Starting phenix.real_space_refine on Wed Mar 20 21:50:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seq_40425/03_2024/8seq_40425_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seq_40425/03_2024/8seq_40425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seq_40425/03_2024/8seq_40425.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seq_40425/03_2024/8seq_40425.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seq_40425/03_2024/8seq_40425_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seq_40425/03_2024/8seq_40425_updated.pdb" } resolution = 3.4 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= 0.027 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 90892 2.51 5 N 24684 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 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.44s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 142952 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 34896 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4376, 34833 Classifications: {'peptide': 4376} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4159} 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: 4376, 34833 Classifications: {'peptide': 4376} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4159} 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: 35542 Chain: "B" Number of atoms: 34896 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4376, 34833 Classifications: {'peptide': 4376} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4159} 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: 4376, 34833 Classifications: {'peptide': 4376} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4159} 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: 35542 Chain: "C" Number of atoms: 34896 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4376, 34833 Classifications: {'peptide': 4376} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4159} 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: 4376, 34833 Classifications: {'peptide': 4376} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4159} 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: 35542 Chain: "D" Number of atoms: 34896 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4376, 34833 Classifications: {'peptide': 4376} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4159} 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: 4376, 34833 Classifications: {'peptide': 4376} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4159} 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: 35542 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 34222 SG CYS A4958 176.002 202.029 85.714 1.00123.83 S ATOM 34247 SG CYS A4961 178.102 202.058 88.744 1.00123.35 S ATOM 69118 SG CYS B4958 179.124 176.023 85.710 1.00123.83 S ATOM 69143 SG CYS B4961 179.101 178.123 88.741 1.00123.35 S ATOM A033I SG CYS C4958 205.225 179.125 85.710 1.00123.83 S ATOM A0347 SG CYS C4961 203.125 179.101 88.741 1.00123.35 S ATOM A0U0U SG CYS D4958 202.123 205.225 85.710 1.00123.83 S ATOM A0U1J SG CYS D4961 202.147 203.126 88.741 1.00123.35 S Time building chain proxies: 100.04, per 1000 atoms: 0.70 Number of scatterers: 142952 At special positions: 0 Unit cell: (382.536, 382.536, 209.944, 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 24684 7.00 C 90892 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: 39.94 Conformation dependent library (CDL) restraints added in 37.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5102 " pdb="ZN ZN A5102 " - pdb=" ND1 HIS A4983 " pdb="ZN ZN A5102 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4958 " pdb=" ZN B5102 " pdb="ZN ZN B5102 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5102 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4958 " pdb=" ZN C5102 " pdb="ZN ZN C5102 " - pdb=" ND1 HIS C4983 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4958 " pdb=" ZN D5102 " pdb="ZN ZN D5102 " - pdb=" ND1 HIS D4983 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4958 " Number of angles added : 8 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 33672 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: 692 helices and 76 sheets defined 58.1% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 45.15 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.754A pdb=" N CYS A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.701A pdb=" N ALA A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N HIS A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 308' Processing helix chain 'A' and resid 364 through 370 Processing helix chain 'A' and resid 394 through 423 removed outlier: 4.510A pdb=" N ARG A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N MET A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLY A 423 " --> pdb=" O ASP A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 453 removed outlier: 3.513A pdb=" N GLY A 450 " --> pdb=" O GLN A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 482 removed outlier: 3.652A pdb=" N GLN A 465 " --> pdb=" O HIS A 461 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SER A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 497 removed outlier: 3.706A pdb=" N VAL A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR A 497 " --> pdb=" O ARG A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.683A pdb=" N TYR A 506 " --> pdb=" O HIS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 531 removed outlier: 3.719A pdb=" N GLU A 513 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 541 removed outlier: 4.021A pdb=" N LEU A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N PHE A 540 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER A 541 " --> pdb=" O CYS A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.547A pdb=" N VAL A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 550 " --> pdb=" O TRP A 546 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU A 551 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASP A 552 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 removed outlier: 3.933A pdb=" N ILE A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 570 " --> pdb=" O CYS A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 578 removed outlier: 3.956A pdb=" N ASN A 576 " --> pdb=" O PRO A 572 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 577 " --> pdb=" O GLU A 573 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 572 through 578' Processing helix chain 'A' and resid 579 through 593 removed outlier: 3.800A pdb=" N LEU A 590 " --> pdb=" O ILE A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 609 removed outlier: 3.936A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N CYS A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 629 removed outlier: 3.634A 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: 4.623A pdb=" N ALA A 814 " --> pdb=" O PRO A 810 " (cutoff:3.500A) removed outlier: 4.563A 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: 3.832A pdb=" N PHE A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) removed outlier: 3.737A 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: 3.560A pdb=" N ILE A 870 " --> pdb=" O HIS A 866 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS A 873 " --> pdb=" O ARG A 869 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 874 " --> pdb=" O ILE A 870 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA A 875 " --> pdb=" O ARG A 871 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE A 878 " --> pdb=" O LEU A 874 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU A 881 " --> pdb=" O ASN A 877 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N TRP A 882 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA A 883 " --> pdb=" O HIS A 879 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.788A 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: 3.928A pdb=" N ASN A 949 " --> pdb=" O LYS A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1004 removed outlier: 3.508A pdb=" N VAL A 995 " --> pdb=" O ASN A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1048 removed outlier: 4.096A pdb=" N SER A1038 " --> pdb=" O SER A1034 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A1039 " --> pdb=" O ASN A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1073 removed outlier: 3.985A pdb=" N ARG A1071 " --> pdb=" O SER A1067 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL A1072 " --> pdb=" O ARG A1068 " (cutoff:3.500A) removed outlier: 4.937A 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: 6.592A pdb=" N GLU A1221 " --> pdb=" O CYS A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1430 removed outlier: 3.532A pdb=" N LEU A1428 " --> pdb=" O PRO A1424 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASN A1429 " --> pdb=" O GLU A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1444 through 1449 removed outlier: 4.046A pdb=" N VAL A1448 " --> pdb=" O GLU A1444 " (cutoff:3.500A) removed outlier: 5.495A 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: 4.739A pdb=" N PHE A1500 " --> pdb=" O TRP A1496 " (cutoff:3.500A) removed outlier: 4.448A 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: 3.844A pdb=" N ALA A1578 " --> pdb=" O PRO A1574 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE A1580 " --> pdb=" O SER A1576 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1657 removed outlier: 4.454A pdb=" N LEU A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER A1654 " --> pdb=" O ILE A1650 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLU A1655 " --> pdb=" O LEU A1651 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU A1657 " --> pdb=" O LEU A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1675 removed outlier: 3.927A pdb=" N PHE A1662 " --> pdb=" O ASP A1658 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1689 removed outlier: 3.920A pdb=" N ALA A1684 " --> pdb=" O ARG A1680 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N CYS A1686 " --> pdb=" O ALA A1682 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER A1687 " --> pdb=" O HIS A1683 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N HIS A1688 " --> pdb=" O ALA A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1690 through 1700 removed outlier: 3.721A 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 1721 through 1734 removed outlier: 3.670A pdb=" N SER A1726 " --> pdb=" O SER A1722 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER A1732 " --> pdb=" O ARG A1728 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU A1733 " --> pdb=" O SER A1729 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR A1734 " --> pdb=" O MET A1730 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1745 removed outlier: 3.675A pdb=" N ILE A1745 " --> pdb=" O GLU A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1825 removed outlier: 3.695A pdb=" N ASP A1809 " --> pdb=" O GLU A1805 " (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 1925 through 1930 removed outlier: 4.156A pdb=" N MET A1929 " --> pdb=" O GLY A1925 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LYS A1930 " --> pdb=" O LEU A1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1925 through 1930' Processing helix chain 'A' and resid 1934 through 1987 removed outlier: 3.706A pdb=" N GLN A1938 " --> pdb=" O SER A1934 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP A1967 " --> pdb=" O GLU A1963 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS A1968 " --> pdb=" O ARG A1964 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE A1984 " --> pdb=" O LEU A1980 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR A1985 " --> pdb=" O MET A1981 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N MET A1986 " --> pdb=" O ARG A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1990 through 2001 removed outlier: 4.399A pdb=" N ARG A1994 " --> pdb=" O GLU A1990 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU A1997 " --> pdb=" O ARG A1993 " (cutoff:3.500A) removed outlier: 4.759A 