVERT: D 4639 MET cc_start: 0.8722 (mtm) cc_final: 0.8270 (mtm) REVERT: D 4680 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.9144 (mtmm) REVERT: D 4684 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8336 (t0) REVERT: D 4730 ASP cc_start: 0.9113 (m-30) cc_final: 0.8848 (p0) REVERT: D 4731 ILE cc_start: 0.9497 (tt) cc_final: 0.9095 (mp) REVERT: D 4874 MET cc_start: 0.8924 (mmm) cc_final: 0.8708 (mmm) REVERT: D 4878 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.7648 (t70) REVERT: D 4902 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7999 (mt-10) REVERT: D 5016 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8700 (pt0) REVERT: D 5020 ASP cc_start: 0.8967 (m-30) cc_final: 0.8716 (t0) REVERT: D 5036 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8068 (mm) outliers start: 440 outliers final: 35 residues processed: 1452 average time/residue: 1.2252 time to fit residues: 3130.2357 Evaluate side-chains 870 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 804 time to evaluate : 12.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4224 GLU Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4546 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4581 LYS Chi-restraints excluded: chain A residue 4628 VAL Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4680 LYS Chi-restraints excluded: chain A residue 4684 ASP Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4739 GLU Chi-restraints excluded: chain A residue 4809 PHE Chi-restraints excluded: chain A residue 4861 LYS Chi-restraints excluded: chain A residue 4878 ASP Chi-restraints excluded: chain A residue 4880 MET Chi-restraints excluded: chain A residue 4945 ASP Chi-restraints excluded: chain A residue 4957 LYS Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain A residue 5036 LEU Chi-restraints excluded: chain B residue 4253 GLU Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4546 VAL Chi-restraints excluded: chain B residue 4577 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4628 VAL Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4680 LYS Chi-restraints excluded: chain B residue 4684 ASP Chi-restraints excluded: chain B residue 4739 GLU Chi-restraints excluded: chain B residue 4797 VAL Chi-restraints excluded: chain B residue 4902 GLU Chi-restraints excluded: chain B residue 4957 LYS Chi-restraints excluded: chain B residue 4958 CYS Chi-restraints excluded: chain B residue 5036 LEU Chi-restraints excluded: chain C residue 4253 GLU Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4546 VAL Chi-restraints excluded: chain C residue 4577 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4628 VAL Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4680 LYS Chi-restraints excluded: chain C residue 4684 ASP Chi-restraints excluded: chain C residue 4739 GLU Chi-restraints excluded: chain C residue 4797 VAL Chi-restraints excluded: chain C residue 4878 ASP Chi-restraints excluded: chain C residue 4902 GLU Chi-restraints excluded: chain C residue 4957 LYS Chi-restraints excluded: chain C residue 4958 CYS Chi-restraints excluded: chain C residue 5036 LEU Chi-restraints excluded: chain D residue 4253 GLU Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4546 VAL Chi-restraints excluded: chain D residue 4577 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4628 VAL Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4680 LYS Chi-restraints excluded: chain D residue 4684 ASP Chi-restraints excluded: chain D residue 4739 GLU Chi-restraints excluded: chain D residue 4797 VAL Chi-restraints excluded: chain D residue 4878 ASP Chi-restraints excluded: chain D residue 4902 GLU Chi-restraints excluded: chain D residue 4957 LYS Chi-restraints excluded: chain D residue 4958 CYS Chi-restraints excluded: chain D residue 5036 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1509 optimal weight: 0.5980 chunk 1355 optimal weight: 4.9990 chunk 751 optimal weight: 20.0000 chunk 462 optimal weight: 20.0000 chunk 914 optimal weight: 8.9990 chunk 724 optimal weight: 30.0000 chunk 1401 optimal weight: 6.9990 chunk 542 optimal weight: 8.9990 chunk 852 optimal weight: 0.7980 chunk 1043 optimal weight: 1.9990 chunk 1623 optimal weight: 7.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1660 GLN ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2284 ASN A2933 ASN ** A3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4043 GLN A4162 ASN A4201 ASN A4246 GLN A4728 HIS A4886 HIS A4984 ASN A5003 HIS ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5035 GLN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1660 GLN ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2247 GLN B2284 ASN B2933 ASN ** B3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4043 GLN B4162 ASN B4201 ASN B4246 GLN B4728 HIS B4886 HIS B4984 ASN B5003 HIS ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5035 GLN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 877 ASN ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN C1660 GLN ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2284 ASN C2933 ASN C2962 GLN ** C3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4043 GLN C4162 ASN C4201 ASN C4246 GLN C4728 HIS C4886 HIS C4984 ASN C5003 HIS ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C5035 GLN ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 919 ASN D1660 GLN ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2247 GLN D2284 ASN D2933 ASN ** D3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4043 GLN D4162 ASN D4201 ASN D4246 GLN D4728 HIS D4886 HIS D4984 ASN D5003 HIS ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5035 GLN E 87 HIS F 87 HIS G 87 HIS H 87 HIS Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 146316 Z= 0.222 Angle : 0.637 13.052 198204 Z= 0.324 Chirality : 0.042 0.329 21788 Planarity : 0.004 0.068 25764 Dihedral : 6.364 146.140 19764 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.10 % Allowed : 6.41 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.01 % 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: 0.22 (0.06), residues: 17840 helix: 1.01 (0.06), residues: 8772 sheet: -0.51 (0.13), residues: 1552 loop : -0.67 (0.07), residues: 7516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1143 HIS 0.007 0.001 HIS D2204 PHE 0.033 0.001 PHE A5028 TYR 0.028 0.001 TYR A 959 ARG 0.012 0.000 ARG D4734 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 815 time to evaluate : 12.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.8223 (tpt) cc_final: 0.7784 (tpp) REVERT: A 483 MET cc_start: 0.8552 (mmm) cc_final: 0.8324 (mmm) REVERT: A 569 ILE cc_start: 0.9520 (tp) cc_final: 0.9224 (pt) REVERT: A 919 ASN cc_start: 0.7839 (t0) cc_final: 0.7353 (p0) REVERT: A 1260 MET cc_start: 0.8636 (mtp) cc_final: 0.8432 (mtm) REVERT: A 1608 MET cc_start: 0.8996 (mtp) cc_final: 0.8648 (mpp) REVERT: A 2008 MET cc_start: 0.9455 (mtm) cc_final: 0.8903 (tmm) REVERT: A 2170 MET cc_start: 0.8748 (mmm) cc_final: 0.8478 (mmm) REVERT: A 2211 MET cc_start: 0.9459 (mmp) cc_final: 0.9237 (mmp) REVERT: A 2312 MET cc_start: 0.4878 (ttt) cc_final: 0.4508 (mtm) REVERT: A 2490 MET cc_start: 0.6614 (mmt) cc_final: 0.6078 (mmt) REVERT: A 2562 ILE cc_start: 0.9255 (mm) cc_final: 0.8945 (tt) REVERT: A 2874 MET cc_start: 0.6819 (mmp) cc_final: 0.5826 (ttp) REVERT: A 3248 ARG cc_start: 0.9024 (tpt-90) cc_final: 0.8379 (ptm160) REVERT: A 3437 MET cc_start: 0.8391 (tpp) cc_final: 0.7801 (tpp) REVERT: A 3573 MET cc_start: 0.8553 (mmm) cc_final: 0.8315 (mmm) REVERT: A 3875 MET cc_start: 0.7687 (mmp) cc_final: 0.7270 (mmp) REVERT: A 3968 TYR cc_start: 0.8772 (m-10) cc_final: 0.8514 (m-80) REVERT: A 4047 MET cc_start: 0.8958 (tmm) cc_final: 0.8687 (tmm) REVERT: A 4064 MET cc_start: 0.8581 (tmm) cc_final: 0.8330 (ppp) REVERT: A 4580 TYR cc_start: 0.7465 (OUTLIER) cc_final: 0.6764 (t80) REVERT: A 4730 ASP cc_start: 0.9183 (m-30) cc_final: 0.8917 (p0) REVERT: A 4731 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9082 (mp) REVERT: A 4953 ASP cc_start: 0.8978 (m-30) cc_final: 0.8760 (m-30) REVERT: A 5016 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8858 (mt-10) REVERT: B 81 MET cc_start: 0.9134 (ttp) cc_final: 0.8864 (ptm) REVERT: B 202 MET cc_start: 0.8231 (tpt) cc_final: 0.7774 (tpp) REVERT: B 513 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8834 (mp0) REVERT: B 569 ILE cc_start: 0.9559 (tp) cc_final: 0.9227 (pt) REVERT: B 1601 MET cc_start: 0.8740 (mmm) cc_final: 0.8353 (mmt) REVERT: B 1608 MET cc_start: 0.9063 (mtp) cc_final: 0.8710 (mpp) REVERT: B 1851 MET cc_start: 0.8847 (mtm) cc_final: 0.8578 (mtp) REVERT: B 2008 MET cc_start: 0.9457 (mtm) cc_final: 0.8920 (tmm) REVERT: B 2312 MET cc_start: 0.5032 (OUTLIER) cc_final: 0.4338 (mtm) REVERT: B 2874 MET cc_start: 0.6472 (mmp) cc_final: 0.5416 (ttp) REVERT: B 3248 ARG cc_start: 0.8963 (tpt-90) cc_final: 0.8297 (ptm160) REVERT: B 3437 MET cc_start: 0.8429 (tpp) cc_final: 0.7881 (tpp) REVERT: B 3552 PHE cc_start: 0.9147 (m-80) cc_final: 0.8936 (m-80) REVERT: B 3638 MET cc_start: 0.4830 (ppp) cc_final: 0.4493 (ppp) REVERT: B 3652 MET cc_start: 0.9256 (pmm) cc_final: 0.8817 (pmm) REVERT: B 3875 MET cc_start: 0.7698 (mmp) cc_final: 0.7331 (mmp) REVERT: B 3968 TYR cc_start: 0.8753 (m-10) cc_final: 0.8473 (m-80) REVERT: B 4044 MET cc_start: 0.9248 (ttm) cc_final: 0.8990 (ttm) REVERT: B 4047 MET cc_start: 0.8934 (tmm) cc_final: 0.8600 (tmm) REVERT: B 4184 MET cc_start: 0.8717 (tpp) cc_final: 0.8499 (tpp) REVERT: B 4580 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.6169 (t80) REVERT: B 4730 ASP cc_start: 0.9130 (m-30) cc_final: 0.8888 (p0) REVERT: B 4731 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.9153 (mp) REVERT: B 4824 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7661 (mtm180) REVERT: B 4874 MET cc_start: 0.8832 (mmm) cc_final: 0.8435 (mmt) REVERT: B 4879 MET cc_start: 0.8298 (mmm) cc_final: 0.7991 (tpp) REVERT: B 5016 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8900 (mt-10) REVERT: C 81 MET cc_start: 0.9134 (ttp) cc_final: 0.8865 (ptm) REVERT: C 202 MET cc_start: 0.8235 (tpt) cc_final: 0.7773 (tpp) REVERT: C 513 GLU cc_start: 0.9281 (mm-30) cc_final: 0.8835 (mp0) REVERT: C 569 ILE cc_start: 0.9559 (tp) cc_final: 0.9227 (pt) REVERT: C 1601 MET cc_start: 0.8741 (mmm) cc_final: 0.8352 (mmt) REVERT: C 1608 MET cc_start: 0.9061 (mtp) cc_final: 0.8710 (mpp) REVERT: C 1851 MET cc_start: 0.8851 (mtm) cc_final: 0.8579 (mtp) REVERT: C 2008 MET cc_start: 0.9457 (mtm) cc_final: 0.8921 (tmm) REVERT: C 2312 MET cc_start: 0.5035 (OUTLIER) cc_final: 0.4341 (mtm) REVERT: C 2874 MET cc_start: 0.6472 (mmp) cc_final: 0.5417 (ttp) REVERT: C 3248 ARG cc_start: 0.8963 (tpt-90) cc_final: 0.8298 (ptm160) REVERT: C 3437 MET cc_start: 0.8427 (tpp) cc_final: 0.7879 (tpp) REVERT: C 3552 PHE cc_start: 0.9146 (m-80) cc_final: 0.8934 (m-80) REVERT: C 3638 MET cc_start: 0.4828 (ppp) cc_final: 0.4489 (ppp) REVERT: C 3652 MET cc_start: 0.9256 (pmm) cc_final: 0.8817 (pmm) REVERT: C 3875 MET cc_start: 0.7684 (mmp) cc_final: 0.7320 (mmp) REVERT: C 3968 TYR cc_start: 0.8752 (m-10) cc_final: 0.8474 (m-80) REVERT: C 4044 MET cc_start: 0.9247 (ttm) cc_final: 0.8990 (ttm) REVERT: C 4047 MET cc_start: 0.8934 (tmm) cc_final: 0.8600 (tmm) REVERT: C 4184 MET cc_start: 0.8717 (tpp) cc_final: 0.8499 (tpp) REVERT: C 4227 GLU cc_start: 0.7365 (pt0) cc_final: 0.6832 (pp20) REVERT: C 4580 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.6172 (t80) REVERT: C 4730 ASP cc_start: 0.9132 (m-30) cc_final: 0.8891 (p0) REVERT: C 4731 ILE cc_start: 0.9458 (OUTLIER) cc_final: 0.9150 (mp) REVERT: C 4824 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7665 (mtm180) REVERT: C 4874 MET cc_start: 0.8857 (mmm) cc_final: 0.8533 (mmm) REVERT: C 4879 MET cc_start: 0.8348 (tpt) cc_final: 0.8120 (tpp) REVERT: C 5016 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8901 (mt-10) REVERT: D 81 MET cc_start: 0.9134 (ttp) cc_final: 0.8866 (ptm) REVERT: D 202 MET cc_start: 0.8230 (tpt) cc_final: 0.7773 (tpp) REVERT: D 513 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8835 (mp0) REVERT: D 569 ILE cc_start: 0.9558 (tp) cc_final: 0.9226 (pt) REVERT: D 1601 MET cc_start: 0.8740 (mmm) cc_final: 0.8352 (mmt) REVERT: D 1608 MET cc_start: 0.9062 (mtp) cc_final: 0.8709 (mpp) REVERT: D 1851 MET cc_start: 0.8846 (mtm) cc_final: 0.8578 (mtp) REVERT: D 2008 MET cc_start: 0.9457 (mtm) cc_final: 0.8922 (tmm) REVERT: D 2312 MET cc_start: 0.5038 (OUTLIER) cc_final: 0.4341 (mtm) REVERT: D 2874 MET cc_start: 0.6472 (mmp) cc_final: 0.5417 (ttp) REVERT: D 3248 ARG cc_start: 0.8964 (tpt-90) cc_final: 0.8298 (ptm160) REVERT: D 3437 MET cc_start: 0.8424 (tpp) cc_final: 0.7875 (tpp) REVERT: D 3552 PHE cc_start: 0.9147 (m-80) cc_final: 0.8935 (m-80) REVERT: D 3638 MET cc_start: 0.4823 (ppp) cc_final: 0.4483 (ppp) REVERT: D 3652 MET cc_start: 0.9256 (pmm) cc_final: 0.8815 (pmm) REVERT: D 3875 MET cc_start: 0.7695 (mmp) cc_final: 0.7328 (mmp) REVERT: D 3968 TYR cc_start: 0.8756 (m-10) cc_final: 0.8478 (m-80) REVERT: D 4044 MET cc_start: 0.9248 (ttm) cc_final: 0.8989 (ttm) REVERT: D 4047 MET cc_start: 0.8936 (tmm) cc_final: 0.8603 (tmm) REVERT: D 4184 MET cc_start: 0.8715 (tpp) cc_final: 0.8499 (tpp) REVERT: D 4227 GLU cc_start: 0.7367 (pt0) cc_final: 0.6831 (pp20) REVERT: D 4580 TYR cc_start: 0.7284 (OUTLIER) cc_final: 0.6163 (t80) REVERT: D 4730 ASP cc_start: 0.9133 (m-30) cc_final: 0.8890 (p0) REVERT: D 4731 ILE cc_start: 0.9457 (OUTLIER) cc_final: 0.9149 (mp) REVERT: D 4874 MET cc_start: 0.8855 (mmm) cc_final: 0.8529 (mmm) REVERT: D 4879 MET cc_start: 0.8351 (tpt) cc_final: 0.8121 (tpp) REVERT: D 5016 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8901 (mt-10) outliers start: 148 outliers final: 67 residues processed: 909 average time/residue: 1.2218 time to fit residues: 2011.9284 Evaluate side-chains 849 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 769 time to evaluate : 12.