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: 3.680A pdb=" N ASN A2007 " --> pdb=" O GLN A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2017 through 2022 removed outlier: 4.428A 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 removed outlier: 3.835A pdb=" N LEU A2039 " --> pdb=" O HIS A2035 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2109 removed outlier: 3.769A pdb=" N SER A2099 " --> pdb=" O GLN A2095 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP A2109 " --> pdb=" O TRP A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2130 removed outlier: 3.975A pdb=" N GLY A2130 " --> pdb=" O ARG A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2131 through 2142 Proline residue: A2139 - end of helix removed outlier: 5.411A pdb=" N TYR A2142 " --> pdb=" O LEU A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2145 through 2169 removed outlier: 4.274A pdb=" N VAL A2149 " --> pdb=" O SER A2145 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLU A2150 " --> pdb=" O PRO A2146 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ASP A2151 " --> pdb=" O SER A2147 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N CYS A2158 " --> pdb=" O SER A2154 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE A2167 " --> pdb=" O ARG A2163 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL A2168 " --> pdb=" O SER A2164 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLN A2169 " --> pdb=" O LEU A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2171 through 2189 removed outlier: 3.693A pdb=" N GLN A2180 " --> pdb=" O ASN A2176 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A2181 " --> pdb=" O LEU A2177 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN A2188 " --> pdb=" O ASN A2184 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LYS A2189 " --> pdb=" O ILE A2185 " (cutoff:3.500A) Processing helix chain 'A' and resid 2194 through 2202 Processing helix chain 'A' and resid 2203 through 2219 removed outlier: 5.000A pdb=" N GLY A2218 " --> pdb=" O VAL A2214 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A2219 " --> pdb=" O LEU A2215 " (cutoff:3.500A) Processing helix chain 'A' and resid 2225 through 2244 removed outlier: 3.582A pdb=" N SER A2231 " --> pdb=" O LYS A2227 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A2241 " --> pdb=" O CYS A2237 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A2242 " --> pdb=" O TYR A2238 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER A2243 " --> pdb=" O PHE A2239 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ARG A2244 " --> pdb=" O CYS A2240 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2255 removed outlier: 4.031A pdb=" N HIS A2253 " --> pdb=" O SER A2249 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A2254 " --> pdb=" O MET A2250 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N SER A2255 " --> pdb=" O PHE A2251 " (cutoff:3.500A) Processing helix chain 'A' and resid 2256 through 2264 removed outlier: 3.787A pdb=" N ASN A2260 " --> pdb=" O TYR A2256 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE A2263 " --> pdb=" O GLU A2259 " (cutoff:3.500A) Processing helix chain 'A' and resid 2271 through 2281 removed outlier: 3.713A pdb=" N VAL A2275 " --> pdb=" O THR A2271 " (cutoff:3.500A) Processing helix chain 'A' and resid 2283 through 2290 Processing helix chain 'A' and resid 2291 through 2309 removed outlier: 3.594A pdb=" N LEU A2295 " --> pdb=" O GLN A2291 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A2297 " --> pdb=" O GLN A2293 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A2298 " --> pdb=" O ASP A2294 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A2307 " --> pdb=" O ALA A2303 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN A2308 " --> pdb=" O GLY A2304 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N SER A2309 " --> pdb=" O CYS A2305 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2317 removed outlier: 3.523A pdb=" N GLY A2317 " --> pdb=" O LEU A2313 " (cutoff:3.500A) Processing helix chain 'A' and resid 2324 through 2340 removed outlier: 3.559A pdb=" N GLY A2328 " --> pdb=" O ASN A2324 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A2334 " --> pdb=" O ARG A2330 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2361 Proline residue: A2361 - end of helix Processing helix chain 'A' and resid 2375 through 2390 removed outlier: 3.570A pdb=" N ALA A2379 " --> pdb=" O GLY A2375 " (cutoff:3.500A) removed outlier: 3.926A 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: 3.837A pdb=" N MET A2423 " --> pdb=" O GLY A2419 " (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: 4.143A pdb=" N LYS A2499 " --> pdb=" O VAL A2495 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A2504 " --> pdb=" O ALA A2500 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE A2505 " --> pdb=" O SER A2501 " (cutoff:3.500A) Processing helix chain 'A' and resid 2514 through 2525 removed outlier: 3.508A pdb=" N VAL A2521 " --> pdb=" O PHE A2517 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL A2524 " --> pdb=" O HIS A2520 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A2525 " --> pdb=" O VAL A2521 " (cutoff:3.500A) Processing helix chain 'A' and resid 2526 through 2538 removed outlier: 3.786A pdb=" N MET A2530 " --> pdb=" O PHE A2526 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N THR A2538 " --> pdb=" O ALA A2534 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2566 removed outlier: 3.575A pdb=" N LEU A2548 " --> pdb=" O THR A2544 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A2549 " --> pdb=" O GLU A2545 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LEU A2559 " --> pdb=" O CYS A2555 " (cutoff:3.500A) Proline residue: A2560 - end of helix Processing helix chain 'A' and resid 2567 through 2573 removed outlier: 5.394A pdb=" N GLY A2571 " --> pdb=" O PRO A2567 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N THR A2572 " --> pdb=" O LEU A2568 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLU A2573 " --> pdb=" O PHE A2569 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2567 through 2573' Processing helix chain 'A' and resid 2575 through 2592 Processing helix chain 'A' and resid 2596 through 2614 Processing helix chain 'A' and resid 2615 through 2630 removed outlier: 4.396A pdb=" N LEU A2619 " --> pdb=" O ARG A2615 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLN A2620 " --> pdb=" O PRO A2616 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N HIS A2621 " --> pdb=" O SER A2617 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU A2622 " --> pdb=" O MET A2618 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A2628 " --> pdb=" O ARG A2624 " (cutoff:3.500A) Processing helix chain 'A' and resid 2634 through 2652 removed outlier: 3.833A pdb=" N LYS A2638 " --> pdb=" O ASN A2634 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N MET A2639 " --> pdb=" O GLU A2635 " (cutoff:3.500A) Proline residue: A2640 - end of helix Processing helix chain 'A' and resid 2669 through 2689 removed outlier: 4.645A pdb=" N HIS A2673 " --> pdb=" O GLU A2669 " (cutoff:3.500A) Processing helix chain 'A' and resid 2693 through 2711 removed outlier: 3.659A pdb=" N ARG A2697 " --> pdb=" O GLN A2693 " (cutoff:3.500A) Proline residue: A2701 - end of helix Proline residue: A2711 - end of helix Processing helix chain 'A' and resid 2751 through 2774 removed outlier: 3.885A pdb=" N LYS A2757 " --> pdb=" O SER A2753 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N HIS A2763 " --> pdb=" O ALA A2759 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN A2774 " --> pdb=" O LYS A2770 " (cutoff:3.500A) Processing helix chain 'A' and resid 2799 through 2819 removed outlier: 3.801A pdb=" N GLU A2803 " --> pdb=" O GLU A2799 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE A2804 " --> pdb=" O LYS A2800 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG A2806 " --> pdb=" O LYS A2802 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N TRP A2807 " --> pdb=" O GLU A2803 " (cutoff:3.500A) Proline residue: A2808 - end of helix removed outlier: 4.108A pdb=" N TRP A2819 " --> pdb=" O ALA A2815 " (cutoff:3.500A) Processing helix chain 'A' and resid 2868 through 2895 removed outlier: 3.593A pdb=" N THR A2885 " --> pdb=" O ASN A2881 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A2893 " --> pdb=" O LYS A2889 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2934 removed outlier: 5.561A pdb=" N ARG A2918 " --> pdb=" O LYS A2914 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ASP A2919 " --> pdb=" O GLU A2915 " (cutoff:3.500A) Processing helix chain 'A' and resid 2949 through 2954 removed outlier: 3.622A pdb=" N ARG A2954 " --> pdb=" O SER A2950 " (cutoff:3.500A) Processing helix chain 'A' and resid 2955 through 2983 removed outlier: 3.927A pdb=" N ILE A2969 " --> pdb=" O ARG A2965 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU A2972 " --> pdb=" O ASP A2968 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE A2973 " --> pdb=" O ILE A2969 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A2974 " --> pdb=" O SER A2970 " (cutoff:3.500A) Processing helix chain 'A' and resid 2991 through 3014 removed outlier: 3.783A pdb=" N LEU A3002 " --> pdb=" O PHE A2998 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU A3003 " --> pdb=" O ALA A2999 " (cutoff:3.500A) Proline residue: A3004 - end of helix removed outlier: 3.548A pdb=" N THR A3011 " --> pdb=" O ASN A3007 " (cutoff:3.500A) Processing helix chain 'A' and resid 3032 through 3051 removed outlier: 3.506A pdb=" N ALA A3048 " --> pdb=" O CYS A3044 " (cutoff:3.500A) Processing helix 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 Processing helix chain 'A' and resid 3085 through 3112 removed outlier: 3.933A pdb=" N GLU A3108 " --> pdb=" O GLU A3104 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN A3109 " --> pdb=" O LYS A3105 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A3112 " --> pdb=" O GLU A3108 " (cutoff:3.500A) Processing helix chain 'A' and resid 3123 through 3151 removed outlier: 3.758A pdb=" N GLN A3127 " --> pdb=" O LYS A3123 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LEU A3137 " --> pdb=" O THR A3133 " (cutoff:3.500A) Proline residue: A3138 - end of helix removed outlier: 3.617A pdb=" N HIS A3150 " --> pdb=" O HIS A3146 " (cutoff:3.500A) Processing helix chain 'A' and resid 3159 through 3176 removed outlier: 4.257A pdb=" N VAL A3163 " --> pdb=" O ASP A3159 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A3174 " --> pdb=" O CYS A3170 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU A3175 " --> pdb=" O SER A3171 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLY A3176 " --> pdb=" O ILE A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3180 through 3201 Proline residue: A3188 - end of helix removed outlier: 3.624A pdb=" N ALA A3200 " --> pdb=" O ARG A3196 " (cutoff:3.500A) Processing helix chain 'A' and resid 3207 through 3212 removed outlier: 4.491A pdb=" N GLU A3212 " --> pdb=" O PRO A3208 " (cutoff:3.500A) Processing helix chain 'A' and resid 3217 through 3222 Processing helix chain 'A' and resid 3226 through 3231 removed outlier: 7.367A pdb=" N LEU A3230 " --> pdb=" O GLU A3226 " (cutoff:3.500A) removed outlier: 5.917A 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 3240 removed outlier: 3.658A pdb=" N MET A3239 " --> pdb=" O SER A3235 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N CYS A3240 " --> pdb=" O VAL A3236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3235 through 3240' Processing helix chain 'A' and resid 3245 through 3260 removed outlier: 3.538A pdb=" N LEU A3249 " --> pdb=" O VAL A3245 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY A3260 " --> pdb=" O LEU A3256 " (cutoff:3.500A) Processing helix chain 'A' and resid 3262 through 3267 Proline residue: A3267 - end of helix Processing helix chain 'A' and resid 3268 through 3285 removed outlier: 4.428A pdb=" N LEU A3274 " --> pdb=" O ILE A3270 " (cutoff:3.500A) Proline residue: A3275 - end of helix Proline residue: A3282 - end of helix Processing helix chain 'A' and resid 3308 through 3328 removed outlier: 3.927A pdb=" N LEU A3312 " --> pdb=" O THR A3308 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A3327 " --> pdb=" O ILE A3323 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLY A3328 " --> pdb=" O VAL A3324 " (cutoff:3.500A) Processing helix chain 'A' and resid 3332 through 3347 removed outlier: 5.302A pdb=" N LYS A3336 " --> pdb=" O ALA A3332 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARG A3337 " --> pdb=" O THR A3333 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A3340 " --> pdb=" O LYS A3336 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A3341 " --> pdb=" O ARG A3337 " (cutoff:3.500A) Proline residue: A3344 - end of helix removed outlier: 5.122A pdb=" N SER A3347 " --> pdb=" O GLN A3343 " (cutoff:3.500A) Processing helix chain 'A' and resid 3350 through 3383 removed outlier: 4.818A pdb=" N LEU A3354 " --> pdb=" O ARG A3350 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N HIS A3355 " --> pdb=" O PRO A3351 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE A3359 " --> pdb=" O HIS A3355 " (cutoff:3.500A) Proline residue: A3360 - end of helix removed outlier: 3.679A pdb=" N GLU A3382 " --> pdb=" O GLN A3378 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA A3383 " --> pdb=" O LEU A3379 " (cutoff:3.500A) Processing helix chain 'A' and resid 3389 through 3413 removed outlier: 6.669A pdb=" N LEU A3393 " --> pdb=" O GLU A3389 " (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 3449 removed outlier: 3.749A pdb=" N GLU A3433 " --> pdb=" O ALA A3429 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A3434 " --> pdb=" O ASN A3430 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N HIS A3449 " --> pdb=" O TRP A3445 " (cutoff:3.500A) Processing helix chain 'A' and resid 3450 through 3463 removed outlier: 3.649A pdb=" N GLN A3456 " --> pdb=" O LYS A3452 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN A3457 " --> pdb=" O ARG A3453 " (cutoff:3.500A) Processing helix chain 'A' and resid 3465 through 3478 removed outlier: 6.738A pdb=" N PHE A3469 " --> pdb=" O ASN A3465 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A3470 " --> pdb=" O ASN A3466 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASP A3473 " --> pdb=" O PHE A3469 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N SER A3474 " --> pdb=" O LEU A3470 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET A3478 " --> pdb=" O SER A3474 " (cutoff:3.500A) Processing helix chain 'A' and resid 3508 through 3526 removed outlier: 3.744A pdb=" N MET A3517 " --> pdb=" O THR A3513 " (cutoff:3.500A) Proline residue: A3519 - end of helix removed outlier: 3.629A pdb=" N CYS A3525 " --> pdb=" O GLY A3521 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ALA A3526 " --> pdb=" O LEU A3522 " (cutoff:3.500A) Processing helix chain 'A' and resid 3529 through 3543 Processing helix chain 'A' and resid 3545 through 3557 removed outlier: 3.558A pdb=" N ARG A3550 " --> pdb=" O ASP A3546 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A3551 " --> pdb=" O GLU A3547 " (cutoff:3.500A) Processing helix chain 'A' and resid 3562 through 3567 removed outlier: 4.112A pdb=" N SER A3566 " --> pdb=" O LYS A3562 " (cutoff:3.500A) Proline residue: A3567 - end of helix No H-bonds generated for 'chain 'A' and resid 3562 through 3567' Processing helix chain 'A' and resid 3568 through 3579 Processing helix chain 'A' and resid 3588 through 3612 removed outlier: 3.586A pdb=" N VAL A3593 " --> pdb=" O PRO A3589 " (cutoff:3.500A) Proline residue: A3612 - end of helix Processing helix chain 'A' and resid 3628 through 3638 removed outlier: 4.503A pdb=" N VAL A3632 " --> pdb=" O ARG A3628 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A3633 " --> pdb=" O ARG A3629 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE A3636 " --> pdb=" O VAL A3632 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG A3637 " --> pdb=" O VAL A3633 " (cutoff:3.500A) Processing helix chain 'A' and resid 3640 through 3645 removed outlier: 3.749A pdb=" N LEU A3644 " --> pdb=" O PRO A3640 " (cutoff:3.500A) Proline residue: A3645 - end of helix No H-bonds generated for 'chain 'A' and resid 3640 through 3645' Processing helix chain 'A' and resid 3646 through 3665 removed outlier: 3.629A pdb=" N GLU A3655 " --> pdb=" O ASN A3651 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU A3663 " --> pdb=" O ALA A3659 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N THR A3664 " --> pdb=" O ALA A3660 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A3665 " --> pdb=" O TRP A3661 " (cutoff:3.500A) Processing helix chain 'A' and resid 3669 through 3679 removed outlier: 3.643A pdb=" N LYS A3679 " --> pdb=" O ASP A3675 " (cutoff:3.500A) Processing helix chain 'A' and resid 3696 through 3711 Processing helix chain 'A' and resid 3719 through 3735 removed outlier: 3.829A pdb=" N CYS A3733 " --> pdb=" O MET A3729 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N HIS A3734 " --> pdb=" O ALA A3730 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU A3735 " --> pdb=" O LYS A3731 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3772 removed outlier: 3.685A pdb=" N LYS A3756 " --> pdb=" O SER A3752 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU A3757 " --> pdb=" O PHE A3753 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET A3758 " --> pdb=" O GLU A3754 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN A3761 " --> pdb=" O GLU A3757 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A3770 " --> pdb=" O GLN A3766 " (cutoff:3.500A) Processing helix chain 'A' and resid 3774 through 3787 removed outlier: 4.295A 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 3826 through 3839 Processing helix chain 'A' and resid 3843 through 3857 removed outlier: 3.656A pdb=" N GLU A3854 " --> pdb=" O GLN A3850 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A3855 " --> pdb=" O ASN A3851 " (cutoff:3.500A) Processing helix chain 'A' and resid 3877 through 3893 removed outlier: 3.550A 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: 3.614A pdb=" N TYR A3937 " --> pdb=" O PHE A3933 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLY A3939 " --> pdb=" O TRP A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3944 through 3970 removed outlier: 3.636A 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: 3.958A pdb=" N ALA A3988 " --> pdb=" O ARG A3984 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS A3998 " --> pdb=" O HIS A3994 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A4005 " --> pdb=" O MET A4001 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP A4006 " --> pdb=" O LYS A4002 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER A4007 " --> pdb=" O LEU A4003 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4032 Processing helix chain 'A' and resid 4038 through 4052 Processing helix chain 'A' and resid 4053 through 4072 removed outlier: 3.748A pdb=" N MET A4064 " --> pdb=" O LYS A4060 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE A4065 " --> pdb=" O PHE A4061 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A4068 " --> pdb=" O MET A4064 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP A4070 " --> pdb=" O LEU A4066 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4082 removed outlier: 3.853A pdb=" N TYR A4080 " --> pdb=" O ALA A4076 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N THR A4082 " --> pdb=" O GLN A4078 " (cutoff:3.500A) Processing helix chain 'A' and resid 4089 through 4101 removed outlier: 4.154A pdb=" N ASP A4098 " --> pdb=" O GLN A4094 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N SER A4099 " --> pdb=" O LYS A4095 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN A4100 " --> pdb=" O ALA A4096 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS A4101 " --> pdb=" O MET A4097 " (cutoff:3.500A) Processing helix chain 'A' and resid 4104 through 4116 removed outlier: 5.495A pdb=" N GLU A4116 " --> pdb=" O LEU A4112 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4155 removed outlier: 4.193A pdb=" N PHE A4128 " --> pdb=" O ASN A4124 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA A4129 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASN A4130 " --> pdb=" O GLU A4126 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N PHE A4132 " --> pdb=" O PHE A4128 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN A4133 " --> pdb=" O ALA A4129 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLU A4134 " --> pdb=" O ASN A4130 " (cutoff:3.500A) Proline residue: A4135 - end of helix removed outlier: 4.215A pdb=" N ASP A4138 " --> pdb=" O GLU A4134 " (cutoff:3.500A) removed outlier: 3.797A 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: 3.579A pdb=" N ASN A4162 " --> pdb=" O PRO A4158 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE A4163 " --> pdb=" O ARG A4159 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A4164 " --> pdb=" O LEU A4160 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU A4165 " --> pdb=" O ARG A4161 " (cutoff:3.500A) Processing helix chain 'A' and resid 4169 through 4175 Processing helix chain 'A' and resid 4198 through 4208 Proline residue: A4208 - end of helix Processing helix chain 'A' and resid 4209 through 4224 Processing helix chain 'A' and resid 4226 through 4252 removed outlier: 4.500A pdb=" N MET A4231 " --> pdb=" O GLU A4227 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLU A4232 " --> pdb=" O ALA A4228 " (cutoff:3.500A) Processing helix chain 'A' and resid 4542 through 4559 Processing helix chain 'A' and resid 4560 through 4580 removed outlier: 3.919A pdb=" N LEU A4567 " --> pdb=" O ARG A4563 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE A4579 " --> pdb=" O PHE A4575 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TYR A4580 " --> pdb=" O ILE A4576 " (cutoff:3.500A) Processing helix chain 'A' and resid 4640 through 4683 removed outlier: 4.035A 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 4709 removed outlier: 3.601A pdb=" N ARG A4703 " --> pdb=" O GLY A4699 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU A4704 " --> pdb=" O GLN A4700 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL A4705 " --> pdb=" O TRP A4701 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASN A4707 " --> pdb=" O ARG A4703 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR A4708 " --> pdb=" O LEU A4704 " (cutoff:3.500A) Proline residue: A4709 - end of helix 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 4749 Processing helix chain 'A' and resid 4772 through 4786 removed outlier: 3.508A pdb=" N ASP A4786 " --> pdb=" O VAL A4782 " (cutoff:3.500A) Processing helix chain 'A' and resid 4787 through 4805 removed outlier: 4.008A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4808 through 4820 removed outlier: 5.097A pdb=" N HIS A4812 " --> pdb=" O PHE A4808 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU A4813 " --> pdb=" O PHE A4809 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU A4814 " --> pdb=" O ALA A4810 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP A4815 " --> pdb=" O ALA A4811 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE A4816 " --> pdb=" O HIS A4812 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA A4817 " --> pdb=" O LEU A4813 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) Processing helix chain 'A' and resid 4821 through 4832 removed outlier: 3.961A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 4.150A 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 4878 through 4893 removed outlier: 3.703A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) Processing helix chain 'A' and resid 4896 through 4901 removed outlier: 4.302A 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: 4.055A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (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: 