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 959 TYR Chi-restraints excluded: chain A residue 1512 THR Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2423 MET Chi-restraints excluded: chain A residue 2514 ASN Chi-restraints excluded: chain A residue 2628 PHE Chi-restraints excluded: chain A residue 2998 PHE Chi-restraints excluded: chain A residue 4156 HIS Chi-restraints excluded: chain A residue 4224 GLU Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4581 LYS Chi-restraints excluded: chain A residue 4628 VAL Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4739 GLU Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4826 ILE Chi-restraints excluded: chain A residue 4945 ASP Chi-restraints excluded: chain A residue 5027 CYS Chi-restraints excluded: chain B residue 959 TYR Chi-restraints excluded: chain B residue 2259 GLU Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2312 MET Chi-restraints excluded: chain B residue 2423 MET Chi-restraints excluded: chain B residue 2514 ASN Chi-restraints excluded: chain B residue 2628 PHE Chi-restraints excluded: chain B residue 2998 PHE Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4628 VAL Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4739 GLU Chi-restraints excluded: chain B residue 4824 ARG Chi-restraints excluded: chain B residue 4826 ILE Chi-restraints excluded: chain B residue 4876 CYS Chi-restraints excluded: chain B residue 4945 ASP Chi-restraints excluded: chain B residue 4957 LYS Chi-restraints excluded: chain B residue 5012 LYS Chi-restraints excluded: chain C residue 959 TYR Chi-restraints excluded: chain C residue 2259 GLU Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2312 MET Chi-restraints excluded: chain C residue 2423 MET Chi-restraints excluded: chain C residue 2514 ASN Chi-restraints excluded: chain C residue 2628 PHE Chi-restraints excluded: chain C residue 2998 PHE Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4628 VAL Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4739 GLU Chi-restraints excluded: chain C residue 4824 ARG Chi-restraints excluded: chain C residue 4826 ILE Chi-restraints excluded: chain C residue 4876 CYS Chi-restraints excluded: chain C residue 4945 ASP Chi-restraints excluded: chain C residue 4957 LYS Chi-restraints excluded: chain C residue 5012 LYS Chi-restraints excluded: chain D residue 959 TYR Chi-restraints excluded: chain D residue 2259 GLU Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2312 MET Chi-restraints excluded: chain D residue 2423 MET Chi-restraints excluded: chain D residue 2514 ASN Chi-restraints excluded: chain D residue 2628 PHE Chi-restraints excluded: chain D residue 2998 PHE Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4628 VAL Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4739 GLU Chi-restraints excluded: chain D residue 4826 ILE Chi-restraints excluded: chain D residue 4876 CYS Chi-restraints excluded: chain D residue 4945 ASP Chi-restraints excluded: chain D residue 4957 LYS Chi-restraints excluded: chain D residue 5012 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 902 optimal weight: 40.0000 chunk 503 optimal weight: 9.9990 chunk 1351 optimal weight: 0.1980 chunk 1105 optimal weight: 20.0000 chunk 447 optimal weight: 5.9990 chunk 1626 optimal weight: 30.0000 chunk 1757 optimal weight: 9.9990 chunk 1448 optimal weight: 40.0000 chunk 1613 optimal weight: 20.0000 chunk 554 optimal weight: 8.9990 chunk 1304 optimal weight: 1.9990 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2247 GLN A2284 ASN ** A3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3611 HIS A3851 ASN A3960 GLN ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A5006 GLN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2284 ASN ** B3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3611 HIS B3851 ASN B3960 GLN ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5006 GLN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 877 ASN ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2247 GLN C2284 ASN C2772 GLN C2962 GLN ** C3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3611 HIS C3851 ASN C3960 GLN ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C5006 GLN ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 919 ASN ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2284 ASN D2772 GLN ** D3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3611 HIS D3851 ASN D3960 GLN ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4973 HIS D5006 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 146316 Z= 0.320 Angle : 0.662 11.848 198204 Z= 0.336 Chirality : 0.042 0.332 21788 Planarity : 0.005 0.058 25764 Dihedral : 6.188 146.473 19677 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.08 % Allowed : 7.97 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.23 % Twisted General : 0.01 % 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: 0.24 (0.06), residues: 17840 helix: 1.03 (0.06), residues: 8840 sheet: -0.60 (0.13), residues: 1632 loop : -0.65 (0.07), residues: 7368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D4644 HIS 0.015 0.001 HIS B3611 PHE 0.032 0.002 PHE D2973 TYR 0.020 0.002 TYR A4851 ARG 0.006 0.001 ARG D4734 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 788 time to evaluate : 12.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 HIS cc_start: 0.7620 (OUTLIER) cc_final: 0.7251 (m90) REVERT: A 202 MET cc_start: 0.8392 (tpt) cc_final: 0.7895 (tpp) REVERT: A 483 MET cc_start: 0.8595 (mmm) cc_final: 0.8357 (mmm) REVERT: A 569 ILE cc_start: 0.9550 (tp) cc_final: 0.9261 (pt) REVERT: A 919 ASN cc_start: 0.7805 (t0) cc_final: 0.7305 (p0) REVERT: A 941 MET cc_start: 0.6738 (tpt) cc_final: 0.6083 (mmp) REVERT: A 960 MET cc_start: 0.1091 (ttm) cc_final: 0.0631 (ttm) REVERT: A 1152 MET cc_start: 0.8418 (mmp) cc_final: 0.8085 (mmp) REVERT: A 1608 MET cc_start: 0.9055 (mtp) cc_final: 0.8690 (mpp) REVERT: A 2008 MET cc_start: 0.9495 (mtm) cc_final: 0.8912 (tmm) REVERT: A 2167 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8632 (pp) REVERT: A 2312 MET cc_start: 0.4869 (OUTLIER) cc_final: 0.4201 (mtm) REVERT: A 2874 MET cc_start: 0.6467 (mmp) cc_final: 0.5375 (ttp) REVERT: A 3239 MET cc_start: 0.5149 (mtt) cc_final: 0.4825 (mmm) REVERT: A 3248 ARG cc_start: 0.8977 (tpt-90) cc_final: 0.8371 (ptm160) REVERT: A 3437 MET cc_start: 0.8442 (tpp) cc_final: 0.8154 (tpp) REVERT: A 3968 TYR cc_start: 0.8911 (m-10) cc_final: 0.8623 (m-80) REVERT: A 4047 MET cc_start: 0.8834 (tmm) cc_final: 0.8482 (tmm) REVERT: A 4580 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.6585 (t80) REVERT: A 4730 ASP cc_start: 0.9171 (m-30) cc_final: 0.8945 (p0) REVERT: A 4731 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.9179 (mp) REVERT: A 4879 MET cc_start: 0.8220 (tpp) cc_final: 0.7471 (tpp) REVERT: A 4989 MET cc_start: 0.9122 (tmm) cc_final: 0.8552 (tmm) REVERT: A 5016 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8877 (mt-10) REVERT: B 12 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8456 (mp10) REVERT: B 81 MET cc_start: 0.9266 (ttp) cc_final: 0.8929 (ptm) REVERT: B 202 MET cc_start: 0.8486 (tpt) cc_final: 0.8013 (tpp) REVERT: B 569 ILE cc_start: 0.9587 (tp) cc_final: 0.9245 (pt) REVERT: B 632 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8594 (mm) REVERT: B 941 MET cc_start: 0.6857 (tpt) cc_final: 0.6489 (mmp) REVERT: B 1170 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8583 (mmm) REVERT: B 1573 MET cc_start: 0.7491 (tpt) cc_final: 0.7280 (tpp) REVERT: B 1601 MET cc_start: 0.8767 (mmm) cc_final: 0.8420 (mmt) REVERT: B 2008 MET cc_start: 0.9440 (mtm) cc_final: 0.8880 (tmm) REVERT: B 2170 MET cc_start: 0.8702 (mmp) cc_final: 0.8182 (mmm) REVERT: B 2312 MET cc_start: 0.5040 (OUTLIER) cc_final: 0.4826 (mtp) REVERT: B 2874 MET cc_start: 0.6517 (mmp) cc_final: 0.5419 (ttp) REVERT: B 3239 MET cc_start: 0.5144 (mtt) cc_final: 0.4878 (mmm) REVERT: B 3248 ARG cc_start: 0.9017 (tpt-90) cc_final: 0.8343 (ptm160) REVERT: B 3437 MET cc_start: 0.8375 (tpp) cc_final: 0.8119 (tpp) REVERT: B 3968 TYR cc_start: 0.8930 (m-10) cc_final: 0.8646 (m-80) REVERT: B 4047 MET cc_start: 0.8908 (tmm) cc_final: 0.8552 (tmm) REVERT: B 4064 MET cc_start: 0.8639 (tmm) cc_final: 0.8272 (ppp) REVERT: B 4184 MET cc_start: 0.8980 (tpp) cc_final: 0.8742 (tpp) REVERT: B 4580 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.6056 (t80) REVERT: B 4730 ASP cc_start: 0.9136 (m-30) cc_final: 0.8919 (p0) REVERT: B 4731 ILE cc_start: 0.9509 (OUTLIER) cc_final: 0.9220 (mp) REVERT: B 4798 MET cc_start: 0.9008 (mmm) cc_final: 0.8721 (mmt) REVERT: B 4879 MET cc_start: 0.8261 (mmm) cc_final: 0.7805 (tpp) REVERT: B 4989 MET cc_start: 0.9069 (tpp) cc_final: 0.8856 (tpp) REVERT: B 5012 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8907 (ptpp) REVERT: B 5016 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8842 (mt-10) REVERT: B 5018 CYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8969 (p) REVERT: C 12 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8455 (mp10) REVERT: C 81 MET cc_start: 0.9266 (ttp) cc_final: 0.8929 (ptm) REVERT: C 202 MET cc_start: 0.8484 (tpt) cc_final: 0.8012 (tpp) REVERT: C 569 ILE cc_start: 0.9587 (tp) cc_final: 0.9246 (pt) REVERT: C 632 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8593 (mm) REVERT: C 941 MET cc_start: 0.6856 (tpt) cc_final: 0.6489 (mmp) REVERT: C 1170 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8582 (mmm) REVERT: C 1573 MET cc_start: 0.7493 (tpt) cc_final: 0.7284 (tpp) REVERT: C 1601 MET cc_start: 0.8768 (mmm) cc_final: 0.8421 (mmt) REVERT: C 2008 MET cc_start: 0.9441 (mtm) cc_final: 0.8880 (tmm) REVERT: C 2170 MET cc_start: 0.8702 (mmp) cc_final: 0.8185 (mmm) REVERT: C 2312 MET cc_start: 0.5045 (OUTLIER) cc_final: 0.4829 (mtp) REVERT: C 2874 MET cc_start: 0.6455 (mmp) cc_final: 0.5410 (ttp) REVERT: C 3239 MET cc_start: 0.5144 (mtt) cc_final: 0.4879 (mmm) REVERT: C 3248 ARG cc_start: 0.9018 (tpt-90) cc_final: 0.8343 (ptm160) REVERT: C 3437 MET cc_start: 0.8374 (tpp) cc_final: 0.8116 (tpp) REVERT: C 3968 TYR cc_start: 0.8929 (m-10) cc_final: 0.8644 (m-80) REVERT: C 4047 MET cc_start: 0.8907 (tmm) cc_final: 0.8551 (tmm) REVERT: C 4064 MET cc_start: 0.8641 (tmm) cc_final: 0.8272 (ppp) REVERT: C 4184 MET cc_start: 0.8982 (tpp) cc_final: 0.8745 (tpp) REVERT: C 4580 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.6059 (t80) REVERT: C 4730 ASP cc_start: 0.9139 (m-30) cc_final: 0.8924 (p0) REVERT: C 4731 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9217 (mp) REVERT: C 4798 MET cc_start: 0.9005 (mmm) cc_final: 0.8717 (mmt) REVERT: C 4879 MET cc_start: 0.8542 (tpt) cc_final: 0.8140 (tpp) REVERT: C 4887 MET cc_start: 0.8362 (mmm) cc_final: 0.8153 (mmm) REVERT: C 4989 MET cc_start: 0.9068 (tpp) cc_final: 0.8857 (tpp) REVERT: C 5012 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8909 (ptpp) REVERT: C 5016 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8843 (mt-10) REVERT: C 5018 CYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8963 (p) REVERT: D 12 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8457 (mp10) REVERT: D 81 MET cc_start: 0.9265 (ttp) cc_final: 0.8929 (ptm) REVERT: D 202 MET cc_start: 0.8512 (tpt) cc_final: 0.8039 (tpp) REVERT: D 569 ILE cc_start: 0.9587 (tp) cc_final: 0.9245 (pt) REVERT: D 632 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8593 (mm) REVERT: D 941 MET cc_start: 0.6853 (tpt) cc_final: 0.6482 (mmp) REVERT: D 1170 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8586 (mmm) REVERT: D 1573 MET cc_start: 0.7492 (tpt) cc_final: 0.7283 (tpp) REVERT: D 1601 MET cc_start: 0.8766 (mmm) cc_final: 0.8423 (mmt) REVERT: D 2008 MET cc_start: 0.9443 (mtm) cc_final: 0.8882 (tmm) REVERT: D 2170 MET cc_start: 0.8702 (mmp) cc_final: 0.8183 (mmm) REVERT: D 2312 MET cc_start: 0.5041 (OUTLIER) cc_final: 0.4829 (mtp) REVERT: D 2874 MET cc_start: 0.6455 (mmp) cc_final: 0.5410 (ttp) REVERT: D 3239 MET cc_start: 0.5145 (mtt) cc_final: 0.4880 (mmm) REVERT: D 3248 ARG cc_start: 0.9017 (tpt-90) cc_final: 0.8344 (ptm160) REVERT: D 3437 MET cc_start: 0.8372 (tpp) cc_final: 0.8116 (tpp) REVERT: D 3968 TYR cc_start: 0.8931 (m-10) cc_final: 0.8648 (m-80) REVERT: D 4047 MET cc_start: 0.8909 (tmm) cc_final: 0.8552 (tmm) REVERT: D 4064 MET cc_start: 0.8639 (tmm) cc_final: 0.8269 (ppp) REVERT: D 4184 MET cc_start: 0.8978 (tpp) cc_final: 0.8740 (tpp) REVERT: D 4580 TYR cc_start: 0.7503 (OUTLIER) cc_final: 0.6052 (t80) REVERT: D 4730 ASP cc_start: 0.9139 (m-30) cc_final: 0.8922 (p0) REVERT: D 4731 ILE cc_start: 0.9440 (OUTLIER) cc_final: 0.9131 (mp) REVERT: D 4798 MET cc_start: 0.9004 (mmm) cc_final: 0.8716 (mmt) REVERT: D 4879 MET cc_start: 0.8542 (tpt) cc_final: 0.8140 (tpp) REVERT: D 4887 MET cc_start: 0.8366 (mmm) cc_final: 0.8160 (mmm) REVERT: D 4942 GLU cc_start: 0.8254 (mm-30) cc_final: 0.8020 (mm-30) REVERT: D 4989 MET cc_start: 0.9070 (tpp) cc_final: 0.8856 (tpp) REVERT: D 5012 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8907 (ptpp) REVERT: D 5016 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8841 (mt-10) REVERT: D 5018 CYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8968 (p) REVERT: E 66 MET cc_start: 0.7468 (pmm) cc_final: 0.7205 (pmm) REVERT: F 66 MET cc_start: 0.7471 (pmm) cc_final: 0.7206 (pmm) REVERT: G 66 MET cc_start: 0.7468 (pmm) cc_final: 0.7204 (pmm) REVERT: H 66 MET cc_start: 0.7464 (pmm) cc_final: 0.7203 (pmm) outliers start: 142 outliers final: 93 residues processed: 876 average time/residue: 1.1570 time to fit residues: 1832.2702 Evaluate side-chains 886 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 767 time to evaluate : 13.