3.813A pdb=" N HIS A5003 " --> pdb=" O ASP A4999 " (cutoff:3.500A) removed outlier: 6.154A 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 255 removed outlier: 4.316A pdb=" N CYS A 253 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A 254 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS A 255 " --> pdb=" O VAL A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 255' Processing helix chain 'A' and resid 3296 through 3302 removed outlier: 4.251A pdb=" N ALA A3300 " --> pdb=" O PRO A3297 " (cutoff:3.500A) Proline residue: A3301 - end of helix Processing helix chain 'A' and resid 3152 through 3157 removed outlier: 4.112A 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: 3.753A pdb=" N CYS B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 303 through 308 removed outlier: 3.701A pdb=" N ALA B 307 " --> pdb=" O ASP B 303 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N HIS B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 303 through 308' Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 394 through 423 removed outlier: 4.510A pdb=" N ARG B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N MET B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLY B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 453 removed outlier: 3.514A pdb=" N GLY B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 482 removed outlier: 3.654A pdb=" N GLN B 465 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 467 " --> pdb=" O GLU B 463 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 497 removed outlier: 3.708A pdb=" N VAL B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N TYR B 497 " --> pdb=" O ARG B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.684A pdb=" N TYR B 506 " --> pdb=" O HIS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 531 removed outlier: 3.720A pdb=" N GLU B 513 " --> pdb=" O GLU B 509 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN B 520 " --> pdb=" O LYS B 516 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 removed outlier: 4.021A pdb=" N LEU B 539 " --> pdb=" O ALA B 535 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N PHE B 540 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER B 541 " --> pdb=" O CYS B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 552 removed outlier: 3.547A pdb=" N VAL B 547 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS B 550 " --> pdb=" O TRP B 546 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASP B 552 " --> pdb=" O VAL B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 571 removed outlier: 3.932A pdb=" N ILE B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU B 570 " --> pdb=" O CYS B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 578 removed outlier: 3.956A pdb=" N ASN B 576 " --> pdb=" O PRO B 572 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE B 577 " --> pdb=" O GLU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.800A pdb=" N LEU B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 609 removed outlier: 3.936A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N CYS B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 629 removed outlier: 3.633A 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: 4.622A pdb=" N ALA B 814 " --> pdb=" O PRO B 810 " (cutoff:3.500A) removed outlier: 4.564A 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: 3.831A pdb=" N PHE B 851 " --> pdb=" O SER B 847 " (cutoff:3.500A) removed outlier: 3.736A 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: 3.560A pdb=" N ILE B 870 " --> pdb=" O HIS B 866 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLU B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU B 874 " --> pdb=" O ILE B 870 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA B 875 " --> pdb=" O ARG B 871 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE B 878 " --> pdb=" O LEU B 874 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU B 880 " --> pdb=" O GLU B 876 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU B 881 " --> pdb=" O ASN B 877 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N TRP B 882 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA B 883 " --> pdb=" O HIS B 879 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR B 885 " --> pdb=" O LEU B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 914 removed outlier: 3.788A 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: 3.928A pdb=" N ASN B 949 " --> pdb=" O LYS B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 1004 removed outlier: 3.507A pdb=" N VAL B 995 " --> pdb=" O ASN B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1048 removed outlier: 4.097A pdb=" N SER B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B1039 " --> pdb=" O ASN B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1073 removed outlier: 3.984A pdb=" N ARG B1071 " --> pdb=" O SER B1067 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL B1072 " --> pdb=" O ARG B1068 " (cutoff:3.500A) removed outlier: 4.937A 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: 6.592A pdb=" N GLU B1221 " --> pdb=" O CYS B1217 " (cutoff:3.500A) Processing helix chain 'B' and resid 1423 through 1430 removed outlier: 3.532A pdb=" N LEU B1428 " --> pdb=" O PRO B1424 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASN B1429 " --> pdb=" O GLU B1425 " (cutoff:3.500A) Processing helix chain 'B' and resid 1444 through 1449 removed outlier: 4.046A pdb=" N VAL B1448 " --> pdb=" O GLU B1444 " (cutoff:3.500A) removed outlier: 5.495A 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: 4.738A pdb=" N PHE B1500 " --> pdb=" O TRP B1496 " (cutoff:3.500A) removed outlier: 4.449A 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: 3.844A pdb=" N ALA B1578 " --> pdb=" O PRO B1574 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE B1580 " --> pdb=" O SER B1576 " (cutoff:3.500A) Processing helix chain 'B' and resid 1649 through 1657 removed outlier: 4.455A pdb=" N LEU B1653 " --> pdb=" O ASP B1649 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER B1654 " --> pdb=" O ILE B1650 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLU B1655 " --> pdb=" O LEU B1651 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU B1657 " --> pdb=" O LEU B1653 " (cutoff:3.500A) Processing helix chain 'B' and resid 1658 through 1675 removed outlier: 3.927A pdb=" N PHE B1662 " --> pdb=" O ASP B1658 " (cutoff:3.500A) Processing helix chain 'B' and resid 1678 through 1689 removed outlier: 3.920A pdb=" N ALA B1684 " --> pdb=" O ARG B1680 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N CYS B1686 " --> pdb=" O ALA B1682 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER B1687 " --> pdb=" O HIS B1683 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N HIS B1688 " --> pdb=" O ALA B1684 " (cutoff:3.500A) Processing helix chain 'B' and resid 1690 through 1700 removed outlier: 3.720A 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 1721 through 1734 removed outlier: 3.670A pdb=" N SER B1726 " --> pdb=" O SER B1722 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER B1732 " --> pdb=" O ARG B1728 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLU B1733 " --> pdb=" O SER B1729 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR B1734 " --> pdb=" O MET B1730 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1745 removed outlier: 3.676A pdb=" N ILE B1745 " --> pdb=" O GLU B1741 " (cutoff:3.500A) Processing helix chain 'B' and resid 1803 through 1825 removed outlier: 3.693A pdb=" N ASP B1809 " --> pdb=" O GLU B1805 " (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 1925 through 1930 removed outlier: 4.155A pdb=" N MET B1929 " --> pdb=" O GLY B1925 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LYS B1930 " --> pdb=" O LEU B1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1925 through 1930' Processing helix chain 'B' and resid 1934 through 1987 removed outlier: 3.707A pdb=" N GLN B1938 " --> pdb=" O SER B1934 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP B1967 " --> pdb=" O GLU B1963 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS B1968 " --> pdb=" O ARG B1964 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE B1984 " --> pdb=" O LEU B1980 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR B1985 " --> pdb=" O MET B1981 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N MET B1986 " --> pdb=" O ARG B1982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1990 through 2001 removed outlier: 4.398A pdb=" N ARG B1994 " --> pdb=" O GLU B1990 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU B1997 " --> pdb=" O ARG B1993 " (cutoff:3.500A) removed outlier: 4.758A 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: 3.679A pdb=" N ASN B2007 " --> pdb=" O GLN B2003 " (cutoff:3.500A) Processing helix chain 'B' and resid 2017 through 2022 removed outlier: 4.429A 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 removed outlier: 3.835A pdb=" N LEU B2039 " --> pdb=" O HIS B2035 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2109 removed outlier: 3.770A pdb=" N SER B2099 " --> pdb=" O GLN B2095 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP B2109 " --> pdb=" O TRP B2105 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2130 removed outlier: 3.975A pdb=" N GLY B2130 " --> pdb=" O ARG B2126 " (cutoff:3.500A) Processing helix chain 'B' and resid 2131 through 2142 Proline residue: B2139 - end of helix removed outlier: 5.411A pdb=" N TYR B2142 " --> pdb=" O LEU B2138 " (cutoff:3.500A) Processing helix chain 'B' and resid 2145 through 2169 removed outlier: 4.275A pdb=" N VAL B2149 " --> pdb=" O SER B2145 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLU B2150 " --> pdb=" O PRO B2146 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ASP B2151 " --> pdb=" O SER B2147 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N CYS B2158 " --> pdb=" O SER B2154 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE B2167 " --> pdb=" O ARG B2163 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL B2168 " --> pdb=" O SER B2164 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLN B2169 " --> pdb=" O LEU B2165 " (cutoff:3.500A) Processing helix chain 'B' and resid 2171 through 2189 removed outlier: 3.692A pdb=" N GLN B2180 " --> pdb=" O ASN B2176 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER B2181 " --> pdb=" O LEU B2177 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN B2188 " --> pdb=" O ASN B2184 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LYS B2189 " --> pdb=" O ILE B2185 " (cutoff:3.500A) Processing helix chain 'B' and resid 2194 through 2202 Processing helix chain 'B' and resid 2203 through 2219 removed outlier: 5.000A pdb=" N GLY B2218 " --> pdb=" O VAL B2214 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU B2219 " --> pdb=" O LEU B2215 " (cutoff:3.500A) Processing helix chain 'B' and resid 2225 through 2244 removed outlier: 3.582A pdb=" N SER B2231 " --> pdb=" O LYS B2227 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B2241 " --> pdb=" O CYS B2237 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE B2242 " --> pdb=" O TYR B2238 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER B2243 " --> pdb=" O PHE B2239 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ARG B2244 " --> pdb=" O CYS B2240 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2255 removed outlier: 4.030A pdb=" N HIS B2253 " --> pdb=" O SER B2249 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B2254 " --> pdb=" O MET B2250 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N SER B2255 " --> pdb=" O PHE B2251 " (cutoff:3.500A) Processing helix chain 'B' and resid 2256 through 2264 removed outlier: 3.788A pdb=" N ASN B2260 " --> pdb=" O TYR B2256 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE B2263 " --> pdb=" O GLU B2259 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2281 removed outlier: 3.714A pdb=" N VAL B2275 " --> pdb=" O THR B2271 " (cutoff:3.500A) Processing helix chain 'B' and resid 2283 through 2290 Processing helix chain 'B' and resid 2291 through 2309 removed outlier: 3.594A pdb=" N LEU B2295 " --> pdb=" O GLN B2291 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS B2297 " --> pdb=" O GLN B2293 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B2298 " --> pdb=" O ASP B2294 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B2307 " --> pdb=" O ALA B2303 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN B2308 " --> pdb=" O GLY B2304 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER B2309 " --> pdb=" O CYS B2305 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2317 removed outlier: 3.523A pdb=" N GLY B2317 " --> pdb=" O LEU B2313 " (cutoff:3.500A) Processing helix chain 'B' and resid 2324 through 2340 removed outlier: 3.559A pdb=" N GLY B2328 " --> pdb=" O ASN B2324 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B2334 " --> pdb=" O ARG B2330 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2361 Proline residue: B2361 - end of helix Processing helix chain 'B' and resid 2375 through 2390 removed outlier: 3.571A pdb=" N ALA B2379 " --> pdb=" O GLY B2375 " (cutoff:3.500A) removed outlier: 3.925A 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: 3.836A pdb=" N MET B2423 " --> pdb=" O GLY B2419 " (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: 4.143A pdb=" N LYS B2499 " --> pdb=" O VAL B2495 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B2504 " --> pdb=" O ALA B2500 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE B2505 " --> pdb=" O SER B2501 " (cutoff:3.500A) Processing helix chain 'B' and resid 2514 through 2525 removed outlier: 3.508A pdb=" N VAL B2521 " --> pdb=" O PHE B2517 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL B2524 " --> pdb=" O HIS B2520 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY B2525 " --> pdb=" O VAL B2521 " (cutoff:3.500A) Processing helix chain 'B' and resid 2526 through 2538 removed outlier: 3.785A pdb=" N MET B2530 " --> pdb=" O PHE B2526 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N THR B2538 " --> pdb=" O ALA B2534 " (cutoff:3.500A) Processing helix chain 'B' and resid 2544 through 2566 removed outlier: 3.574A pdb=" N LEU B2548 " --> pdb=" O THR B2544 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B2549 " --> pdb=" O GLU B2545 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU B2559 " --> pdb=" O CYS B2555 " (cutoff:3.500A) Proline residue: B2560 - end of helix Processing helix chain 'B' and resid 2567 through 2573 removed outlier: 5.394A pdb=" N GLY B2571 " --> pdb=" O PRO B2567 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N THR B2572 " --> pdb=" O LEU B2568 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLU B2573 " --> pdb=" O PHE B2569 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2567 through 2573' Processing helix chain 'B' and resid 2575 through 2592 Processing helix chain 'B' and resid 2596 through 2614 Processing helix chain 'B' and resid 2615 through 2630 removed outlier: 4.396A pdb=" N LEU B2619 " --> pdb=" O ARG B2615 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLN B2620 " --> pdb=" O PRO B2616 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N HIS B2621 " --> pdb=" O SER B2617 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU B2622 " --> pdb=" O MET B2618 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE B2628 " --> pdb=" O ARG B2624 " (cutoff:3.500A) Processing helix chain 'B' and resid 2634 through 2652 removed outlier: 3.832A pdb=" N LYS B2638 " --> pdb=" O ASN B2634 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N MET B2639 " --> pdb=" O GLU B2635 " (cutoff:3.500A) Proline residue: B2640 - end of helix Processing helix chain 'B' and resid 2669 through 2689 removed outlier: 4.645A pdb=" N HIS B2673 " --> pdb=" O GLU B2669 " (cutoff:3.500A) Processing helix chain 'B' and resid 2693 through 2711 removed outlier: 3.659A pdb=" N ARG B2697 " --> pdb=" O GLN B2693 " (cutoff:3.500A) Proline residue: B2701 - end of helix Proline residue: B2711 - end of helix Processing helix chain 'B' and resid 2751 through 2774 removed outlier: 3.885A pdb=" N LYS B2757 " --> pdb=" O SER B2753 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N HIS B2763 " --> pdb=" O ALA B2759 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN B2774 " --> pdb=" O LYS B2770 " (cutoff:3.500A) Processing helix chain 'B' and resid 2799 through 2819 removed outlier: 3.801A pdb=" N GLU B2803 " --> pdb=" O GLU B2799 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE B2804 " --> pdb=" O LYS B2800 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG B2806 " --> pdb=" O LYS B2802 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N TRP B2807 " --> pdb=" O GLU B2803 " (cutoff:3.500A) Proline residue: B2808 - end of helix removed outlier: 4.108A pdb=" N TRP B2819 " --> pdb=" O ALA B2815 " (cutoff:3.500A) Processing helix chain 'B' and resid 2868 through 2895 removed outlier: 3.592A pdb=" N THR B2885 " --> pdb=" O ASN B2881 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B2893 " --> pdb=" O LYS B2889 " (cutoff:3.500A) Processing helix chain 'B' and resid 2912 through 2934 removed outlier: 5.561A pdb=" N ARG B2918 " --> pdb=" O LYS B2914 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ASP B2919 " --> pdb=" O GLU B2915 " (cutoff:3.500A) Processing helix chain 'B' and resid 2949 through 2954 removed outlier: 3.623A pdb=" N ARG B2954 " --> pdb=" O SER B2950 " (cutoff:3.500A) Processing helix chain 'B' and resid 2955 through 2983 removed outlier: 3.927A pdb=" N ILE B2969 " --> pdb=" O ARG B2965 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU B2972 " --> pdb=" O ASP B2968 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE B2973 " --> pdb=" O ILE B2969 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B2974 " --> pdb=" O SER B2970 " (cutoff:3.500A) Processing helix chain 'B' and resid 2991 through 3014 removed outlier: 3.784A pdb=" N LEU B3002 " --> pdb=" O PHE B2998 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU B3003 " --> pdb=" O ALA B2999 " (cutoff:3.500A) Proline residue: B3004 - end of helix removed outlier: 3.548A pdb=" N THR B3011 " --> pdb=" O ASN B3007 " (cutoff:3.500A) Processing helix chain 'B' and resid 3032 through 3051 removed outlier: 3.505A pdb=" N ALA B3048 " --> pdb=" O CYS B3044 " (cutoff:3.500A) Processing helix 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 Processing helix chain 'B' and resid 3085 through 3112 removed outlier: 3.933A pdb=" N GLU B3108 " --> pdb=" O GLU B3104 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN B3109 " --> pdb=" O LYS B3105 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B3112 " --> pdb=" O GLU B3108 " (cutoff:3.500A) Processing helix chain 'B' and resid 3123 through 3151 removed outlier: 3.758A pdb=" N GLN B3127 " --> pdb=" O LYS B3123 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LEU B3137 " --> pdb=" O THR B3133 " (cutoff:3.500A) Proline residue: B3138 - end of helix removed outlier: 3.617A pdb=" N HIS B3150 " --> pdb=" O HIS B3146 " (cutoff:3.500A) Processing helix chain 'B' and resid 3159 through 3176 removed outlier: 4.257A pdb=" N VAL B3163 " --> pdb=" O ASP B3159 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B3174 " --> pdb=" O CYS B3170 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU B3175 " --> pdb=" O SER B3171 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLY B3176 " --> pdb=" O ILE B3172 " (cutoff:3.500A) Processing helix chain 'B' and resid 3180 through 3201 Proline residue: B3188 - end of helix removed outlier: 3.624A pdb=" N ALA B3200 " --> pdb=" O ARG B3196 " (cutoff:3.500A) Processing helix chain 'B' and resid 3207 through 3212 removed outlier: 4.491A pdb=" N GLU B3212 " --> pdb=" O PRO B3208 " (cutoff:3.500A) Processing helix chain 'B' and resid 3217 through 3222 Processing helix chain 'B' and resid 3226 through 3231 removed outlier: 7.368A pdb=" N LEU B3230 " --> pdb=" O GLU B3226 " (cutoff:3.500A) removed outlier: 5.917A 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 3240 removed outlier: 3.658A pdb=" N MET B3239 " --> pdb=" O SER B3235 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N CYS B3240 " --> pdb=" O VAL B3236 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3235 through 3240' Processing helix chain 'B' and resid 3245 through 3260 removed outlier: 3.539A pdb=" N LEU B3249 " --> pdb=" O VAL B3245 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY B3260 " --> pdb=" O LEU B3256 " (cutoff:3.500A) Processing helix chain 'B' and resid 3262 through 3267 Proline residue: B3267 - end of helix Processing helix chain 'B' and resid 3268 through 3285 removed outlier: 4.427A pdb=" N LEU B3274 " --> pdb=" O ILE B3270 " (cutoff:3.500A) Proline residue: B3275 - end of helix Proline residue: B3282 - end of helix Processing helix chain 'B' and resid 3308 through 3328 removed outlier: 3.926A pdb=" N LEU B3312 " --> pdb=" O THR B3308 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B3327 " --> pdb=" O ILE B3323 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLY B3328 " --> pdb=" O VAL B3324 " (cutoff:3.500A) Processing helix chain 'B' and resid 3332 through 3347 removed outlier: 5.302A pdb=" N LYS B3336 " --> pdb=" O ALA B3332 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ARG B3337 " --> pdb=" O THR B3333 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B3340 " --> pdb=" O LYS B3336 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B3341 " --> pdb=" O ARG B3337 " (cutoff:3.500A) Proline residue: B3344 - end of helix removed outlier: 5.121A pdb=" N SER B3347 " --> pdb=" O GLN B3343 " (cutoff:3.500A) Processing helix chain 'B' and resid 3350 through 3383 removed outlier: 4.818A pdb=" N LEU B3354 " --> pdb=" O ARG B3350 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N HIS B3355 " --> pdb=" O PRO B3351 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE B3359 " --> pdb=" O HIS B3355 " (cutoff:3.500A) Proline residue: B3360 - end of helix removed outlier: 3.678A pdb=" N GLU B3382 " --> pdb=" O GLN B3378 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA B3383 " --> pdb=" O LEU B3379 " (cutoff:3.500A) Processing helix chain 'B' and resid 3389 through 3413 removed outlier: 6.670A pdb=" N LEU B3393 " --> pdb=" O GLU B3389 " (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 3449 removed outlier: 3.749A pdb=" N GLU B3433 " --> pdb=" O ALA B3429 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B3434 " --> pdb=" O ASN B3430 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N HIS B3449 " --> pdb=" O TRP B3445 " (cutoff:3.500A) Processing helix chain 'B' and resid 3450 through 3463 removed outlier: 3.649A pdb=" N GLN B3456 " --> pdb=" O LYS B3452 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN B3457 " --> pdb=" O ARG B3453 " (cutoff:3.500A) Processing helix chain 'B' and resid 3465 through 3478 removed outlier: 6.737A pdb=" N PHE B3469 " --> pdb=" O ASN B3465 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU B3470 " --> pdb=" O ASN B3466 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASP B3473 " --> pdb=" O PHE B3469 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N SER B3474 " --> pdb=" O LEU B3470 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET B3478 " --> pdb=" O SER B3474 " (cutoff:3.500A) Processing helix chain 'B' and resid 3508 through 3526 removed outlier: 3.744A pdb=" N MET B3517 " --> pdb=" O THR B3513 " (cutoff:3.500A) Proline residue: B3519 - end of helix removed outlier: 3.629A pdb=" N CYS B3525 " --> pdb=" O GLY B3521 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ALA B3526 " --> pdb=" O LEU B3522 " (cutoff:3.500A) Processing helix chain 'B' and resid 3529 through 3543 Processing helix chain 'B' and resid 3545 through 3557 removed outlier: 3.558A pdb=" N ARG B3550 " --> pdb=" O ASP B3546 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B3551 " --> pdb=" O GLU B3547 " (cutoff:3.500A) Processing helix chain 'B' and resid 3562 