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 959 TYR Chi-restraints excluded: chain A residue 1512 THR Chi-restraints excluded: chain A residue 2167 ILE Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2312 MET Chi-restraints excluded: chain A residue 2514 ASN Chi-restraints excluded: chain A residue 2628 PHE Chi-restraints excluded: chain A residue 2998 PHE Chi-restraints excluded: chain A residue 3518 LEU Chi-restraints excluded: chain A residue 4156 HIS Chi-restraints excluded: chain A residue 4224 GLU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4581 LYS Chi-restraints excluded: chain A residue 4585 SER Chi-restraints excluded: chain A residue 4628 VAL Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4710 SER Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4739 GLU Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4822 THR Chi-restraints excluded: chain A residue 4826 ILE Chi-restraints excluded: chain A residue 4925 ILE Chi-restraints excluded: chain A residue 4945 ASP Chi-restraints excluded: chain A residue 5027 CYS Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 959 TYR Chi-restraints excluded: chain B residue 1170 MET Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 2208 MET Chi-restraints excluded: chain B residue 2259 GLU Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2312 MET Chi-restraints excluded: chain B residue 2514 ASN Chi-restraints excluded: chain B residue 2628 PHE Chi-restraints excluded: chain B residue 2998 PHE Chi-restraints excluded: chain B residue 3412 LEU Chi-restraints excluded: chain B residue 3518 LEU Chi-restraints excluded: chain B residue 3758 MET Chi-restraints excluded: chain B residue 4156 HIS Chi-restraints excluded: chain B residue 4207 MET Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4585 SER Chi-restraints excluded: chain B residue 4628 VAL Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4710 SER Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4739 GLU Chi-restraints excluded: chain B residue 4822 THR Chi-restraints excluded: chain B residue 4826 ILE Chi-restraints excluded: chain B residue 4876 CYS Chi-restraints excluded: chain B residue 4945 ASP Chi-restraints excluded: chain B residue 5012 LYS Chi-restraints excluded: chain B residue 5018 CYS Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 959 TYR Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 2259 GLU Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2312 MET Chi-restraints excluded: chain C residue 2514 ASN Chi-restraints excluded: chain C residue 2628 PHE Chi-restraints excluded: chain C residue 2998 PHE Chi-restraints excluded: chain C residue 3412 LEU Chi-restraints excluded: chain C residue 3518 LEU Chi-restraints excluded: chain C residue 3758 MET Chi-restraints excluded: chain C residue 4156 HIS Chi-restraints excluded: chain C residue 4207 MET Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4585 SER Chi-restraints excluded: chain C residue 4628 VAL Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4710 SER Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4739 GLU Chi-restraints excluded: chain C residue 4822 THR Chi-restraints excluded: chain C residue 4826 ILE Chi-restraints excluded: chain C residue 4876 CYS Chi-restraints excluded: chain C residue 4945 ASP Chi-restraints excluded: chain C residue 5012 LYS Chi-restraints excluded: chain C residue 5018 CYS Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 959 TYR Chi-restraints excluded: chain D residue 1170 MET Chi-restraints excluded: chain D residue 1599 MET Chi-restraints excluded: chain D residue 2208 MET Chi-restraints excluded: chain D residue 2259 GLU Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2312 MET Chi-restraints excluded: chain D residue 2514 ASN Chi-restraints excluded: chain D residue 2628 PHE Chi-restraints excluded: chain D residue 2998 PHE Chi-restraints excluded: chain D residue 3412 LEU Chi-restraints excluded: chain D residue 3518 LEU Chi-restraints excluded: chain D residue 3758 MET Chi-restraints excluded: chain D residue 4156 HIS Chi-restraints excluded: chain D residue 4207 MET Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4585 SER Chi-restraints excluded: chain D residue 4628 VAL Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4710 SER Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4739 GLU Chi-restraints excluded: chain D residue 4822 THR Chi-restraints excluded: chain D residue 4826 ILE Chi-restraints excluded: chain D residue 4876 CYS Chi-restraints excluded: chain D residue 4945 ASP Chi-restraints excluded: chain D residue 5012 LYS Chi-restraints excluded: chain D residue 5018 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1607 optimal weight: 9.9990 chunk 1222 optimal weight: 7.9990 chunk 844 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 chunk 776 optimal weight: 1.9990 chunk 1092 optimal weight: 20.0000 chunk 1632 optimal weight: 8.9990 chunk 1728 optimal weight: 0.7980 chunk 852 optimal weight: 0.8980 chunk 1547 optimal weight: 20.0000 chunk 465 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2247 GLN A2520 HIS ** A3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3555 ASN ** A3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2247 GLN B2520 HIS ** B3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3555 ASN ** B3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1066 GLN ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2247 GLN C2520 HIS ** C3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3555 ASN ** C3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2520 HIS ** D3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3555 ASN ** D3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 146316 Z= 0.178 Angle : 0.580 11.268 198204 Z= 0.291 Chirality : 0.040 0.294 21788 Planarity : 0.004 0.071 25764 Dihedral : 6.045 145.851 19663 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.06 % Allowed : 9.15 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.11 % Twisted General : 0.01 % 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: 0.46 (0.06), residues: 17840 helix: 1.23 (0.06), residues: 8856 sheet: -0.48 (0.13), residues: 1620 loop : -0.58 (0.07), residues: 7364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A4644 HIS 0.015 0.001 HIS A2520 PHE 0.031 0.001 PHE D2973 TYR 0.016 0.001 TYR B 959 ARG 0.009 0.000 ARG B3403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 787 time to evaluate : 12.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8710 (tp) REVERT: A 202 MET cc_start: 0.8396 (tpt) cc_final: 0.7960 (tpp) REVERT: A 483 MET cc_start: 0.8605 (mmm) cc_final: 0.8358 (mmm) REVERT: A 569 ILE cc_start: 0.9550 (tp) cc_final: 0.9261 (pt) REVERT: A 919 ASN cc_start: 0.7930 (t0) cc_final: 0.7453 (m110) REVERT: A 1152 MET cc_start: 0.8553 (mmp) cc_final: 0.8040 (mmp) REVERT: A 1608 MET cc_start: 0.9071 (mtp) cc_final: 0.8723 (mpp) REVERT: A 2008 MET cc_start: 0.9488 (mtm) cc_final: 0.8885 (tmm) REVERT: A 2170 MET cc_start: 0.8943 (mmm) cc_final: 0.8688 (mmm) REVERT: A 2874 MET cc_start: 0.6426 (mmp) cc_final: 0.5393 (ttp) REVERT: A 3437 MET cc_start: 0.8461 (tpp) cc_final: 0.8139 (tpp) REVERT: A 3442 PHE cc_start: 0.8870 (t80) cc_final: 0.8582 (m-80) REVERT: A 3573 MET cc_start: 0.8503 (mmm) cc_final: 0.8280 (mmm) REVERT: A 3968 TYR cc_start: 0.8762 (m-10) cc_final: 0.8443 (m-80) REVERT: A 4047 MET cc_start: 0.8853 (tmm) cc_final: 0.8495 (tmm) REVERT: A 4580 TYR cc_start: 0.7521 (OUTLIER) cc_final: 0.6157 (t80) REVERT: A 4730 ASP cc_start: 0.9148 (m-30) cc_final: 0.8914 (p0) REVERT: A 4731 ILE cc_start: 0.9435 (tt) cc_final: 0.9153 (mp) REVERT: A 4879 MET cc_start: 0.7976 (tpp) cc_final: 0.7275 (tpp) REVERT: A 4989 MET cc_start: 0.9205 (tmm) cc_final: 0.8608 (tmm) REVERT: A 5016 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8846 (mt-10) REVERT: B 12 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8469 (mp10) REVERT: B 81 MET cc_start: 0.9260 (ttp) cc_final: 0.8929 (ptm) REVERT: B 202 MET cc_start: 0.8421 (tpt) cc_final: 0.7971 (tpp) REVERT: B 569 ILE cc_start: 0.9582 (tp) cc_final: 0.9249 (pt) REVERT: B 960 MET cc_start: 0.1174 (mtt) cc_final: 0.0496 (ttm) REVERT: B 1152 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8361 (mmp) REVERT: B 1170 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8358 (mmm) REVERT: B 1601 MET cc_start: 0.8715 (mmm) cc_final: 0.8356 (mmt) REVERT: B 2008 MET cc_start: 0.9431 (mtm) cc_final: 0.8863 (tmm) REVERT: B 2170 MET cc_start: 0.8688 (mmp) cc_final: 0.8153 (mmm) REVERT: B 2211 MET cc_start: 0.9500 (mmm) cc_final: 0.9265 (mmp) REVERT: B 2312 MET cc_start: 0.5050 (ttt) cc_final: 0.4417 (mtm) REVERT: B 2874 MET cc_start: 0.6480 (mmp) cc_final: 0.5416 (ttp) REVERT: B 3437 MET cc_start: 0.8494 (tpp) cc_final: 0.8197 (tpp) REVERT: B 3442 PHE cc_start: 0.8861 (t80) cc_final: 0.8623 (m-80) REVERT: B 3652 MET cc_start: 0.9253 (pmm) cc_final: 0.8868 (pmm) REVERT: B 4047 MET cc_start: 0.8888 (tmm) cc_final: 0.8530 (tmm) REVERT: B 4580 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.5787 (t80) REVERT: B 4730 ASP cc_start: 0.9164 (m-30) cc_final: 0.8901 (p0) REVERT: B 4731 ILE cc_start: 0.9482 (tt) cc_final: 0.9215 (mp) REVERT: B 4798 MET cc_start: 0.8890 (mmm) cc_final: 0.8565 (mmt) REVERT: B 4879 MET cc_start: 0.8168 (mmm) cc_final: 0.7948 (tpp) REVERT: B 5012 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8826 (ptpp) REVERT: B 5016 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8814 (mt-10) REVERT: C 12 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8468 (mp10) REVERT: C 81 MET cc_start: 0.9260 (ttp) cc_final: 0.8930 (ptm) REVERT: C 202 MET cc_start: 0.8417 (tpt) cc_final: 0.7947 (tpp) REVERT: C 569 ILE cc_start: 0.9582 (tp) cc_final: 0.9249 (pt) REVERT: C 1152 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8358 (mmp) REVERT: C 1170 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8359 (mmm) REVERT: C 1601 MET cc_start: 0.8714 (mmm) cc_final: 0.8357 (mmt) REVERT: C 2008 MET cc_start: 0.9432 (mtm) cc_final: 0.8864 (tmm) REVERT: C 2170 MET cc_start: 0.8689 (mmp) cc_final: 0.8155 (mmm) REVERT: C 2211 MET cc_start: 0.9499 (mmm) cc_final: 0.9272 (mmp) REVERT: C 2312 MET cc_start: 0.5055 (ttt) cc_final: 0.4420 (mtm) REVERT: C 2874 MET cc_start: 0.6484 (mmp) cc_final: 0.5417 (ttp) REVERT: C 3437 MET cc_start: 0.8491 (tpp) cc_final: 0.8194 (tpp) REVERT: C 3442 PHE cc_start: 0.8859 (t80) cc_final: 0.8621 (m-80) REVERT: C 3652 MET cc_start: 0.9253 (pmm) cc_final: 0.8866 (pmm) REVERT: C 4047 MET cc_start: 0.8890 (tmm) cc_final: 0.8532 (tmm) REVERT: C 4580 TYR cc_start: 0.7420 (OUTLIER) cc_final: 0.5790 (t80) REVERT: C 4730 ASP cc_start: 0.9168 (m-30) cc_final: 0.8906 (p0) REVERT: C 4731 ILE cc_start: 0.9477 (tt) cc_final: 0.9211 (mp) REVERT: C 4798 MET cc_start: 0.8891 (mmm) cc_final: 0.8586 (mmt) REVERT: C 5012 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8828 (ptpp) REVERT: C 5016 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8814 (mt-10) REVERT: D 12 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8470 (mp10) REVERT: D 81 MET cc_start: 0.9260 (ttp) cc_final: 0.8929 (ptm) REVERT: D 202 MET cc_start: 0.8430 (tpt) cc_final: 0.7970 (tpp) REVERT: D 569 ILE cc_start: 0.9581 (tp) cc_final: 0.9249 (pt) REVERT: D 1152 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8364 (mmp) REVERT: D 1170 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8361 (mmm) REVERT: D 1601 MET cc_start: 0.8716 (mmm) cc_final: 0.8357 (mmt) REVERT: D 2008 MET cc_start: 0.9433 (mtm) cc_final: 0.8865 (tmm) REVERT: D 2170 MET cc_start: 0.8689 (mmp) cc_final: 0.8154 (mmm) REVERT: D 2211 MET cc_start: 0.9501 (mmm) cc_final: 0.9265 (mmp) REVERT: D 2312 MET cc_start: 0.5054 (ttt) cc_final: 0.4421 (mtm) REVERT: D 2874 MET cc_start: 0.6483 (mmp) cc_final: 0.5416 (ttp) REVERT: D 3437 MET cc_start: 0.8490 (tpp) cc_final: 0.8194 (tpp) REVERT: D 3442 PHE cc_start: 0.8860 (t80) cc_final: 0.8621 (m-80) REVERT: D 3652 MET cc_start: 0.9254 (pmm) cc_final: 0.8868 (pmm) REVERT: D 4047 MET cc_start: 0.8890 (tmm) cc_final: 0.8532 (tmm) REVERT: D 4580 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.5769 (t80) REVERT: D 4730 ASP cc_start: 0.9167 (m-30) cc_final: 0.8903 (p0) REVERT: D 4731 ILE cc_start: 0.9477 (tt) cc_final: 0.9212 (mp) REVERT: D 4798 MET cc_start: 0.8887 (mmm) cc_final: 0.8585 (mmt) REVERT: D 5012 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8826 (ptpp) REVERT: D 5016 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8812 (mt-10) REVERT: E 66 MET cc_start: 0.7444 (pmm) cc_final: 0.7181 (pmm) REVERT: F 66 MET cc_start: 0.7448 (pmm) cc_final: 0.7183 (pmm) REVERT: G 66 MET cc_start: 0.7441 (pmm) cc_final: 0.7178 (pmm) REVERT: H 66 MET cc_start: 0.7443 (pmm) cc_final: 0.7180 (pmm) outliers start: 139 outliers final: 74 residues processed: 879 average time/residue: 1.1768 time to fit residues: 1873.8494 Evaluate side-chains 846 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 758 time to evaluate : 12.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 959 TYR Chi-restraints excluded: chain A residue 1512 THR Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2514 ASN Chi-restraints excluded: chain A residue 2628 PHE Chi-restraints excluded: chain A residue 3518 LEU Chi-restraints excluded: chain A residue 3758 MET Chi-restraints excluded: chain A residue 4224 GLU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4581 LYS Chi-restraints excluded: chain A residue 4628 VAL Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4710 SER Chi-restraints excluded: chain A residue 4739 GLU Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4826 ILE Chi-restraints excluded: chain A residue 4925 ILE Chi-restraints excluded: chain A residue 4945 ASP Chi-restraints excluded: chain A residue 5027 CYS Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 959 TYR Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1170 MET Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2514 ASN Chi-restraints excluded: chain B residue 2628 PHE Chi-restraints excluded: chain B residue 2998 PHE Chi-restraints excluded: chain B residue 3518 LEU Chi-restraints excluded: chain B residue 3758 MET Chi-restraints excluded: chain B residue 4156 HIS Chi-restraints excluded: chain B residue 4207 MET Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4628 VAL Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4710 SER Chi-restraints excluded: chain B residue 4739 GLU Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4826 ILE Chi-restraints excluded: chain B residue 4876 CYS Chi-restraints excluded: chain B residue 4945 ASP Chi-restraints excluded: chain B residue 5012 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 959 TYR Chi-restraints excluded: chain C residue 1152 MET Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2514 ASN Chi-restraints excluded: chain C residue 2628 PHE Chi-restraints excluded: chain C residue 2998 PHE Chi-restraints excluded: chain C residue 3518 LEU Chi-restraints excluded: chain C residue 3758 MET Chi-restraints excluded: chain C residue 4156 HIS Chi-restraints excluded: chain C residue 4207 MET Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4628 VAL Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4710 SER Chi-restraints excluded: chain C residue 4739 GLU Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4826 ILE Chi-restraints excluded: chain C residue 4853 VAL Chi-restraints excluded: chain C residue 4876 CYS Chi-restraints excluded: chain C residue 4945 ASP Chi-restraints excluded: chain C residue 5012 LYS Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 959 TYR Chi-restraints excluded: chain D residue 1152 MET Chi-restraints excluded: chain D residue 1170 MET Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2514 ASN Chi-restraints excluded: chain D residue 2628 PHE Chi-restraints excluded: chain D residue 2998 PHE Chi-restraints excluded: chain D residue 3518 LEU Chi-restraints excluded: chain D residue 3758 MET Chi-restraints excluded: chain D residue 4156 HIS Chi-restraints excluded: chain D residue 4207 MET Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4628 VAL Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4710 SER Chi-restraints excluded: chain D residue 4739 GLU Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4826 ILE Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4876 CYS Chi-restraints excluded: chain D residue 4945 ASP Chi-restraints excluded: chain D residue 5012 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1439 optimal weight: 20.0000 chunk 981 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 1286 optimal weight: 4.9990 chunk 713 optimal weight: 50.0000 chunk 1474 optimal weight: 5.9990 chunk 1194 optimal weight: 40.0000 chunk 2 optimal weight: 20.0000 chunk 882 optimal weight: 20.0000 chunk 1551 optimal weight: 30.0000 chunk 436 optimal weight: 4.9990 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 GLN ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1631 GLN ** A1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2247 GLN A2291 GLN ** A3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3555 ASN ** A3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4246 GLN ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4973 HIS B 98 HIS ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN B 705 ASN B 765 GLN ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1631 GLN ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2247 GLN B2291 GLN B2520 HIS ** B3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3555 ASN ** B3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4246 GLN ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 HIS ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 ASN C 705 ASN C 765 GLN ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1631 GLN ** C1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2247 GLN C2291 GLN C2520 HIS ** C3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3555 ASN ** C3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4246 GLN ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 HIS ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 705 ASN D 765 GLN ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1631 GLN ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2291 GLN D2520 HIS ** D3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3555 ASN ** D3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4246 GLN ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.138 146316 Z= 0.503 Angle : 0.799 13.498 198204 Z= 0.406 Chirality : 0.046 0.309 21788 Planarity : 0.006 0.084 25764 Dihedral : 6.435 144.557 19657 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.27 % Allowed : 10.09 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.11 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.06), residues: 17840 helix: 0.74 (0.05), residues: 8832 sheet: -0.87 (0.13), residues: 1680 loop : -0.77 (0.07), residues: 7328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 148 HIS 0.012 0.002 HIS A4978 PHE 0.034 0.003 PHE A4807 TYR 0.044 0.003 TYR A1051 ARG 0.015 0.001 ARG A1180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 907 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 737 time to evaluate : 12.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8579 (mp10) REVERT: A 483 MET cc_start: 0.8666 (mmm) cc_final: 0.8325 (mmm) REVERT: A 569 ILE cc_start: 0.9613 (tp) cc_final: 0.9299 (pt) REVERT: A 1152 MET cc_start: 0.8792 (mmp) cc_final: 0.8224 (mmp) REVERT: A 2008 MET cc_start: 0.9457 (mtm) cc_final: 0.8783 (tmm) REVERT: A 2490 MET cc_start: 0.8074 (mmt) cc_final: 0.7453 (mmt) REVERT: A 2874 MET cc_start: 0.6472 (mmp) cc_final: 0.5420 (ttp) REVERT: A 3442 PHE cc_start: 0.9071 (t80) cc_final: 0.8678 (m-80) REVERT: A 3836 MET cc_start: 0.9379 (ttp) cc_final: 0.9176 (ttt) REVERT: A 3968 TYR cc_start: 0.9119 (m-10) cc_final: 0.8834 (m-80) REVERT: A 3999 MET cc_start: 0.9300 (mmm) cc_final: 0.8818 (tpp) REVERT: A 4047 MET cc_start: 0.8865 (tmm) cc_final: 0.8465 (tmm) REVERT: A 4580 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.6115 (t80) REVERT: A 4730 ASP cc_start: 0.9204 (m-30) cc_final: 0.8959 (p0) REVERT: A 4731 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9093 (mp) REVERT: A 4879 MET cc_start: 0.8442 (tpp) cc_final: 0.8100 (tpp) REVERT: A 4989 MET cc_start: 0.9193 (tmm) cc_final: 0.8905 (tmm) REVERT: B 12 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8627 (mp10) REVERT: B 81 MET cc_start: 0.9300 (ttp) cc_final: 0.8861 (ptm) REVERT: B 569 ILE cc_start: 0.9600 (tp) cc_final: 0.9260 (pt) REVERT: B 1152 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.7869 (mmp) REVERT: B 1170 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8422 (mmm) REVERT: B 1601 MET cc_start: 0.8715 (mmm) cc_final: 0.8380 (mmt) REVERT: B 2008 MET cc_start: 0.9450 (mtm) cc_final: 0.8798 (tmm) REVERT: B 2874 MET cc_start: 0.6491 (mmp) cc_final: 0.5396 (ttp) REVERT: B 3442 PHE cc_start: 0.9081 (t80) cc_final: 0.8687 (m-80) REVERT: B 3968 TYR cc_start: 0.9115 (m-10) cc_final: 0.8831 (m-80) REVERT: B 4047 MET cc_start: 0.8860 (tmm) cc_final: 0.8455 (tmm) REVERT: B 4580 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.6082 (t80) REVERT: B 4730 ASP cc_start: 0.9261 (m-30) cc_final: 0.8945 (p0) REVERT: B 4731 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.9063 (mp) REVERT: C 12 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8626 (mp10) REVERT: C 81 MET cc_start: 0.9300 (ttp) cc_final: 0.8861 (ptm) REVERT: C 569 ILE cc_start: 0.9600 (tp) cc_final: 0.9260 (pt) REVERT: C 1152 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.7866 (mmp) REVERT: C 1170 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8421 (mmm) REVERT: C 1601 MET cc_start: 0.8717 (mmm) cc_final: 0.8380 (mmt) REVERT: C 2008 MET cc_start: 0.9450 (mtm) cc_final: 0.8798 (tmm) REVERT: C 2874 MET cc_start: 0.6497 (mmp) cc_final: 0.5397 (ttp) REVERT: C 3442 PHE cc_start: 0.9080 (t80) cc_final: 0.8689 (m-80) REVERT: C 3968 TYR cc_start: 0.9115 (m-10) cc_final: 0.8831 (m-80) REVERT: C 4047 MET cc_start: 0.8858 (tmm) cc_final: 0.8454 (tmm) REVERT: C 4580 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.6086 (t80) REVERT: C 4730 ASP cc_start: 0.9261 (m-30) cc_final: 0.8949 (p0) REVERT: C 4731 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.9060 (mp) REVERT: C 4879 MET cc_start: 0.8611 (tpp) cc_final: 0.8020 (tpp) REVERT: D 12 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8627 (mp10) REVERT: D 81 MET cc_start: 0.9298 (ttp) cc_final: 0.8860 (ptm) REVERT: D 569 ILE cc_start: 0.9599 (tp) cc_final: 0.9260 (pt) REVERT: D 1152 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.7871 (mmp) REVERT: D 1170 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8422 (mmm) REVERT: D 1601 MET cc_start: 0.8718 (mmm) cc_final: 0.8381 (mmt) REVERT: D 2008 MET cc_start: 0.9451 (mtm) cc_final: 0.8799 (tmm) REVERT: D 2256 TYR cc_start: 0.8807 (t80) cc_final: 0.8554 (t80) REVERT: D 2874 MET cc_start: 0.6498 (mmp) cc_final: 0.5399 (ttp) REVERT: D 3442 PHE cc_start: 0.9081 (t80) cc_final: 0.8688 (m-80) REVERT: D 3968 TYR cc_start: 0.9115 (m-10) cc_final: 0.8832 (m-80) REVERT: D 4047 MET cc_start: 0.8859 (tmm) cc_final: 0.8454 (tmm) REVERT: D 4580 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.6233 (t80) REVERT: D 4730 ASP cc_start: 0.9262 (m-30) cc_final: 0.8948 (p0) REVERT: D 4731 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9061 (mp) REVERT: D 4879 MET cc_start: 0.8610 (tpp) cc_final: 0.8018 (tpp) REVERT: E 57 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.9050 (tptp) REVERT: E 66 MET cc_start: 0.7476 (pmm) cc_final: 0.7211 (pmm) REVERT: F 57 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.9049 (tptp) REVERT: F 66 MET cc_start: 0.7481 (pmm) cc_final: 0.7216 (pmm) REVERT: G 57 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.9048 (tptp) REVERT: G 66 MET cc_start: 0.7478 (pmm) cc_final: 0.7211 (pmm) REVERT: H 57 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.9049 (tptp) REVERT: H 66 MET cc_start: 0.7476 (pmm) cc_final: 0.7213 (pmm) outliers start: 170 outliers final: 112 residues processed: 857 average time/residue: 1.1529 time to fit residues: 1789.7394 Evaluate side-chains 853 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 723 time to evaluate : 12.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 959 TYR Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1944 GLU Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2514 ASN Chi-restraints excluded: chain A residue 2628 PHE Chi-restraints excluded: chain A residue 2998 PHE Chi-restraints excluded: chain A residue 3412 LEU Chi-restraints excluded: chain A residue 3518 LEU Chi-restraints excluded: chain A residue 4156 HIS Chi-restraints excluded: chain A residue 4224 GLU Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4581 LYS Chi-restraints excluded: chain A residue 4585 SER Chi-restraints excluded: chain A residue 4628 VAL Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4710 SER Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4739 GLU Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4826 ILE Chi-restraints excluded: chain A residue 4876 CYS Chi-restraints excluded: chain A residue 4925 ILE Chi-restraints excluded: chain A residue 4945 ASP Chi-restraints excluded: chain A residue 5027 CYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 959 TYR Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1170 MET Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2490 MET Chi-restraints excluded: chain B residue 2514 ASN Chi-restraints excluded: chain B residue 2628 PHE Chi-restraints excluded: chain B residue 2998 PHE Chi-restraints excluded: chain B residue 3412 LEU Chi-restraints excluded: chain B residue 3518 LEU Chi-restraints excluded: chain B residue 3753 PHE Chi-restraints excluded: chain B residue 4156 HIS Chi-restraints excluded: chain B residue 4207 MET Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4585 SER Chi-restraints excluded: chain B residue 4628 VAL Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4710 SER Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4739 GLU Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4824 ARG Chi-restraints excluded: chain B residue 4825 THR Chi-restraints excluded: chain B residue 4826 ILE Chi-restraints excluded: chain B residue 4876 CYS Chi-restraints excluded: chain B residue 4925 ILE Chi-restraints excluded: chain B residue 4945 ASP Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 959 TYR Chi-restraints excluded: chain C residue 1152 MET Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 1731 LEU Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2490 MET Chi-restraints excluded: chain C residue 2514 ASN Chi-restraints excluded: chain C residue 2628 PHE Chi-restraints excluded: chain C residue 2998 PHE Chi-restraints excluded: chain C residue 3412 LEU Chi-restraints excluded: chain C residue 3518 LEU Chi-restraints excluded: chain C residue 3753 PHE Chi-restraints excluded: chain C residue 4156 HIS Chi-restraints excluded: chain C residue 4207 MET Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4585 SER Chi-restraints excluded: chain C residue 4628 VAL Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4710 SER Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4739 GLU Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4826 ILE Chi-restraints excluded: chain C residue 4876 CYS Chi-restraints excluded: chain C residue 4925 ILE Chi-restraints excluded: chain C residue 4945 ASP Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 959 TYR Chi-restraints excluded: chain D residue 1152 MET Chi-restraints excluded: chain D residue 1170 MET Chi-restraints excluded: chain D residue 1599 MET Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 2259 GLU Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2490 MET Chi-restraints excluded: chain D residue 2514 ASN Chi-restraints excluded: chain D residue 2628 PHE Chi-restraints excluded: chain D residue 2998 PHE Chi-restraints excluded: chain D residue 3412 LEU Chi-restraints excluded: chain D residue 3518 LEU Chi-restraints excluded: chain D residue 3753 PHE Chi-restraints excluded: chain D residue 4156 HIS Chi-restraints excluded: chain D residue 4207 MET Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4585 SER Chi-restraints excluded: chain D residue 4628 VAL Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4710 SER Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4739 GLU Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4825 THR Chi-restraints excluded: chain D residue 4826 ILE Chi-restraints excluded: chain D residue 4876 CYS Chi-restraints excluded: chain D residue 4925 ILE Chi-restraints excluded: chain D residue 4945 ASP Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain H residue 57 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 581 optimal weight: 9.9990 chunk 1556 optimal weight: 6.9990 chunk 341 optimal weight: 7.9990 chunk 1014 optimal weight: 6.9990 chunk 426 optimal weight: 0.6980 chunk 1729 optimal weight: 0.7980 chunk 1436 optimal weight: 0.0170 chunk 800 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 572 optimal weight: 0.6980 chunk 908 optimal weight: 20.0000 overall best weight: 1.2420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1220 GLN ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2247 GLN A2520 HIS ** A3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3555 ASN ** A3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 ASN B1220 GLN ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2247 GLN B2520 HIS B2772 GLN ** B3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3555 ASN ** B3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1203 ASN C1220 GLN ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2247 GLN C2520 HIS ** C3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3555 ASN ** C3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1203 ASN D1220 GLN ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2247 GLN D2520 HIS ** D3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3555 ASN ** D3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 146316 Z= 0.167 Angle : 0.597 11.568 198204 Z= 0.299 Chirality : 0.041 0.272 21788 Planarity : 0.004 0.088 25764 Dihedral : 6.142 144.032 19657 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.06 % Allowed : 10.92 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.11 % Twisted General : 0.01 % 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: 0.38 (0.06), residues: 17840 helix: 1.20 (0.06), residues: 8860 sheet: -0.68 (0.13), residues: 1652 loop : -0.63 (0.07), residues: 7328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A4644 HIS 0.015 0.001 HIS D2520 PHE 0.028 0.002 PHE C3095 TYR 0.018 0.001 TYR A3922 ARG 0.008 0.000 ARG B3403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 752 time to evaluate : 13.