through 3567 removed outlier: 4.112A pdb=" N SER B3566 " --> pdb=" O LYS B3562 " (cutoff:3.500A) Proline residue: B3567 - end of helix No H-bonds generated for 'chain 'B' and resid 3562 through 3567' Processing helix chain 'B' and resid 3568 through 3579 Processing helix chain 'B' and resid 3588 through 3612 removed outlier: 3.585A pdb=" N VAL B3593 " --> pdb=" O PRO B3589 " (cutoff:3.500A) Proline residue: B3612 - end of helix Processing helix chain 'B' and resid 3628 through 3638 removed outlier: 4.504A pdb=" N VAL B3632 " --> pdb=" O ARG B3628 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B3633 " --> pdb=" O ARG B3629 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE B3636 " --> pdb=" O VAL B3632 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG B3637 " --> pdb=" O VAL B3633 " (cutoff:3.500A) Processing helix chain 'B' and resid 3640 through 3645 removed outlier: 3.749A pdb=" N LEU B3644 " --> pdb=" O PRO B3640 " (cutoff:3.500A) Proline residue: B3645 - end of helix No H-bonds generated for 'chain 'B' and resid 3640 through 3645' Processing helix chain 'B' and resid 3646 through 3665 removed outlier: 3.629A pdb=" N GLU B3655 " --> pdb=" O ASN B3651 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU B3663 " --> pdb=" O ALA B3659 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N THR B3664 " --> pdb=" O ALA B3660 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B3665 " --> pdb=" O TRP B3661 " (cutoff:3.500A) Processing helix chain 'B' and resid 3669 through 3679 removed outlier: 3.643A pdb=" N LYS B3679 " --> pdb=" O ASP B3675 " (cutoff:3.500A) Processing helix chain 'B' and resid 3696 through 3711 Processing helix chain 'B' and resid 3719 through 3735 removed outlier: 3.830A pdb=" N CYS B3733 " --> pdb=" O MET B3729 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N HIS B3734 " --> pdb=" O ALA B3730 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU B3735 " --> pdb=" O LYS B3731 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3772 removed outlier: 3.686A pdb=" N LYS B3756 " --> pdb=" O SER B3752 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU B3757 " --> pdb=" O PHE B3753 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET B3758 " --> pdb=" O GLU B3754 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN B3761 " --> pdb=" O GLU B3757 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B3770 " --> pdb=" O GLN B3766 " (cutoff:3.500A) Processing helix chain 'B' and resid 3774 through 3787 removed outlier: 4.295A 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 3826 through 3839 Processing helix chain 'B' and resid 3843 through 3857 removed outlier: 3.656A pdb=" N GLU B3854 " --> pdb=" O GLN B3850 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY B3855 " --> pdb=" O ASN B3851 " (cutoff:3.500A) Processing helix chain 'B' and resid 3877 through 3893 removed outlier: 3.549A 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: 3.614A pdb=" N TYR B3937 " --> pdb=" O PHE B3933 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLY B3939 " --> pdb=" O TRP B3935 " (cutoff:3.500A) Processing helix chain 'B' and resid 3944 through 3970 removed outlier: 3.636A 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: 3.958A pdb=" N ALA B3988 " --> pdb=" O ARG B3984 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS B3998 " --> pdb=" O HIS B3994 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B4005 " --> pdb=" O MET B4001 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP B4006 " --> pdb=" O LYS B4002 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER B4007 " --> pdb=" O LEU B4003 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4032 Processing helix chain 'B' and resid 4038 through 4052 Processing helix chain 'B' and resid 4053 through 4072 removed outlier: 3.748A pdb=" N MET B4064 " --> pdb=" O LYS B4060 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE B4065 " --> pdb=" O PHE B4061 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B4068 " --> pdb=" O MET B4064 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP B4070 " --> pdb=" O LEU B4066 " (cutoff:3.500A) Processing helix chain 'B' and resid 4074 through 4082 removed outlier: 3.853A pdb=" N TYR B4080 " --> pdb=" O ALA B4076 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N THR B4082 " --> pdb=" O GLN B4078 " (cutoff:3.500A) Processing helix chain 'B' and resid 4089 through 4101 removed outlier: 4.154A pdb=" N ASP B4098 " --> pdb=" O GLN B4094 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N SER B4099 " --> pdb=" O LYS B4095 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN B4100 " --> pdb=" O ALA B4096 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS B4101 " --> pdb=" O MET B4097 " (cutoff:3.500A) Processing helix chain 'B' and resid 4104 through 4116 removed outlier: 5.495A pdb=" N GLU B4116 " --> pdb=" O LEU B4112 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4155 removed outlier: 4.192A pdb=" N PHE B4128 " --> pdb=" O ASN B4124 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA B4129 " --> pdb=" O PHE B4125 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASN B4130 " --> pdb=" O GLU B4126 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N PHE B4132 " --> pdb=" O PHE B4128 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN B4133 " --> pdb=" O ALA B4129 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLU B4134 " --> pdb=" O ASN B4130 " (cutoff:3.500A) Proline residue: B4135 - end of helix removed outlier: 4.214A pdb=" N ASP B4138 " --> pdb=" O GLU B4134 " (cutoff:3.500A) removed outlier: 3.796A 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: 3.579A pdb=" N ASN B4162 " --> pdb=" O PRO B4158 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE B4163 " --> pdb=" O ARG B4159 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B4164 " --> pdb=" O LEU B4160 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU B4165 " --> pdb=" O ARG B4161 " (cutoff:3.500A) Processing helix chain 'B' and resid 4169 through 4175 Processing helix chain 'B' and resid 4198 through 4208 Proline residue: B4208 - end of helix Processing helix chain 'B' and resid 4209 through 4224 Processing helix chain 'B' and resid 4226 through 4252 removed outlier: 4.500A pdb=" N MET B4231 " --> pdb=" O GLU B4227 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLU B4232 " --> pdb=" O ALA B4228 " (cutoff:3.500A) Processing helix chain 'B' and resid 4542 through 4559 Processing helix chain 'B' and resid 4560 through 4580 removed outlier: 3.919A pdb=" N LEU B4567 " --> pdb=" O ARG B4563 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE B4579 " --> pdb=" O PHE B4575 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TYR B4580 " --> pdb=" O ILE B4576 " (cutoff:3.500A) Processing helix chain 'B' and resid 4640 through 4683 removed outlier: 4.035A 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 4709 removed outlier: 3.600A pdb=" N ARG B4703 " --> pdb=" O GLY B4699 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU B4704 " --> pdb=" O GLN B4700 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL B4705 " --> pdb=" O TRP B4701 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B4706 " --> pdb=" O ASP B4702 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASN B4707 " --> pdb=" O ARG B4703 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR B4708 " --> pdb=" O LEU B4704 " (cutoff:3.500A) Proline residue: B4709 - end of helix 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 4749 Processing helix chain 'B' and resid 4772 through 4786 removed outlier: 3.508A pdb=" N ASP B4786 " --> pdb=" O VAL B4782 " (cutoff:3.500A) Processing helix chain 'B' and resid 4787 through 4805 removed outlier: 4.008A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4808 through 4820 removed outlier: 5.096A pdb=" N HIS B4812 " --> pdb=" O PHE B4808 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU B4813 " --> pdb=" O PHE B4809 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU B4814 " --> pdb=" O ALA B4810 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP B4815 " --> pdb=" O ALA B4811 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE B4816 " --> pdb=" O HIS B4812 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ALA B4817 " --> pdb=" O LEU B4813 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) Processing helix chain 'B' and resid 4821 through 4832 removed outlier: 3.962A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 4.150A 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 4878 through 4893 removed outlier: 3.704A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) Processing helix chain 'B' and resid 4896 through 4901 removed outlier: 4.301A 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: 4.056A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (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: 3.813A pdb=" N HIS B5003 " --> pdb=" O ASP B4999 " (cutoff:3.500A) removed outlier: 6.153A 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 255 removed outlier: 4.316A pdb=" N CYS B 253 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 254 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS B 255 " --> pdb=" O VAL B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 250 through 255' Processing helix chain 'B' and resid 3296 through 3302 removed outlier: 4.251A pdb=" N ALA B3300 " --> pdb=" O PRO B3297 " (cutoff:3.500A) Proline residue: B3301 - end of helix Processing helix chain 'B' and resid 3152 through 3157 removed outlier: 4.112A 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: 3.752A pdb=" N CYS C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 303 through 308 removed outlier: 3.702A pdb=" N ALA C 307 " --> pdb=" O ASP C 303 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N HIS C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 308' Processing helix chain 'C' and resid 364 through 370 Processing helix chain 'C' and resid 394 through 423 removed outlier: 4.509A pdb=" N ARG C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N MET C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLY C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 453 removed outlier: 3.513A pdb=" N GLY C 450 " --> pdb=" O GLN C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 482 removed outlier: 3.653A pdb=" N GLN C 465 " --> pdb=" O HIS C 461 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SER C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 497 removed outlier: 3.708A pdb=" N VAL C 496 " --> pdb=" O ASP C 492 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR C 497 " --> pdb=" O ARG C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.683A pdb=" N TYR C 506 " --> pdb=" O HIS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 531 removed outlier: 3.720A pdb=" N GLU C 513 " --> pdb=" O GLU C 509 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLU C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN C 520 " --> pdb=" O LYS C 516 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR C 523 " --> pdb=" O VAL C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 541 removed outlier: 4.021A pdb=" N LEU C 539 " --> pdb=" O ALA C 535 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N PHE C 540 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER C 541 " --> pdb=" O CYS C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 552 removed outlier: 3.547A pdb=" N VAL C 547 " --> pdb=" O ASN C 543 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS C 550 " --> pdb=" O TRP C 546 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU C 551 " --> pdb=" O VAL C 547 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASP C 552 " --> pdb=" O VAL C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 571 removed outlier: 3.933A pdb=" N ILE C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU C 570 " --> pdb=" O CYS C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 578 removed outlier: 3.956A pdb=" N ASN