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8580 (mp10) REVERT: A 127 MET cc_start: 0.7728 (mmm) cc_final: 0.7209 (ptt) REVERT: A 483 MET cc_start: 0.8718 (mmm) cc_final: 0.8424 (mmm) REVERT: A 569 ILE cc_start: 0.9575 (tp) cc_final: 0.9307 (pt) REVERT: A 919 ASN cc_start: 0.7869 (t0) cc_final: 0.7417 (p0) REVERT: A 1152 MET cc_start: 0.8871 (mmp) cc_final: 0.8419 (mmp) REVERT: A 1170 MET cc_start: 0.8732 (mmm) cc_final: 0.8467 (mmm) REVERT: A 2008 MET cc_start: 0.9436 (mtm) cc_final: 0.8664 (tmm) REVERT: A 2254 LEU cc_start: 0.8996 (tp) cc_final: 0.8657 (tp) REVERT: A 2490 MET cc_start: 0.7888 (mmt) cc_final: 0.7353 (mmt) REVERT: A 2761 TYR cc_start: 0.6181 (OUTLIER) cc_final: 0.5850 (m-80) REVERT: A 2874 MET cc_start: 0.6423 (mmp) cc_final: 0.5408 (ttp) REVERT: A 3437 MET cc_start: 0.8447 (tpp) cc_final: 0.8216 (tpp) REVERT: A 3442 PHE cc_start: 0.9041 (t80) cc_final: 0.8660 (t80) REVERT: A 3524 MET cc_start: 0.8264 (ppp) cc_final: 0.7639 (ppp) REVERT: A 3968 TYR cc_start: 0.8763 (m-10) cc_final: 0.8400 (m-80) REVERT: A 4047 MET cc_start: 0.8893 (tmm) cc_final: 0.8504 (tmm) REVERT: A 4580 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.6065 (t80) REVERT: A 4730 ASP cc_start: 0.9190 (m-30) cc_final: 0.8970 (p0) REVERT: A 4731 ILE cc_start: 0.9505 (tt) cc_final: 0.9232 (mp) REVERT: A 4989 MET cc_start: 0.9238 (tmm) cc_final: 0.8583 (tmm) REVERT: B 12 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8600 (mp10) REVERT: B 81 MET cc_start: 0.9276 (ttp) cc_final: 0.8828 (ptm) REVERT: B 127 MET cc_start: 0.7750 (mmm) cc_final: 0.7225 (ptt) REVERT: B 202 MET cc_start: 0.8631 (tpp) cc_final: 0.7837 (tpp) REVERT: B 1170 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8255 (mmm) REVERT: B 1601 MET cc_start: 0.8751 (mmm) cc_final: 0.8430 (mmt) REVERT: B 2008 MET cc_start: 0.9415 (mtm) cc_final: 0.8724 (tmm) REVERT: B 2874 MET cc_start: 0.6505 (mmp) cc_final: 0.5411 (ttp) REVERT: B 3437 MET cc_start: 0.8475 (tpp) cc_final: 0.8250 (tpp) REVERT: B 3968 TYR cc_start: 0.8764 (m-10) cc_final: 0.8426 (m-80) REVERT: B 4047 MET cc_start: 0.8893 (tmm) cc_final: 0.8509 (tmm) REVERT: B 4122 MET cc_start: 0.2955 (tpp) cc_final: 0.2742 (tpp) REVERT: B 4207 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8402 (ttt) REVERT: B 4580 TYR cc_start: 0.7387 (OUTLIER) cc_final: 0.5622 (t80) REVERT: B 4730 ASP cc_start: 0.9198 (m-30) cc_final: 0.8950 (p0) REVERT: B 4731 ILE cc_start: 0.9499 (OUTLIER) cc_final: 0.9218 (mp) REVERT: B 4879 MET cc_start: 0.8124 (mmm) cc_final: 0.7795 (tpp) REVERT: B 5013 MET cc_start: 0.9299 (mtp) cc_final: 0.9015 (ttp) REVERT: C 12 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8598 (mp10) REVERT: C 81 MET cc_start: 0.9276 (ttp) cc_final: 0.8830 (ptm) REVERT: C 202 MET cc_start: 0.8717 (tpp) cc_final: 0.8039 (tpp) REVERT: C 960 MET cc_start: 0.2058 (mtt) cc_final: 0.1420 (ttm) REVERT: C 1170 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8211 (mmm) REVERT: C 1601 MET cc_start: 0.8750 (mmm) cc_final: 0.8426 (mmt) REVERT: C 2008 MET cc_start: 0.9416 (mtm) cc_final: 0.8725 (tmm) REVERT: C 2250 MET cc_start: 0.9129 (tpp) cc_final: 0.8922 (tpt) REVERT: C 2874 MET cc_start: 0.6450 (mmp) cc_final: 0.5388 (ttp) REVERT: C 3437 MET cc_start: 0.8473 (tpp) cc_final: 0.8249 (tpp) REVERT: C 3573 MET cc_start: 0.8627 (mmm) cc_final: 0.8274 (mmm) REVERT: C 3968 TYR cc_start: 0.8765 (m-10) cc_final: 0.8425 (m-80) REVERT: C 4047 MET cc_start: 0.8892 (tmm) cc_final: 0.8509 (tmm) REVERT: C 4122 MET cc_start: 0.2954 (tpp) cc_final: 0.2744 (tpp) REVERT: C 4207 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8403 (ttt) REVERT: C 4580 TYR cc_start: 0.7391 (OUTLIER) cc_final: 0.5623 (t80) REVERT: C 4730 ASP cc_start: 0.9202 (m-30) cc_final: 0.8954 (p0) REVERT: C 4731 ILE cc_start: 0.9489 (OUTLIER) cc_final: 0.9210 (mp) REVERT: C 4879 MET cc_start: 0.8371 (tpp) cc_final: 0.7642 (tpp) REVERT: C 5013 MET cc_start: 0.9304 (mtp) cc_final: 0.9020 (ttp) REVERT: D 12 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8599 (mp10) REVERT: D 81 MET cc_start: 0.9277 (ttp) cc_final: 0.8831 (ptm) REVERT: D 202 MET cc_start: 0.8732 (tpp) cc_final: 0.8044 (tpp) REVERT: D 960 MET cc_start: 0.2051 (mtt) cc_final: 0.1416 (ttm) REVERT: D 1170 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8215 (mmm) REVERT: D 1601 MET cc_start: 0.8751 (mmm) cc_final: 0.8429 (mmt) REVERT: D 2008 MET cc_start: 0.9417 (mtm) cc_final: 0.8726 (tmm) REVERT: D 2874 MET cc_start: 0.6450 (mmp) cc_final: 0.5388 (ttp) REVERT: D 3437 MET cc_start: 0.8470 (tpp) cc_final: 0.8247 (tpp) REVERT: D 3968 TYR cc_start: 0.8764 (m-10) cc_final: 0.8426 (m-80) REVERT: D 4047 MET cc_start: 0.8894 (tmm) cc_final: 0.8510 (tmm) REVERT: D 4122 MET cc_start: 0.2953 (tpp) cc_final: 0.2742 (tpp) REVERT: D 4207 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8403 (ttt) REVERT: D 4580 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.5694 (t80) REVERT: D 4730 ASP cc_start: 0.9199 (m-30) cc_final: 0.8953 (p0) REVERT: D 4731 ILE cc_start: 0.9489 (OUTLIER) cc_final: 0.9210 (mp) REVERT: D 4879 MET cc_start: 0.8372 (tpp) cc_final: 0.7645 (tpp) REVERT: D 4942 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7605 (mt-10) REVERT: D 5013 MET cc_start: 0.9300 (mtp) cc_final: 0.9016 (ttp) REVERT: E 66 MET cc_start: 0.7447 (pmm) cc_final: 0.7156 (pmm) REVERT: F 66 MET cc_start: 0.7451 (pmm) cc_final: 0.7160 (pmm) REVERT: G 66 MET cc_start: 0.7447 (pmm) cc_final: 0.7158 (pmm) REVERT: H 66 MET cc_start: 0.7449 (pmm) cc_final: 0.7160 (pmm) outliers start: 137 outliers final: 81 residues processed: 850 average time/residue: 1.1406 time to fit residues: 1761.2764 Evaluate side-chains 820 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 725 time to evaluate : 12.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 959 TYR Chi-restraints excluded: chain A residue 1573 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2514 ASN Chi-restraints excluded: chain A residue 2520 HIS Chi-restraints excluded: chain A residue 2628 PHE Chi-restraints excluded: chain A residue 2761 TYR Chi-restraints excluded: chain A residue 2998 PHE Chi-restraints excluded: chain A residue 3518 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4581 LYS Chi-restraints excluded: chain A residue 4628 VAL Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4710 SER Chi-restraints excluded: chain A residue 4739 GLU Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4826 ILE Chi-restraints excluded: chain A residue 4876 CYS Chi-restraints excluded: chain A residue 4945 ASP Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 1170 MET Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2514 ASN Chi-restraints excluded: chain B residue 2628 PHE Chi-restraints excluded: chain B residue 2998 PHE Chi-restraints excluded: chain B residue 3518 LEU Chi-restraints excluded: chain B residue 3753 PHE Chi-restraints excluded: chain B residue 3758 MET Chi-restraints excluded: chain B residue 4156 HIS Chi-restraints excluded: chain B residue 4207 MET Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4628 VAL Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4710 SER Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4739 GLU Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4945 ASP Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1731 LEU Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2514 ASN Chi-restraints excluded: chain C residue 2628 PHE Chi-restraints excluded: chain C residue 2998 PHE Chi-restraints excluded: chain C residue 3518 LEU Chi-restraints excluded: chain C residue 3753 PHE Chi-restraints excluded: chain C residue 3758 MET Chi-restraints excluded: chain C residue 4156 HIS Chi-restraints excluded: chain C residue 4207 MET Chi-restraints excluded: chain C residue 4227 GLU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4628 VAL Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4710 SER Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4739 GLU Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4826 ILE Chi-restraints excluded: chain C residue 4876 CYS Chi-restraints excluded: chain C residue 4945 ASP Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 1170 MET Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 2254 LEU Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2514 ASN Chi-restraints excluded: chain D residue 2628 PHE Chi-restraints excluded: chain D residue 2998 PHE Chi-restraints excluded: chain D residue 3518 LEU Chi-restraints excluded: chain D residue 3753 PHE Chi-restraints excluded: chain D residue 3758 MET Chi-restraints excluded: chain D residue 4156 HIS Chi-restraints excluded: chain D residue 4207 MET Chi-restraints excluded: chain D residue 4227 GLU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4628 VAL Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4710 SER Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4739 GLU Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4876 CYS Chi-restraints excluded: chain D residue 4945 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1667 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 985 optimal weight: 20.0000 chunk 1263 optimal weight: 4.9990 chunk 978 optimal weight: 0.2980 chunk 1456 optimal weight: 5.9990 chunk 966 optimal weight: 50.0000 chunk 1723 optimal weight: 7.9990 chunk 1078 optimal weight: 0.9980 chunk 1050 optimal weight: 9.9990 chunk 795 optimal weight: 9.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1665 HIS ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2247 GLN A2520 HIS ** A3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 ASN B1665 HIS ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2247 GLN B2520 HIS ** B3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1203 ASN C1665 HIS ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2247 GLN C2520 HIS ** C3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1203 ASN D1665 HIS ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2247 GLN D2520 HIS ** D3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 146316 Z= 0.235 Angle : 0.615 14.140 198204 Z= 0.307 Chirality : 0.041 0.280 21788 Planarity : 0.004 0.078 25764 Dihedral : 6.100 144.230 19654 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.06 % Allowed : 11.25 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.11 % Twisted General : 0.01 % 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: 0.46 (0.06), residues: 17840 helix: 1.25 (0.06), residues: 8876 sheet: -0.72 (0.13), residues: 1668 loop : -0.55 (0.07), residues: 7296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A4644 HIS 0.024 0.001 HIS A2520 PHE 0.029 0.002 PHE A2973 TYR 0.021 0.001 TYR D3722 ARG 0.009 0.000 ARG C3403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 732 time to evaluate : 12.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8588 (mp10) REVERT: A 483 MET cc_start: 0.8715 (mmm) cc_final: 0.8417 (mmm) REVERT: A 569 ILE cc_start: 0.9589 (tp) cc_final: 0.9326 (pt) REVERT: A 919 ASN cc_start: 0.7844 (t0) cc_final: 0.7421 (m110) REVERT: A 1152 MET cc_start: 0.8848 (mmp) cc_final: 0.8403 (mmp) REVERT: A 1170 MET cc_start: 0.8800 (mmm) cc_final: 0.8501 (mmm) REVERT: A 1865 MET cc_start: 0.9060 (mtm) cc_final: 0.8643 (mpp) REVERT: A 2008 MET cc_start: 0.9426 (mtm) cc_final: 0.8728 (tmm) REVERT: A 2254 LEU cc_start: 0.8912 (tp) cc_final: 0.8575 (tp) REVERT: A 2490 MET cc_start: 0.7946 (mmt) cc_final: 0.7357 (mmt) REVERT: A 2761 TYR cc_start: 0.6191 (OUTLIER) cc_final: 0.5852 (m-80) REVERT: A 2874 MET cc_start: 0.6472 (mmp) cc_final: 0.5435 (ttp) REVERT: A 3437 MET cc_start: 0.8424 (tpp) cc_final: 0.8181 (tpp) REVERT: A 3442 PHE cc_start: 0.9046 (t80) cc_final: 0.8699 (t80) REVERT: A 3968 TYR cc_start: 0.8861 (m-10) cc_final: 0.8520 (m-80) REVERT: A 4047 MET cc_start: 0.8883 (tmm) cc_final: 0.8469 (tmm) REVERT: A 4580 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.6204 (t80) REVERT: A 4730 ASP cc_start: 0.9189 (m-30) cc_final: 0.8957 (p0) REVERT: A 4731 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9232 (mp) REVERT: A 4879 MET cc_start: 0.8292 (tpp) cc_final: 0.7628 (tpp) REVERT: A 4989 MET cc_start: 0.9201 (tmm) cc_final: 0.8568 (tmm) REVERT: B 12 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8639 (mp10) REVERT: B 81 MET cc_start: 0.9289 (ttp) cc_final: 0.8871 (ptm) REVERT: B 202 MET cc_start: 0.8682 (tpp) cc_final: 0.8010 (tpp) REVERT: B 1170 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8268 (mmm) REVERT: B 1601 MET cc_start: 0.8736 (mmm) cc_final: 0.8426 (mmt) REVERT: B 2008 MET cc_start: 0.9421 (mtm) cc_final: 0.8742 (tmm) REVERT: B 2546 MET cc_start: 0.6088 (mmm) cc_final: 0.5579 (mpp) REVERT: B 2874 MET cc_start: 0.6488 (mmp) cc_final: 0.5408 (ttp) REVERT: B 3437 MET cc_start: 0.8448 (tpp) cc_final: 0.8212 (tpp) REVERT: B 3442 PHE cc_start: 0.9008 (t80) cc_final: 0.8637 (m-80) REVERT: B 3968 TYR cc_start: 0.8865 (m-10) cc_final: 0.8515 (m-80) REVERT: B 4047 MET