C 576 " --> pdb=" O PRO C 572 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE C 577 " --> pdb=" O GLU C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 593 removed outlier: 3.800A pdb=" N LEU C 590 " --> pdb=" O ILE C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 609 removed outlier: 3.936A pdb=" N LEU C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL C 608 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N CYS C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 629 removed outlier: 3.633A 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: 4.622A pdb=" N ALA C 814 " --> pdb=" O PRO C 810 " (cutoff:3.500A) removed outlier: 4.564A 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: 3.831A pdb=" N PHE C 851 " --> pdb=" O SER C 847 " (cutoff:3.500A) removed outlier: 3.737A 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: 3.560A pdb=" N ILE C 870 " --> pdb=" O HIS C 866 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLU C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS C 873 " --> pdb=" O ARG C 869 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU C 874 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA C 875 " --> pdb=" O ARG C 871 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE C 878 " --> pdb=" O LEU C 874 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU C 880 " --> pdb=" O GLU C 876 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU C 881 " --> pdb=" O ASN C 877 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N TRP C 882 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA C 883 " --> pdb=" O HIS C 879 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR C 885 " --> pdb=" O LEU C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 914 removed outlier: 3.788A 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: 3.928A pdb=" N ASN C 949 " --> pdb=" O LYS C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 1004 removed outlier: 3.507A pdb=" N VAL C 995 " --> pdb=" O ASN C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1048 removed outlier: 4.096A pdb=" N SER C1038 " --> pdb=" O SER C1034 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C1039 " --> pdb=" O ASN C1035 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1073 removed outlier: 3.984A pdb=" N ARG C1071 " --> pdb=" O SER C1067 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL C1072 " --> pdb=" O ARG C1068 " (cutoff:3.500A) removed outlier: 4.937A 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: 6.592A pdb=" N GLU C1221 " --> pdb=" O CYS C1217 " (cutoff:3.500A) Processing helix chain 'C' and resid 1423 through 1430 removed outlier: 3.532A pdb=" N LEU C1428 " --> pdb=" O PRO C1424 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASN C1429 " --> pdb=" O GLU C1425 " (cutoff:3.500A) Processing helix chain 'C' and resid 1444 through 1449 removed outlier: 4.046A pdb=" N VAL C1448 " --> pdb=" O GLU C1444 " (cutoff:3.500A) removed outlier: 5.495A 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: 4.738A pdb=" N PHE C1500 " --> pdb=" O TRP C1496 " (cutoff:3.500A) removed outlier: 4.449A 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: 3.845A pdb=" N ALA C1578 " --> pdb=" O PRO C1574 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE C1580 " --> pdb=" O SER C1576 " (cutoff:3.500A) Processing helix chain 'C' and resid 1649 through 1657 removed outlier: 4.455A pdb=" N LEU C1653 " --> pdb=" O ASP C1649 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER C1654 " --> pdb=" O ILE C1650 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLU C1655 " --> pdb=" O LEU C1651 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU C1657 " --> pdb=" O LEU C1653 " (cutoff:3.500A) Processing helix chain 'C' and resid 1658 through 1675 removed outlier: 3.928A pdb=" N PHE C1662 " --> pdb=" O ASP C1658 " (cutoff:3.500A) Processing helix chain 'C' and resid 1678 through 1689 removed outlier: 3.921A pdb=" N ALA C1684 " --> pdb=" O ARG C1680 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N CYS C1686 " --> pdb=" O ALA C1682 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER C1687 " --> pdb=" O HIS C1683 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS C1688 " --> pdb=" O ALA C1684 " (cutoff:3.500A) Processing helix chain 'C' and resid 1690 through 1700 removed outlier: 3.721A 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 1721 through 1734 removed outlier: 3.670A pdb=" N SER C1726 " --> pdb=" O SER C1722 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER C1732 " --> pdb=" O ARG C1728 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLU C1733 " --> pdb=" O SER C1729 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR C1734 " --> pdb=" O MET C1730 " (cutoff:3.500A) Processing helix chain 'C' and resid 1739 through 1745 removed outlier: 3.676A pdb=" N ILE C1745 " --> pdb=" O GLU C1741 " (cutoff:3.500A) Processing helix chain 'C' and resid 1803 through 1825 removed outlier: 3.694A pdb=" N ASP C1809 " --> pdb=" O GLU C1805 " (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 1925 through 1930 removed outlier: 4.155A pdb=" N MET C1929 " --> pdb=" O GLY C1925 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LYS C1930 " --> pdb=" O LEU C1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1925 through 1930' Processing helix chain 'C' and resid 1934 through 1987 removed outlier: 3.706A pdb=" N GLN C1938 " --> pdb=" O SER C1934 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP C1967 " --> pdb=" O GLU C1963 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS C1968 " --> pdb=" O ARG C1964 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE C1984 " --> pdb=" O LEU C1980 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR C1985 " --> pdb=" O MET C1981 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N MET C1986 " --> pdb=" O ARG C1982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1990 through 2001 removed outlier: 4.398A pdb=" N ARG C1994 " --> pdb=" O GLU C1990 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU C1997 " --> pdb=" O ARG C1993 " (cutoff:3.500A) removed outlier: 4.758A 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: 3.680A pdb=" N ASN C2007 " --> pdb=" O GLN C2003 " (cutoff:3.500A) Processing helix chain 'C' and resid 2017 through 2022 removed outlier: 4.429A 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 removed outlier: 3.835A pdb=" N LEU C2039 " --> pdb=" O HIS C2035 " (cutoff:3.500A) Processing helix chain 'C' and resid 2093 through 2109 removed outlier: 3.770A pdb=" N SER C2099 " --> pdb=" O GLN C2095 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP C2109 " --> pdb=" O TRP C2105 " (cutoff:3.500A) Processing helix chain 'C' and resid 2113 through 2130 removed outlier: 3.975A pdb=" N GLY C2130 " --> pdb=" O ARG C2126 " (cutoff:3.500A) Processing helix chain 'C' and resid 2131 through 2142 Proline residue: C2139 - end of helix removed outlier: 5.411A pdb=" N TYR C2142 " --> pdb=" O LEU C2138 " (cutoff:3.500A) Processing helix chain 'C' and resid 2145 through 2169 removed outlier: 4.274A pdb=" N VAL C2149 " --> pdb=" O SER C2145 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLU C2150 " --> pdb=" O PRO C2146 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ASP C2151 " --> pdb=" O SER C2147 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N CYS C2158 " --> pdb=" O SER C2154 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE C2167 " --> pdb=" O ARG C2163 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL C2168 " --> pdb=" O SER C2164 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLN C2169 " --> pdb=" O LEU C2165 " (cutoff:3.500A) Processing helix chain 'C' and resid 2171 through 2189 removed outlier: 3.692A pdb=" N GLN C2180 " --> pdb=" O ASN C2176 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER C2181 " --> pdb=" O LEU C2177 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN C2188 " --> pdb=" O ASN C2184 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS C2189 " --> pdb=" O ILE C2185 " (cutoff:3.500A) Processing helix chain 'C' and resid 2194 through 2202 Processing helix chain 'C' and resid 2203 through 2219 removed outlier: 5.000A pdb=" N GLY C2218 " --> pdb=" O VAL C2214 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU C2219 " --> pdb=" O LEU C2215 " (cutoff:3.500A) Processing helix chain 'C' and resid 2225 through 2244 removed outlier: 3.582A pdb=" N SER C2231 " --> pdb=" O LYS C2227 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG C2241 " --> pdb=" O CYS C2237 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE C2242 " --> pdb=" O TYR C2238 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER C2243 " --> pdb=" O PHE C2239 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ARG C2244 " --> pdb=" O CYS C2240 " (cutoff:3.500A) Processing helix chain 'C' and resid 2245 through 2255 removed outlier: 4.030A pdb=" N HIS C2253 " --> pdb=" O SER C2249 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C2254 " --> pdb=" O MET C2250 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N SER C2255 " --> pdb=" O PHE C2251 " (cutoff:3.500A) Processing helix chain 'C' and resid 2256 through 2264 removed outlier: 3.788A pdb=" N ASN C2260 " --> pdb=" O TYR C2256 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE C2263 " --> pdb=" O GLU C2259 " (cutoff:3.500A) Processing helix chain 'C' and resid 2271 through 2281 removed outlier: 3.714A pdb=" N VAL C2275 " --> pdb=" O THR C2271 " (cutoff:3.500A) Processing helix chain 'C' and resid 2283 through 2290 Processing helix chain 'C' and resid 2291 through 2309 removed outlier: 3.594A pdb=" N LEU C2295 " --> pdb=" O GLN C2291 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C2297 " --> pdb=" O GLN C2293 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL C2298 " --> pdb=" O ASP C2294 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU C2307 " --> pdb=" O ALA C2303 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN C2308 " --> pdb=" O GLY C2304 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER C2309 " --> pdb=" O CYS C2305 " (cutoff:3.500A) Processing helix chain 'C' and resid 2310 through 2317 removed outlier: 3.523A pdb=" N GLY C2317 " --> pdb=" O LEU C2313 " (cutoff:3.500A) Processing helix chain 'C' and resid 2324 through 2340 removed outlier: 3.559A pdb=" N GLY C2328 " --> pdb=" O ASN C2324 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE C2334 " --> pdb=" O ARG C2330 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2361 Proline residue: C2361 - end of helix Processing helix chain 'C' and resid 2375 through 2390 removed outlier: 3.571A pdb=" N ALA C2379 " --> pdb=" O GLY C2375 " (cutoff:3.500A) removed outlier: 3.925A 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: 3.836A pdb=" N MET C2423 " --> pdb=" O GLY C2419 " (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: 4.143A pdb=" N LYS C2499 " --> pdb=" O VAL C2495 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU C2504 " --> pdb=" O ALA C2500 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE C2505 " --> pdb=" O SER C2501 " (cutoff:3.500A) Processing helix chain 'C' and resid 2514 through 2525 removed outlier: 3.509A pdb=" N VAL C2521 " --> pdb=" O PHE C2517 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL C2524 " --> pdb=" O HIS C2520 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY C2525 " --> pdb=" O VAL C2521 " (cutoff:3.500A) Processing helix chain 'C' and resid 2526 through 2538 removed outlier: 3.785A pdb=" N MET C2530 " --> pdb=" O PHE C2526 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N THR C2538 " --> pdb=" O ALA C2534 " (cutoff:3.500A) Processing helix chain 'C' and resid 2544 through 2566 removed outlier: 3.574A pdb=" N LEU C2548 " --> pdb=" O THR C2544 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA C2549 " --> pdb=" O GLU C2545 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU C2559 " --> pdb=" O CYS C2555 " (cutoff:3.500A) Proline residue: C2560 - end of