cc_start: 0.8882 (tmm) cc_final: 0.8475 (tmm) REVERT: B 4122 MET cc_start: 0.3125 (tpp) cc_final: 0.2875 (tpp) REVERT: B 4207 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8486 (ttt) REVERT: B 4580 TYR cc_start: 0.7445 (OUTLIER) cc_final: 0.5786 (t80) REVERT: B 4730 ASP cc_start: 0.9245 (m-30) cc_final: 0.8971 (p0) REVERT: B 4731 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.9225 (mp) REVERT: B 4798 MET cc_start: 0.8964 (mmm) cc_final: 0.8658 (mmt) REVERT: B 4879 MET cc_start: 0.8171 (mmm) cc_final: 0.7601 (tpp) REVERT: B 5013 MET cc_start: 0.9300 (mtp) cc_final: 0.9029 (ttp) REVERT: C 12 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8638 (mp10) REVERT: C 81 MET cc_start: 0.9291 (ttp) cc_final: 0.8872 (ptm) REVERT: C 202 MET cc_start: 0.8751 (tpp) cc_final: 0.8520 (tpp) REVERT: C 1170 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8271 (mmm) REVERT: C 1601 MET cc_start: 0.8736 (mmm) cc_final: 0.8425 (mmt) REVERT: C 2008 MET cc_start: 0.9421 (mtm) cc_final: 0.8743 (tmm) REVERT: C 2250 MET cc_start: 0.9092 (tpp) cc_final: 0.8828 (tpt) REVERT: C 2546 MET cc_start: 0.6089 (mmm) cc_final: 0.5580 (mpp) REVERT: C 2874 MET cc_start: 0.6494 (mmp) cc_final: 0.5411 (ttp) REVERT: C 3437 MET cc_start: 0.8448 (tpp) cc_final: 0.8214 (tpp) REVERT: C 3442 PHE cc_start: 0.9010 (t80) cc_final: 0.8638 (m-80) REVERT: C 3573 MET cc_start: 0.8743 (mmm) cc_final: 0.8398 (mmm) REVERT: C 3968 TYR cc_start: 0.8865 (m-10) cc_final: 0.8515 (m-80) REVERT: C 4047 MET cc_start: 0.8882 (tmm) cc_final: 0.8475 (tmm) REVERT: C 4122 MET cc_start: 0.3122 (tpp) cc_final: 0.2871 (tpp) REVERT: C 4207 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8485 (ttt) REVERT: C 4580 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.5788 (t80) REVERT: C 4730 ASP cc_start: 0.9247 (m-30) cc_final: 0.8976 (p0) REVERT: C 4731 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9218 (mp) REVERT: C 4798 MET cc_start: 0.8963 (mmm) cc_final: 0.8655 (mmt) REVERT: C 4879 MET cc_start: 0.8435 (tpp) cc_final: 0.7867 (tpp) REVERT: C 5013 MET cc_start: 0.9301 (mtp) cc_final: 0.9029 (ttp) REVERT: D 12 GLN cc_start: 0.9111 (mm-40) cc_final: 0.8637 (mp10) REVERT: D 81 MET cc_start: 0.9292 (ttp) cc_final: 0.8872 (ptm) REVERT: D 202 MET cc_start: 0.8696 (tpp) cc_final: 0.8484 (tpp) REVERT: D 1170 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8274 (mmm) REVERT: D 1601 MET cc_start: 0.8736 (mmm) cc_final: 0.8427 (mmt) REVERT: D 2008 MET cc_start: 0.9422 (mtm) cc_final: 0.8744 (tmm) REVERT: D 2546 MET cc_start: 0.6091 (mmm) cc_final: 0.5581 (mpp) REVERT: D 2874 MET cc_start: 0.6494 (mmp) cc_final: 0.5411 (ttp) REVERT: D 3437 MET cc_start: 0.8449 (tpp) cc_final: 0.8215 (tpp) REVERT: D 3442 PHE cc_start: 0.9010 (t80) cc_final: 0.8638 (m-80) REVERT: D 3968 TYR cc_start: 0.8864 (m-10) cc_final: 0.8515 (m-80) REVERT: D 4047 MET cc_start: 0.8881 (tmm) cc_final: 0.8474 (tmm) REVERT: D 4122 MET cc_start: 0.3126 (tpp) cc_final: 0.2877 (tpp) REVERT: D 4207 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8486 (ttt) REVERT: D 4580 TYR cc_start: 0.7461 (OUTLIER) cc_final: 0.5878 (t80) REVERT: D 4730 ASP cc_start: 0.9246 (m-30) cc_final: 0.8975 (p0) REVERT: D 4731 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9218 (mp) REVERT: D 4798 MET cc_start: 0.8959 (mmm) cc_final: 0.8651 (mmt) REVERT: D 4879 MET cc_start: 0.8436 (tpp) cc_final: 0.7869 (tpp) REVERT: D 4942 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7611 (mt-10) REVERT: D 5013 MET cc_start: 0.9302 (mtp) cc_final: 0.9029 (ttp) REVERT: E 66 MET cc_start: 0.7675 (pmm) cc_final: 0.7412 (pmm) REVERT: F 29 MET cc_start: 0.7716 (tpp) cc_final: 0.7401 (tpp) REVERT: F 66 MET cc_start: 0.7681 (pmm) cc_final: 0.7414 (pmm) REVERT: G 66 MET cc_start: 0.7678 (pmm) cc_final: 0.7412 (pmm) REVERT: H 29 MET cc_start: 0.7716 (tpp) cc_final: 0.7400 (tpp) REVERT: H 66 MET cc_start: 0.7678 (pmm) cc_final: 0.7413 (pmm) outliers start: 137 outliers final: 98 residues processed: 824 average time/residue: 1.1736 time to fit residues: 1752.4008 Evaluate side-chains 842 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 729 time to evaluate : 12.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 959 TYR Chi-restraints excluded: chain A residue 1573 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2514 ASN Chi-restraints excluded: chain A residue 2628 PHE Chi-restraints excluded: chain A residue 2761 TYR Chi-restraints excluded: chain A residue 2998 PHE Chi-restraints excluded: chain A residue 3518 LEU Chi-restraints excluded: chain A residue 4156 HIS Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4581 LYS Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4710 SER Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4739 GLU Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4826 ILE Chi-restraints excluded: chain A residue 4876 CYS Chi-restraints excluded: chain A residue 4925 ILE Chi-restraints excluded: chain A residue 4945 ASP Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 1170 MET Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2514 ASN Chi-restraints excluded: chain B residue 2520 HIS Chi-restraints excluded: chain B residue 2628 PHE Chi-restraints excluded: chain B residue 2998 PHE Chi-restraints excluded: chain B residue 3412 LEU Chi-restraints excluded: chain B residue 3518 LEU Chi-restraints excluded: chain B residue 3753 PHE Chi-restraints excluded: chain B residue 4156 HIS Chi-restraints excluded: chain B residue 4207 MET Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4628 VAL Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4710 SER Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4739 GLU Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4826 ILE Chi-restraints excluded: chain B residue 4945 ASP Chi-restraints excluded: chain B residue 5027 CYS Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 1731 LEU Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2514 ASN Chi-restraints excluded: chain C residue 2520 HIS Chi-restraints excluded: chain C residue 2628 PHE Chi-restraints excluded: chain C residue 2998 PHE Chi-restraints excluded: chain C residue 3412 LEU Chi-restraints excluded: chain C residue 3518 LEU Chi-restraints excluded: chain C residue 3753 PHE Chi-restraints excluded: chain C residue 4156 HIS Chi-restraints excluded: chain C residue 4207 MET Chi-restraints excluded: chain C residue 4227 GLU Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4628 VAL Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4710 SER Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4739 GLU Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4826 ILE Chi-restraints excluded: chain C residue 4876 CYS Chi-restraints excluded: chain C residue 4945 ASP Chi-restraints excluded: chain C residue 5027 CYS Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 1170 MET Chi-restraints excluded: chain D residue 1599 MET Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2514 ASN Chi-restraints excluded: chain D residue 2520 HIS Chi-restraints excluded: chain D residue 2628 PHE Chi-restraints excluded: chain D residue 2998 PHE Chi-restraints excluded: chain D residue 3412 LEU Chi-restraints excluded: chain D residue 3518 LEU Chi-restraints excluded: chain D residue 3753 PHE Chi-restraints excluded: chain D residue 4156 HIS Chi-restraints excluded: chain D residue 4207 MET Chi-restraints excluded: chain D residue 4227 GLU Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4628 VAL Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4710 SER Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4739 GLU Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4826 ILE Chi-restraints excluded: chain D residue 4876 CYS Chi-restraints excluded: chain D residue 4945 ASP Chi-restraints excluded: chain D residue 5027 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1066 optimal weight: 6.9990 chunk 688 optimal weight: 50.0000 chunk 1029 optimal weight: 10.0000 chunk 519 optimal weight: 1.9990 chunk 338 optimal weight: 9.9990 chunk 333 optimal weight: 7.9990 chunk 1095 optimal weight: 0.9990 chunk 1174 optimal weight: 20.0000 chunk 852 optimal weight: 0.8980 chunk 160 optimal weight: 5.9990 chunk 1354 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2520 HIS ** A3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2520 HIS ** B3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2520 HIS ** C3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1203 ASN ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2520 HIS ** D3162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 146316 Z= 0.227 Angle : 0.611 13.487 198204 Z= 0.303 Chirality : 0.041 0.281 21788 Planarity : 0.004 0.073 25764 Dihedral : 6.074 144.231 19653 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.94 % Allowed : 11.53 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.11 % Twisted General : 0.01 % 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: 0.51 (0.06), residues: 17840 helix: 1.28 (0.06), residues: 8900 sheet: -0.67 (0.13), residues: 1648 loop : -0.53 (0.07), residues: 7292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A4644 HIS 0.045 0.001 HIS D2520 PHE 0.029 0.001 PHE A2973 TYR 0.024 0.001 TYR D3722 ARG 0.005 0.000 ARG C 869 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 735 time to evaluate : 12.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8634 (mp10) REVERT: A 127 MET cc_start: 0.7897 (mmp) cc_final: 0.7589 (mmp) REVERT: A 483 MET cc_start: 0.8749 (mmm) cc_final: 0.8441 (mmm) REVERT: A 569 ILE cc_start: 0.9590 (tp) cc_final: 0.9328 (pt) REVERT: A 919 ASN cc_start: 0.7818 (t0) cc_final: 0.7403 (m110) REVERT: A 1152 MET cc_start: 0.8854 (mmp) cc_final: 0.8533 (mmp) REVERT: A 1170 MET cc_start: 0.8852 (mmm) cc_final: 0.8600 (mmm) REVERT: A 1851 MET cc_start: 0.8651 (mtp) cc_final: 0.8443 (mmm) REVERT: A 2008 MET cc_start: 0.9422 (mtm) cc_final: 0.8721 (tmm) REVERT: A 2170 MET cc_start: 0.8698 (mmm) cc_final: 0.8398 (tpp) REVERT: A 2254 LEU cc_start: 0.8943 (tp) cc_final: 0.8618 (tp) REVERT: A 2490 MET cc_start: 0.7894 (mmt) cc_final: 0.7159 (mmt) REVERT: A 2761 TYR cc_start: 0.6115 (OUTLIER) cc_final: 0.5884 (m-80) REVERT: A 2874 MET cc_start: 0.6456 (mmp) cc_final: 0.5430 (ttp) REVERT: A 3201 MET cc_start: 0.7880 (tpt) cc_final: 0.7508 (tmm) REVERT: A 3437 MET cc_start: 0.8471 (tpp) cc_final: 0.8220 (tpp) REVERT: A 3442 PHE cc_start: 0.9033 (t80) cc_final: 0.8690 (t80) REVERT: A 3524 MET cc_start: 0.8283 (ppp) cc_final: 0.7633 (ppp) REVERT: A 3968 TYR cc_start: 0.8838 (m-10) cc_final: 0.8507 (m-80) REVERT: A 4047 MET cc_start: 0.8886 (tmm) cc_final: 0.8466 (tmm) REVERT: A 4207 MET cc_start: 0.8737 (ttt) cc_final: 0.8366 (ttt) REVERT: A 4580 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.6206 (t80) REVERT: A 4730 ASP cc_start: 0.9194 (m-30) cc_final: 0.8958 (p0) REVERT: A 4731 ILE cc_start: 0.9492 (OUTLIER) cc_final: 0.9226 (mp) REVERT: A 4879 MET cc_start: 0.8385 (tpp) cc_final: 0.7045 (tpp) REVERT: A 4989 MET cc_start: 0.9206 (tmm) cc_final: 0.8559 (tmm) REVERT: B 12 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8645 (mp10) REVERT: B 81 MET cc_start: 0.9219 (ttp) cc_final: 0.8873 (ptm) REVERT: B 127 MET cc_start: 0.7997 (mmp) cc_final: 0.7667 (mmp) REVERT: B 202 MET cc_start: 0.8687 (tpp) cc_final: 0.8447 (tpp) REVERT: B 1170 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8171 (mmm) REVERT: B 1601 MET cc_start: 0.8745 (mmm) cc_final: 0.8432 (mmt) REVERT: B 2008 MET cc_start: 0.9419 (mtm) cc_final: 0.8736 (tmm) REVERT: B 2211 MET cc_start: 0.9407 (mmm) cc_final: 0.9053 (mmp) REVERT: B 2874 MET cc_start: 0.6474 (mmp) cc_final: 0.5404 (ttp) REVERT: B 3437 MET cc_start: 0.8507 (tpp) cc_final: 0.8266 (tpp) REVERT: B 3442 PHE cc_start: 0.9057 (t80) cc_final: 0.8675 (m-80) REVERT: B 3968 TYR cc_start: 0.8840 (m-10) cc_final: 0.8512 (m-80) REVERT: B 4047 MET cc_start: 0.8888 (tmm) cc_final: 0.8471 (tmm) REVERT: B 4207 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8480 (ttt) REVERT: B 4580 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.5775 (t80) REVERT: B 4730 ASP cc_start: 0.9244 (m-30) cc_final: 0.8976 (p0) REVERT: B 4731 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9109 (mp) REVERT: B 4798 MET cc_start: 0.8947 (mmm) cc_final: 0.8647 (mmt) REVERT: B 4879 MET cc_start: 0.8153 (mmm) cc_final: 0.7618 (tpp) REVERT: C 12 GLN cc_start: 0.9116 (mm-40) cc_final: 0.8644 (mp10) REVERT: C 81 MET cc_start: 0.9220 (ttp) cc_final: 0.8872 (ptm) REVERT: C 202 MET cc_start: 0.8699 (tpp) cc_final: 0.8476 (tpp) REVERT: C 1170 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8426 (mmp) REVERT: C 1601 MET cc_start: 0.8748 (mmm) cc_final: 0.8433 (mmt) REVERT: C 2008 MET cc_start: 0.9418 (mtm) cc_final: 0.8737 (tmm) REVERT: C 2874 MET cc_start: 0.6480 (mmp) cc_final: 0.5407 (ttp) REVERT: C 3437 MET cc_start: 0.8507 (tpp) cc_final: 0.8267 (tpp) REVERT: C 3442 PHE cc_start: 0.9057 (t80) cc_final: 0.8677 (m-80) REVERT: C 3573 MET cc_start: 0.8747 (mmm) cc_final: 0.8391 (mmm) REVERT: C 3968 TYR cc_start: 0.8840 (m-10) cc_final: 0.8512 (m-80) REVERT: C 4047 MET cc_start: 0.8889 (tmm) cc_final: 0.8472 (tmm) REVERT: C 4207 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8481 (ttt) REVERT: C 4580 TYR cc_start: 0.7435 (OUTLIER) cc_final: 0.5778 (t80) REVERT: C 4730 ASP cc_start: 0.9247 (m-30) cc_final: 0.8980 (p0) REVERT: C 4731 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9103 (mp) REVERT: C 4798 MET cc_start: 0.8949 (mmm) cc_final: 0.8648 (mmt) REVERT: C 4879 MET cc_start: 0.8395 (tpp) cc_final: 0.7869 (tpp) REVERT: D 12 GLN cc_start: 0.9116 (mm-40) cc_final: 0.8645 (mp10) REVERT: D 81 MET cc_start: 0.9220 (ttp) cc_final: 0.8873 (ptm) REVERT: D 1170 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8427 (mmp) REVERT: D 1601 MET cc_start: 0.8745 (mmm) cc_final: 0.8434 (mmt) REVERT: D 2008 MET cc_start: 0.9419 (mtm) cc_final: 0.8737 (tmm) REVERT: D 2874 MET cc_start: 0.6478 (mmp) cc_final: 0.5407 (ttp) REVERT: D 3437 MET cc_start: 0.8506 (tpp) cc_final: 0.8267 (tpp) REVERT: D 3442 PHE cc_start: 0.9058 (t80) cc_final: 0.8677 (m-80) REVERT: D 3968 TYR cc_start: 0.8841 (m-10) cc_final: 0.8513 (m-80) REVERT: D 4047 MET cc_start: 0.8888 (tmm) cc_final: 0.8470 (tmm) REVERT: D 4207 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8481 (ttt) REVERT: D 4580 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.5794 (t80) REVERT: D 4730 ASP cc_start: 0.9246 (m-30) cc_final: 0.8979 (p0) REVERT: D 4731 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9102 (mp) REVERT: D 4798 MET cc_start: 0.8945 (mmm) cc_final: 0.8645 (mmt) REVERT: D 4879 MET cc_start: 0.8394 (tpp) cc_final: 0.7870 (tpp) REVERT: D 4942 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7597 (mt-10) REVERT: E 29 MET cc_start: 0.7679 (tpp) cc_final: 0.7381 (tpp) REVERT: E 66 MET cc_start: 0.7668 (pmm) cc_final: 0.7402 (pmm) REVERT: F 66 MET cc_start: 0.7674 (pmm) cc_final: 0.7405 (pmm) REVERT: G 29 MET cc_start: 0.7680 (tpp) cc_final: 0.7362 (tpp) REVERT: G 66 MET cc_start: 0.7673 (pmm) cc_final: 0.7406 (pmm) REVERT: H 66 MET cc_start: 0.7673 (pmm) cc_final: 0.7407 (pmm) outliers start: 119 outliers final: 89 residues processed: 815 average time/residue: 1.1714 time to fit residues: 1734.8353 Evaluate side-chains 837 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 733 time to evaluate : 12.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 1573 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2514 ASN Chi-restraints excluded: chain A residue 2761 TYR Chi-restraints excluded: chain A residue 2998 PHE Chi-restraints excluded: chain A residue 3518 LEU Chi-restraints excluded: chain A residue 4156 HIS Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4581 LYS Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4710 SER Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4739 GLU Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4826 ILE Chi-restraints excluded: chain A residue 4876 CYS Chi-restraints excluded: chain A residue 4945 ASP Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 1170 MET Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2514 ASN Chi-restraints excluded: chain B residue 2520 HIS Chi-restraints excluded: chain B residue 2628 PHE Chi-restraints excluded: chain B residue 2998 PHE Chi-restraints excluded: chain B residue 3518 LEU Chi-restraints excluded: chain B residue 3753 PHE Chi-restraints excluded: chain B residue 4156 HIS Chi-restraints excluded: chain B residue 4207 MET Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4628 VAL Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4710 SER Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4739 GLU Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4826 ILE Chi-restraints excluded: chain B residue 4945 ASP Chi-restraints excluded: chain B residue 5027 CYS Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 1731 LEU Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2514 ASN Chi-restraints excluded: chain C residue 2520 HIS Chi-restraints excluded: chain C residue 2628 PHE Chi-restraints excluded: chain C residue 2998 PHE Chi-restraints excluded: chain C residue 3518 LEU Chi-restraints excluded: chain C residue 3753 PHE Chi-restraints excluded: chain C residue 4156 HIS Chi-restraints excluded: chain C residue 4207 MET Chi-restraints excluded: chain C residue 4227 GLU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4628 VAL Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4710 SER Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4739 GLU Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4826 ILE Chi-restraints excluded: chain C residue 4945 ASP Chi-restraints excluded: chain C residue 5027 CYS Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 1170 MET Chi-restraints excluded: chain D residue 1599 MET Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2514 ASN Chi-restraints excluded: chain D residue 2520 HIS Chi-restraints excluded: chain D residue 2628 PHE Chi-restraints excluded: chain D residue 2998 PHE Chi-restraints excluded: chain D residue 3518 LEU Chi-restraints excluded: chain D residue 3753 PHE Chi-restraints excluded: chain D residue 4156 HIS Chi-restraints excluded: chain D residue 4207 MET Chi-restraints excluded: chain D residue 4227 GLU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4628 VAL Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4710 SER Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4739 GLU Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4826 ILE Chi-restraints excluded: chain D residue 4945 ASP Chi-restraints excluded: chain D residue 5027 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1567 optimal weight: 20.0000 chunk 1651 optimal weight: 5.9990 chunk 1506 optimal weight: 0.7980 chunk 1605 optimal weight: 20.0000 chunk 1650 optimal weight: 1.9990 chunk 966 optimal weight: 50.0000 chunk 699 optimal weight: 0.8980 chunk 1261 optimal weight: 5.9990 chunk 492 optimal weight: 10.0000 chunk 1451 optimal weight: 0.8980 chunk 1518 optimal weight: 6.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1631 GLN ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2520 HIS A3162 GLN ** A3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2247 GLN B2520 HIS B3162 GLN ** B3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3851 ASN ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2247 GLN C2520 HIS C3162 GLN ** C3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3851 ASN ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1203 ASN ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2520 HIS D3162 GLN ** D3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3851 ASN ** D4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 146316 Z= 0.183 Angle : 0.597 14.175 198204 Z= 0.294 Chirality : 0.040 0.276 21788 Planarity : 0.004 0.069 25764 Dihedral : 6.021 144.471 19653 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.90 % Allowed : 11.74 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.11 % Twisted General : 0.01 % 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: 0.58 (0.06), residues: 17840 helix: 1.37 (0.06), residues: 8904 sheet: -0.66 (0.13), residues: 1616 loop : -0.52 (0.07), residues: 7320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A4644 HIS 0.035 0.001 HIS D2520 PHE 0.028 0.001 PHE A2973 TYR 0.024 0.001 TYR B3722 ARG 0.005 0.000 ARG C 869 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 743 time to evaluate : 12.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8637 (mp10) REVERT: A 127 MET cc_start: 0.7930 (mmp) cc_final: 0.7677 (mmp) REVERT: A 202 MET cc_start: 0.8305 (tpp) cc_final: 0.7549 (tpp) REVERT: A 483 MET cc_start: 0.8742 (mmm) cc_final: 0.8434 (mmm) REVERT: A 569 ILE cc_start: 0.9592 (tp) cc_final: 0.9334 (pt) REVERT: A 919 ASN cc_start: 0.7844 (t0) cc_final: 0.7444 (m110) REVERT: A 1152 MET cc_start: 0.8830 (mmp) cc_final: 0.8545 (mmp) REVERT: A 1170 MET cc_start: 0.8849 (mmm) cc_final: 0.8589 (mmm) REVERT: A 2008 MET cc_start: 0.9414 (mtm) cc_final: 0.8709 (tmm) REVERT: A 2170 MET cc_start: 0.8670 (mmm) cc_final: 0.8388 (tpp) REVERT: A 2254 LEU cc_start: 0.8919 (tp) cc_final: 0.8580 (tp) REVERT: A 2490 MET cc_start: 0.8051 (mmt) cc_final: 0.7361 (mmt) REVERT: A 2761 TYR cc_start: 0.6113 (OUTLIER) cc_final: 0.5889 (m-80) REVERT: A 2874 MET cc_start: 0.6433 (mmp) cc_final: 0.5427 (ttp) REVERT: A 3201 MET cc_start: 0.7890 (tpt) cc_final: 0.7570 (tmm) REVERT: A 3437 MET cc_start: 0.8471 (tpp) cc_final: 0.8212 (tpp) REVERT: A 3442 PHE cc_start: 0.9005 (t80) cc_final: 0.8655 (t80) REVERT: A 3524 MET cc_start: 0.8316 (ppp) cc_final: 0.7631 (ppp) REVERT: A 4047 MET cc_start: 0.8906 (tmm) cc_final: 0.8476 (tmm) REVERT: A 4207 MET cc_start: 0.8718 (ttt) cc_final: 0.8343 (ttt) REVERT: A 4580 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.6163 (t80) REVERT: A 4730 ASP cc_start: 0.9190 (m-30) cc_final: 0.8960 (p0) REVERT: A 4731 ILE cc_start: 0.9489 (OUTLIER) cc_final: 0.9257 (mp) REVERT: A 4879 MET cc_start: 0.8328 (tpp) cc_final: 0.6891 (tpp) REVERT: A 4989 MET cc_start: 0.9225 (tmm) cc_final: 0.8550 (tmm) REVERT: B 12 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8647 (mp10) REVERT: B 81 MET cc_start: 0.9210 (ttp) cc_final: 0.8869 (ptm) REVERT: B 127 MET cc_start: 0.7914 (mmp) cc_final: 0.7602 (mmp) REVERT: B 202 MET cc_start: 0.8659 (tpp) cc_final: 0.7847 (tpp) REVERT: B 1601 MET cc_start: 0.8727 (mmm) cc_final: 0.8416 (mmt) REVERT: B 2008 MET cc_start: 0.9411 (mtm) cc_final: 0.8722 (tmm) REVERT: B 2211 MET cc_start: 0.9422 (mmm) cc_final: 0.9063 (mmp) REVERT: B 2874 MET cc_start: 0.6492 (mmp) cc_final: 0.5461 (ttp) REVERT: B 3437 MET cc_start: 0.8508 (tpp) cc_final: 0.8259 (tpp) REVERT: B 3442 PHE cc_start: 0.9027 (t80) cc_final: 0.8691 (m-80) REVERT: B 4047 MET cc_start: 0.8888 (tmm) cc_final: 0.8469 (tmm) REVERT: B 4207 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8472 (ttt) REVERT: B 4580 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.5747 (t80) REVERT: B 4730 ASP cc_start: 0.9222 (m-30) cc_final: 0.8976 (p0) REVERT: B 4731 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9093 (mp) REVERT: B 4798 MET cc_start: 0.8918 (mmm) cc_final: 0.8632 (mmt) REVERT: B 4879 MET cc_start: 0.8150 (mmm) cc_final: 0.7736 (tpp) REVERT: C 12 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8645 (mp10) REVERT: C 81 MET cc_start: 0.9211 (ttp) cc_final: 0.8869 (ptm) REVERT: C 202 MET cc_start: 0.8723 (tpp) cc_final: 0.7928 (tpp) REVERT: C 1601 MET cc_start: 0.8725 (mmm) cc_final: 0.8415 (mmt) REVERT: C 2008 MET cc_start: 0.9411 (mtm) cc_final: 0.8722 (tmm) REVERT: C 2874 MET cc_start: 0.6496 (mmp) cc_final: 0.5463 (ttp) REVERT: C 3437 MET cc_start: 0.8509 (tpp) cc_final: 0.8260 (tpp) REVERT: C 3442 PHE cc_start: 0.9027 (t80) cc_final: 0.8693 (m-80) REVERT: C 3573 MET cc_start: 0.8753 (mmm) cc_final: 0.8395 (mmm) REVERT: C 4047 MET cc_start: 0.8890 (tmm) cc_final: 0.8471 (tmm) REVERT: C 4207 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8472 (ttt) REVERT: C 4580 TYR cc_start: 0.7382 (OUTLIER) cc_final: 0.5748 (t80) REVERT: C 4730 ASP cc_start: 0.9222 (m-30) cc_final: 0.8981 (p0) REVERT: C 4731 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9086 (mp) REVERT: C 4798 MET cc_start: 0.8918 (mmm) cc_final: 0.8630 (mmt) REVERT: C 4879 MET cc_start: 0.8380 (tpp) cc_final: 0.7854 (tpp) REVERT: C 4942 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7471 (mt-10) REVERT: D 12 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8646 (mp10) REVERT: D 81 MET cc_start: 0.9211 (ttp) cc_final: 0.8870 (ptm) REVERT: D 202 MET cc_start: 0.8310 (tpp) cc_final: 0.7570 (tpp) REVERT: D 1601 MET cc_start: 0.8725 (mmm) cc_final: 0.8414 (mmt) REVERT: D 2008 MET cc_start: 0.9411 (mtm) cc_final: 0.8723 (tmm) REVERT: D 2874 MET cc_start: 0.6495 (mmp) cc_final: 0.5464 (ttp) REVERT: D 3437 MET cc_start: 0.8507 (tpp) cc_final: 0.8260 (tpp) REVERT: D 3442 PHE cc_start: 0.9028 (t80) cc_final: 0.8694 (m-80) REVERT: D 4047 MET cc_start: 0.8889 (tmm) cc_final: 0.8471 (tmm) REVERT: D 4207 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8471 (ttt) REVERT: D 4580 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.5723 (t80) REVERT: D 4730 ASP cc_start: 0.9221 (m-30) cc_final: 0.8980 (p0) REVERT: D 4731 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9087 (mp) REVERT: D 4798 MET cc_start: 0.8914 (mmm) cc_final: 0.8629 (mmt) REVERT: D 4879 MET cc_start: 0.8379 (tpp) cc_final: 0.7851 (tpp) REVERT: D 4942 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7602 (mt-10) REVERT: E 29 MET cc_start: 0.7992 (tpp) cc_final: 0.7742 (tpp) REVERT: E 66 MET cc_start: 0.7664 (pmm) cc_final: 0.7398 (pmm) REVERT: F 66 MET cc_start: 0.7667 (pmm) cc_final: 0.7399 (pmm) REVERT: G 29 MET cc_start: 0.7788 (tpp) cc_final: 0.7471 (tpp) REVERT: G 66 MET cc_start: 0.7667 (pmm) cc_final: 0.7400 (pmm) REVERT: H 66 MET cc_start: 0.7667 (pmm) cc_final: 0.7400 (pmm) outliers start: 112 outliers final: 93 residues processed: 819 average time/residue: 1.1642 time to fit residues: 1737.5783 Evaluate side-chains 840 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 735 time to evaluate : 12.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 1573 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2514 ASN Chi-restraints excluded: chain A residue 2520 HIS Chi-restraints excluded: chain A residue 2761 TYR Chi-restraints excluded: chain A residue 2998 PHE Chi-restraints excluded: chain A residue 3518 LEU Chi-restraints excluded: chain A residue 4156 HIS Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4581 LYS Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4710 SER Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4739 GLU Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4826 ILE Chi-restraints excluded: chain A residue 4876 CYS Chi-restraints excluded: chain A residue 4945 ASP Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 1170 MET Chi-restraints excluded: chain B residue 1512 THR Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2514 ASN Chi-restraints excluded: chain B residue 2520 HIS Chi-restraints excluded: chain B residue 2998 PHE Chi-restraints excluded: chain B residue 3412 LEU Chi-restraints excluded: chain B residue 3518 LEU Chi-restraints excluded: chain B residue 3753 PHE Chi-restraints excluded: chain B residue 4156 HIS Chi-restraints excluded: chain B residue 4207 MET Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4710 SER Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4739 GLU Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4826 ILE Chi-restraints excluded: chain B residue 4945 ASP Chi-restraints excluded: chain B residue 5027 CYS Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1512 THR Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 1731 LEU Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2514 ASN Chi-restraints excluded: chain C residue 2520 HIS Chi-restraints excluded: chain C residue 2998 PHE Chi-restraints excluded: chain C residue 3412 LEU Chi-restraints excluded: chain C residue 3518 LEU Chi-restraints excluded: chain C residue 3753 PHE Chi-restraints excluded: chain C residue 4156 HIS Chi-restraints excluded: chain C residue 4207 MET Chi-restraints excluded: chain C residue 4227 GLU Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4710 SER Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4739 GLU Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4826 ILE Chi-restraints excluded: chain C residue 4945 ASP Chi-restraints excluded: chain C residue 5027 CYS Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 1170 MET Chi-restraints excluded: chain D residue 1512 THR Chi-restraints excluded: chain D residue 1599 MET Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2514 ASN Chi-restraints excluded: chain D residue 2520 HIS Chi-restraints excluded: chain D residue 2998 PHE Chi-restraints excluded: chain D residue 3412 LEU Chi-restraints excluded: chain D residue 3518 LEU Chi-restraints excluded: chain D residue 3753 PHE Chi-restraints excluded: chain D residue 4156 HIS Chi-restraints excluded: chain D residue 4207 MET Chi-restraints excluded: chain D residue 4227 GLU Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4710 SER Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4739 GLU Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4826 ILE Chi-restraints excluded: chain D residue 4945 ASP Chi-restraints excluded: chain D residue 5027 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1600 optimal weight: 5.9990 chunk 1054 optimal weight: 9.9990 chunk 1698 optimal weight: 0.3980 chunk 1036 optimal weight: 0.9990 chunk 805 optimal weight: 7.9990 chunk 1180 optimal weight: 6.9990 chunk 1781 optimal weight: 9.9990 chunk 1639 optimal weight: 30.0000 chunk 1418 optimal weight: 20.0000 chunk 147 optimal weight: 4.9990 chunk 1095 optimal weight: 1.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2520 HIS A2924 GLN ** A3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1062 GLN ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2247 GLN B2520 HIS ** B3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 GLN ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2247 GLN C2520 HIS ** C3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 GLN ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2520 HIS ** D3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 146316 Z= 0.208 Angle : 0.608 15.282 198204 Z= 0.299 Chirality : 0.040 0.278 21788 Planarity : 0.004 0.067 25764 Dihedral : 5.998 144.473 19647 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.89 % Allowed : 11.95 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.11 % Twisted General : 0.01 % 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: 0.60 (0.06), residues: 17840 helix: 1.37 (0.06), residues: 8928 sheet: -0.64 (0.13), residues: 1612 loop : -0.49 (0.07), residues: 7300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A4644 HIS 0.026 0.001 HIS C2520 PHE 0.029 0.001 PHE A2973 TYR 0.024 0.001 TYR B3722 ARG 0.005 0.000 ARG C 869 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 741 time to evaluate : 12.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8626 (mp10) REVERT: A 202 MET cc_start: 0.8309 (tpp) cc_final: 0.7508 (tpp) REVERT: A 483 MET cc_start: 0.8809 (mmm) cc_final: 0.8524 (mmm) REVERT: A 919 ASN cc_start: 0.7869 (t0) cc_final: 0.7474 (m110) REVERT: A 1152 MET cc_start: 0.8832 (mmp) cc_final: 0.8506 (mmp) REVERT: A 1170 MET cc_start: 0.8861 (mmm) cc_final: 0.8600 (mmm) REVERT: A 1851 MET cc_start: 0.8763 (mmm) cc_final: 0.8558 (mmm) REVERT: A 2008 MET cc_start: 0.9414 (mtm) cc_final: 0.8714 (tmm) REVERT: A 2170 MET cc_start: 0.8685 (mmm) cc_final: 0.8364 (tpp) REVERT: A 2254 LEU cc_start: 0.8939 (tp) cc_final: 0.8603 (tp) REVERT: A 2490 MET cc_start: 0.7892 (mmt) cc_final: 0.7160 (mmt) REVERT: A 2761 TYR cc_start: 0.6115 (OUTLIER) cc_final: 0.5894 (m-80) REVERT: A 2874 MET cc_start: 0.6422 (mmp) cc_final: 0.5425 (ttp) REVERT: A 3201 MET cc_start: 0.7866 (tpt) cc_final: 0.7543 (tmm) REVERT: A 3437 MET cc_start: 0.8467 (tpp) cc_final: 0.8205 (tpp) REVERT: A 3442 PHE cc_start: 0.9003 (t80) cc_final: 0.8649 (t80) REVERT: A 3524 MET cc_start: 0.8316 (ppp) cc_final: 0.7628 (ppp) REVERT: A 4047 MET cc_start: 0.8882 (tmm) cc_final: 0.8438 (tmm) REVERT: A 4207 MET cc_start: 0.8724 (ttt) cc_final: 0.8346 (ttt) REVERT: A 4580 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.6207 (t80) REVERT: A 4730 ASP cc_start: 0.9212 (m-30) cc_final: 0.8981 (p0) REVERT: A 4731 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9100 (mp) REVERT: A 4879 MET cc_start: 0.8381 (tpp) cc_final: 0.6978 (tpp) REVERT: A 4989 MET cc_start: 0.9225 (tmm) cc_final: 0.8549 (tmm) REVERT: B 12 GLN cc_start: 0.9115 (mm-40) cc_final: 0.8638 (mp10) REVERT: B 81 MET cc_start: 0.9129 (ttp) cc_final: 0.8878 (ptm) REVERT: B 202 MET cc_start: 0.8662 (tpp) cc_final: 0.7854 (tpp) REVERT: B 1170 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8165 (mmm) REVERT: B 1601 MET cc_start: 0.8727 (mmm) cc_final: 0.8418 (mmt) REVERT: B 2008 MET cc_start: 0.9413 (mtm) cc_final: 0.8727 (tmm) REVERT: B 2211 MET cc_start: 0.9421 (mmm) cc_final: 0.9063 (mmp) REVERT: B 2254 LEU cc_start: 0.8849 (tp) cc_final: 0.8525 (tp) REVERT: B 2490 MET cc_start: 0.7896 (mmm) cc_final: 0.7588 (mmp) REVERT: B 2874 MET cc_start: 0.6483 (mmp) cc_final: 0.5461 (ttp) REVERT: B 3213 TYR cc_start: 0.8587 (m-80) cc_final: 0.8224 (m-80) REVERT: B 3437 MET cc_start: 0.8505 (tpp) cc_final: 0.8253 (tpp) REVERT: B 3442 PHE cc_start: 0.9026 (t80) cc_final: 0.8713 (m-80) REVERT: B 4047 MET cc_start: 0.8888 (tmm) cc_final: 0.8468 (tmm) REVERT: B 4207 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8474 (ttt) REVERT: B 4580 TYR cc_start: 0.7393 (OUTLIER) cc_final: 0.5754 (t80) REVERT: B 4688 ILE cc_start: 0.9289 (mp) cc_final: 0.9077 (mt) REVERT: B 4730 ASP cc_start: 0.9222 (m-30) cc_final: 0.8964 (p0) REVERT: B 4731 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9087 (mp) REVERT: B 4879 MET cc_start: 0.8155 (mmm) cc_final: 0.7679 (tpp) REVERT: C 12 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8636 (mp10) REVERT: C 81 MET cc_start: 0.9130 (ttp) cc_final: 0.8878 (ptm) REVERT: C 127 MET cc_start: 0.7564 (mmm) cc_final: 0.7047 (ptt) REVERT: C 202 MET cc_start: 0.8672 (tpp) cc_final: 0.7853 (tpp) REVERT: C 1170 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8166 (mmm) REVERT: C 1601 MET cc_start: 0.8728 (mmm) cc_final: 0.8418 (mmt) REVERT: C 2008 MET cc_start: 0.9413 (mtm) cc_final: 0.8728 (tmm) REVERT: C 2490 MET cc_start: 0.7897 (mmm) cc_final: 0.7587 (mmp) REVERT: C 2874 MET cc_start: 0.6486 (mmp) cc_final: 0.5461 (ttp) REVERT: C 3213 TYR cc_start: 0.8587 (m-80) cc_final: 0.8224 (m-80) REVERT: C 3437 MET cc_start: 0.8504 (tpp) cc_final: 0.8253 (tpp) REVERT: C 3442 PHE cc_start: 0.9026 (t80) cc_final: 0.8715 (m-80) REVERT: C 3573 MET cc_start: 0.8751 (mmm) cc_final: 0.8383 (mmm) REVERT: C 4047 MET cc_start: 0.8888 (tmm) cc_final: 0.8470 (tmm) REVERT: C 4207 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8476 (ttt) REVERT: C 4580 TYR cc_start: 0.7393 (OUTLIER) cc_final: 0.5756 (t80) REVERT: C 4688 ILE cc_start: 0.9290 (mp) cc_final: 0.9078 (mt) REVERT: C 4730 ASP cc_start: 0.9223 (m-30) cc_final: 0.8970 (p0) REVERT: C 4731 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9082 (mp) REVERT: C 4798 MET cc_start: 0.8917 (mmm) cc_final: 0.8628 (mmt) REVERT: C 4879 MET cc_start: 0.8409 (tpp) cc_final: 0.7900 (tpp) REVERT: C 4942 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7500 (mt-10) REVERT: D 12 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8637 (mp10) REVERT: D 81 MET cc_start: 0.9131 (ttp) cc_final: 0.8880 (ptm) REVERT: D 127 MET cc_start: 0.7565 (mmm) cc_final: 0.7048 (ptt) REVERT: D 202 MET cc_start: 0.8396 (tpp) cc_final: 0.7641 (tpp) REVERT: D 1170 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8169 (mmm) REVERT: D 1601 MET cc_start: 0.8728 (mmm) cc_final: 0.8419 (mmt) REVERT: D 2008 MET cc_start: 0.9414 (mtm) cc_final: 0.8729 (tmm) REVERT: D 2490 MET cc_start: 0.7899 (mmm) cc_final: 0.7588 (mmp) REVERT: D 2874 MET cc_start: 0.6484 (mmp) cc_final: 0.5464 (ttp) REVERT: D 3437 MET cc_start: 0.8504 (tpp) cc_final: 0.8252 (tpp) REVERT: D 3442 PHE cc_start: 0.9027 (t80) cc_final: 0.8714 (m-80) REVERT: D 4047 MET cc_start: 0.8888 (tmm) cc_final: 0.8470 (tmm) REVERT: D 4207 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8475 (ttt) REVERT: D 4580 TYR cc_start: 0.7386 (OUTLIER) cc_final: 0.5723 (t80) REVERT: D 4688 ILE cc_start: 0.9290 (mp) cc_final: 0.9078 (mt) REVERT: D 4730 ASP cc_start: 0.9223 (m-30) cc_final: 0.8969 (p0) REVERT: D 4731 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9082 (mp) REVERT: D 4798 MET cc_start: 0.8917 (mmm) cc_final: 0.8630 (mmt) REVERT: D 4879 MET cc_start: 0.8410 (tpp) cc_final: 0.7901 (tpp) REVERT: D 4942 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7612 (mt-10) REVERT: E 29 MET cc_start: 0.8000 (tpp) cc_final: 0.7740 (tpp) REVERT: E 66 MET cc_start: 0.7670 (pmm) cc_final: 0.7403 (pmm) REVERT: F 66 MET cc_start: 0.7670 (pmm) cc_final: 0.7404 (pmm) REVERT: G 29 MET cc_start: 0.8002 (tpp) cc_final: 0.7744 (tpp) REVERT: G 66 MET cc_start: 0.7672 (pmm) cc_final: 0.7405 (pmm) REVERT: H 66 MET cc_start: 0.7671 (pmm) cc_final: 0.7404 (pmm) outliers start: 110 outliers final: 91 residues processed: 814 average time/residue: 1.1555 time to fit residues: 1719.7430 Evaluate side-chains 844 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 738 time to evaluate : 12.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 1573 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2514 ASN Chi-restraints excluded: chain A residue 2520 HIS Chi-restraints excluded: chain A residue 2761 TYR Chi-restraints excluded: chain A residue 2998 PHE Chi-restraints excluded: chain A residue 3518 LEU Chi-restraints excluded: chain A residue 3758 MET Chi-restraints excluded: chain A residue 4156 HIS Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4581 LYS Chi-restraints excluded: chain A residue 4710 SER Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4739 GLU Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4826 ILE Chi-restraints excluded: chain A residue 4876 CYS Chi-restraints excluded: chain A residue 4925 ILE Chi-restraints excluded: chain A residue 4945 ASP Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 1170 MET Chi-restraints excluded: chain B residue 1512 THR Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2514 ASN Chi-restraints excluded: chain B residue 2520 HIS Chi-restraints excluded: chain B residue 2998 PHE Chi-restraints excluded: chain B residue 3412 LEU Chi-restraints excluded: chain B residue 3518 LEU Chi-restraints excluded: chain B residue 3753 PHE Chi-restraints excluded: chain B residue 4156 HIS Chi-restraints excluded: chain B residue 4207 MET Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4710 SER Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4739 GLU Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4826 ILE Chi-restraints excluded: chain B residue 4945 ASP Chi-restraints excluded: chain B residue 5027 CYS Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1512 THR Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 1731 LEU Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2514 ASN Chi-restraints excluded: chain C residue 2520 HIS Chi-restraints excluded: chain C residue 2998 PHE Chi-restraints excluded: chain C residue 3412 LEU Chi-restraints excluded: chain C residue 3518 LEU Chi-restraints excluded: chain C residue 3753 PHE Chi-restraints excluded: chain C residue 4156 HIS Chi-restraints excluded: chain C residue 4207 MET Chi-restraints excluded: chain C residue 4227 GLU Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4710 SER Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4739 GLU Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4826 ILE Chi-restraints excluded: chain C residue 4945 ASP Chi-restraints excluded: chain C residue 5027 CYS Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 1170 MET Chi-restraints excluded: chain D residue 1512 THR Chi-restraints excluded: chain D residue 1599 MET Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2514 ASN Chi-restraints excluded: chain D residue 2520 HIS Chi-restraints excluded: chain D residue 2998 PHE Chi-restraints excluded: chain D residue 3412 LEU Chi-restraints excluded: chain D residue 3518 LEU Chi-restraints excluded: chain D residue 3753 PHE Chi-restraints excluded: chain D residue 4156 HIS Chi-restraints excluded: chain D residue 4207 MET Chi-restraints excluded: chain D residue 4227 GLU Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4710 SER Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4739 GLU Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4826 ILE Chi-restraints excluded: chain D residue 4945 ASP Chi-restraints excluded: chain D residue 5027 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 869 optimal weight: 7.9990 chunk 1126 optimal weight: 50.0000 chunk 1510 optimal weight: 7.9990 chunk 434 optimal weight: 2.9990 chunk 1307 optimal weight: 0.4980 chunk 209 optimal weight: 9.9990 chunk 394 optimal weight: 4.9990 chunk 1420 optimal weight: 10.0000 chunk 594 optimal weight: 6.9990 chunk 1458 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2520 HIS ** A3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3998 HIS ** A4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2520 HIS B2924 GLN B3211 ASN ** B3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2520 HIS C2924 GLN C3211 ASN ** C3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2520 HIS D3211 ASN ** D3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.073588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.054511 restraints weight = 2285764.692| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 10.32 r_work: 0.3164 rms_B_bonded: 8.45 restraints_weight: 2.0000 r_work: 0.3265 rms_B_bonded: 5.59 restraints_weight: 4.0000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 146316 Z= 0.266 Angle : 0.633 15.487 198204 Z= 0.313 Chirality : 0.041 0.284 21788 Planarity : 0.004 0.066 25764 Dihedral : 6.027 144.304 19646 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.89 % Allowed : 12.01 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.11 % Twisted General : 0.01 % 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: 0.54 (0.06), residues: 17840 helix: 1.32 (0.06), residues: 8944 sheet: -0.70 (0.13), residues: 1612 loop : -0.52 (0.08), residues: 7284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A4644 HIS 0.039 0.001 HIS C2520 PHE 0.029 0.002 PHE A2973 TYR 0.023 0.001 TYR B3722 ARG 0.005 0.000 ARG C 869 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 41929.61 seconds wall clock time: 730 minutes 29.96 seconds (43829.96 seconds total)