helix Processing helix chain 'C' and resid 2567 through 2573 removed outlier: 5.394A pdb=" N GLY C2571 " --> pdb=" O PRO C2567 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N THR C2572 " --> pdb=" O LEU C2568 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLU C2573 " --> pdb=" O PHE C2569 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2567 through 2573' Processing helix chain 'C' and resid 2575 through 2592 Processing helix chain 'C' and resid 2596 through 2614 Processing helix chain 'C' and resid 2615 through 2630 removed outlier: 4.396A pdb=" N LEU C2619 " --> pdb=" O ARG C2615 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLN C2620 " --> pdb=" O PRO C2616 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N HIS C2621 " --> pdb=" O SER C2617 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU C2622 " --> pdb=" O MET C2618 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE C2628 " --> pdb=" O ARG C2624 " (cutoff:3.500A) Processing helix chain 'C' and resid 2634 through 2652 removed outlier: 3.832A pdb=" N LYS C2638 " --> pdb=" O ASN C2634 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N MET C2639 " --> pdb=" O GLU C2635 " (cutoff:3.500A) Proline residue: C2640 - end of helix Processing helix chain 'C' and resid 2669 through 2689 removed outlier: 4.645A pdb=" N HIS C2673 " --> pdb=" O GLU C2669 " (cutoff:3.500A) Processing helix chain 'C' and resid 2693 through 2711 removed outlier: 3.659A pdb=" N ARG C2697 " --> pdb=" O GLN C2693 " (cutoff:3.500A) Proline residue: C2701 - end of helix Proline residue: C2711 - end of helix Processing helix chain 'C' and resid 2751 through 2774 removed outlier: 3.885A pdb=" N LYS C2757 " --> pdb=" O SER C2753 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N HIS C2763 " --> pdb=" O ALA C2759 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN C2774 " --> pdb=" O LYS C2770 " (cutoff:3.500A) Processing helix chain 'C' and resid 2799 through 2819 removed outlier: 3.801A pdb=" N GLU C2803 " --> pdb=" O GLU C2799 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE C2804 " --> pdb=" O LYS C2800 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG C2806 " --> pdb=" O LYS C2802 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N TRP C2807 " --> pdb=" O GLU C2803 " (cutoff:3.500A) Proline residue: C2808 - end of helix removed outlier: 4.108A pdb=" N TRP C2819 " --> pdb=" O ALA C2815 " (cutoff:3.500A) Processing helix chain 'C' and resid 2868 through 2895 removed outlier: 3.592A pdb=" N THR C2885 " --> pdb=" O ASN C2881 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C2893 " --> pdb=" O LYS C2889 " (cutoff:3.500A) Processing helix chain 'C' and resid 2912 through 2934 removed outlier: 5.561A pdb=" N ARG C2918 " --> pdb=" O LYS C2914 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ASP C2919 " --> pdb=" O GLU C2915 " (cutoff:3.500A) Processing helix chain 'C' and resid 2949 through 2954 removed outlier: 3.623A pdb=" N ARG C2954 " --> pdb=" O SER C2950 " (cutoff:3.500A) Processing helix chain 'C' and resid 2955 through 2983 removed outlier: 3.927A pdb=" N ILE C2969 " --> pdb=" O ARG C2965 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU C2972 " --> pdb=" O ASP C2968 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE C2973 " --> pdb=" O ILE C2969 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE C2974 " --> pdb=" O SER C2970 " (cutoff:3.500A) Processing helix chain 'C' and resid 2991 through 3014 removed outlier: 3.784A pdb=" N LEU C3002 " --> pdb=" O PHE C2998 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU C3003 " --> pdb=" O ALA C2999 " (cutoff:3.500A) Proline residue: C3004 - end of helix removed outlier: 3.548A pdb=" N THR C3011 " --> pdb=" O ASN C3007 " (cutoff:3.500A) Processing helix chain 'C' and resid 3032 through 3051 removed outlier: 3.505A pdb=" N ALA C3048 " --> pdb=" O CYS C3044 " (cutoff:3.500A) Processing helix 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 Processing helix chain 'C' and resid 3085 through 3112 removed outlier: 3.934A pdb=" N GLU C3108 " --> pdb=" O GLU C3104 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN C3109 " --> pdb=" O LYS C3105 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU C3112 " --> pdb=" O GLU C3108 " (cutoff:3.500A) Processing helix chain 'C' and resid 3123 through 3151 removed outlier: 3.758A pdb=" N GLN C3127 " --> pdb=" O LYS C3123 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LEU C3137 " --> pdb=" O THR C3133 " (cutoff:3.500A) Proline residue: C3138 - end of helix removed outlier: 3.617A pdb=" N HIS C3150 " --> pdb=" O HIS C3146 " (cutoff:3.500A) Processing helix chain 'C' and resid 3159 through 3176 removed outlier: 4.257A pdb=" N VAL C3163 " --> pdb=" O ASP C3159 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C3174 " --> pdb=" O CYS C3170 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU C3175 " --> pdb=" O SER C3171 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLY C3176 " --> pdb=" O ILE C3172 " (cutoff:3.500A) Processing helix chain 'C' and resid 3180 through 3201 Proline residue: C3188 - end of helix removed outlier: 3.625A pdb=" N ALA C3200 " --> pdb=" O ARG C3196 " (cutoff:3.500A) Processing helix chain 'C' and resid 3207 through 3212 removed outlier: 4.491A pdb=" N GLU C3212 " --> pdb=" O PRO C3208 " (cutoff:3.500A) Processing helix chain 'C' and resid 3217 through 3222 Processing helix chain 'C' and resid 3226 through 3231 removed outlier: 7.368A pdb=" N LEU C3230 " --> pdb=" O GLU C3226 " (cutoff:3.500A) removed outlier: 5.917A 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 3240 removed outlier: 3.658A pdb=" N MET C3239 " --> pdb=" O SER C3235 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N CYS C3240 " --> pdb=" O VAL C3236 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3235 through 3240' Processing helix chain 'C' and resid 3245 through 3260 removed outlier: 3.539A pdb=" N LEU C3249 " --> pdb=" O VAL C3245 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY C3260 " --> pdb=" O LEU C3256 " (cutoff:3.500A) Processing helix chain 'C' and resid 3262 through 3267 Proline residue: C3267 - end of helix Processing helix chain 'C' and resid 3268 through 3285 removed outlier: 4.427A pdb=" N LEU C3274 " --> pdb=" O ILE C3270 " (cutoff:3.500A) Proline residue: C3275 - end of helix Proline residue: C3282 - end of helix Processing helix chain 'C' and resid 3308 through 3328 removed outlier: 3.927A pdb=" N LEU C3312 " --> pdb=" O THR C3308 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU C3327 " --> pdb=" O ILE C3323 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLY C3328 " --> pdb=" O VAL C3324 " (cutoff:3.500A) Processing helix chain 'C' and resid 3332 through 3347 removed outlier: 5.303A pdb=" N LYS C3336 " --> pdb=" O ALA C3332 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ARG C3337 " --> pdb=" O THR C3333 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C3340 " --> pdb=" O LYS C3336 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C3341 " --> pdb=" O ARG C3337 " (cutoff:3.500A) Proline residue: C3344 - end of helix removed outlier: 5.122A pdb=" N SER C3347 " --> pdb=" O GLN C3343 " (cutoff:3.500A) Processing helix chain 'C' and resid 3350 through 3383 removed outlier: 4.818A pdb=" N LEU C3354 " --> pdb=" O ARG C3350 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N HIS C3355 " --> pdb=" O PRO C3351 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE C3359 " --> pdb=" O HIS C3355 " (cutoff:3.500A) Proline residue: C3360 - end of helix removed outlier: 3.678A pdb=" N GLU C3382 " --> pdb=" O GLN C3378 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA C3383 " --> pdb=" O LEU C3379 " (cutoff:3.500A) Processing helix chain 'C' and resid 3389 through 3413 removed outlier: 6.670A pdb=" N LEU C3393 " --> pdb=" O GLU C3389 " (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 3449 removed outlier: 3.749A pdb=" N GLU C3433 " --> pdb=" O ALA C3429 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C3434 " --> pdb=" O ASN C3430 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N HIS C3449 " --> pdb=" O TRP C3445 " (cutoff:3.500A) Processing helix chain 'C' and resid 3450 through 3463 removed outlier: 3.649A pdb=" N GLN C3456 " --> pdb=" O LYS C3452 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN C3457 " --> pdb=" O ARG C3453 " (cutoff:3.500A) Processing helix chain 'C' and resid 3465 through 3478 removed outlier: 6.737A pdb=" N PHE C3469 " --> pdb=" O ASN C3465 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU C3470 " --> pdb=" O ASN C3466 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASP C3473 " --> pdb=" O PHE C3469 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N SER C3474 " --> pdb=" O LEU C3470 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET C3478 " --> pdb=" O SER C3474 " (cutoff:3.500A) Processing helix chain 'C' and resid 3508 through 3526 removed outlier: 3.744A pdb=" N MET C3517 " --> pdb=" O THR C3513 " (cutoff:3.500A) Proline residue: C3519 - end of helix removed outlier: 3.628A pdb=" N CYS C3525 " --> pdb=" O GLY C3521 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ALA C3526 " --> pdb=" O LEU C3522 " (cutoff:3.500A) Processing helix chain 'C' and resid 3529 through 3543 Processing helix chain 'C' and resid 3545 through 3557 removed outlier: 3.559A pdb=" N ARG C3550 " --> pdb=" O ASP C3546 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C3551 " --> pdb=" O GLU C3547 " (cutoff:3.500A) Processing helix chain 'C' and resid 3562 through 3567 removed outlier: 4.113A pdb=" N SER C3566 " --> pdb=" O LYS C3562 " (cutoff:3.500A) Proline residue: C3567 - end of helix No H-bonds generated for 'chain 'C' and resid 3562 through 3567' Processing helix chain 'C' and resid 3568 through 3579 Processing helix chain 'C' and resid 3588 through 3612 removed outlier: 3.585A pdb=" N VAL C3593 " --> pdb=" O PRO C3589 " (cutoff:3.500A) Proline residue: C3612 - end of helix Processing helix chain 'C' and resid 3628 through 3638 removed outlier: 4.503A pdb=" N VAL C3632 " --> pdb=" O ARG C3628 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL C3633 " --> pdb=" O ARG C3629 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE C3636 " --> pdb=" O VAL C3632 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG C3637 " --> pdb=" O VAL C3633 " (cutoff:3.500A) Processing helix chain 'C' and resid 3640 through 3645 removed outlier: 3.749A pdb=" N LEU C3644 " --> pdb=" O PRO C3640 " (cutoff:3.500A) Proline residue: C3645 - end of helix No H-bonds generated for 'chain 'C' and resid 3640 through 3645' Processing helix chain 'C' and resid 3646 through 3665 removed outlier: 3.629A pdb=" N GLU C3655 " --> pdb=" O ASN C3651 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU C3663 " --> pdb=" O ALA C3659 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N THR C3664 " --> pdb=" O ALA C3660 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU C3665 " --> pdb=" O TRP C3661 " (cutoff:3.500A) Processing helix chain 'C' and resid 3669 through 3679 removed outlier: 3.644A pdb=" N LYS C3679 " --> pdb=" O ASP C3675 " (cutoff:3.500A) Processing helix chain 'C' and resid 3696 through 3711 Processing helix chain 'C' and resid 3719 through 3735 removed outlier: 3.830A pdb=" N CYS C3733 " --> pdb=" O MET C3729 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N HIS C3734 " --> pdb=" O ALA C3730 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU C3735 " --> pdb=" O LYS C3731 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3772 removed outlier: 3.685A pdb=" N LYS C3756 " --> pdb=" O SER C3752 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU C3757 " --> pdb=" O PHE C3753 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET C3758 " --> pdb=" O GLU C3754 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN C3761 " --> pdb=" O GLU C3757 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU C3770 " --> pdb=" O GLN C3766 " (cutoff:3.500A) Processing helix chain 'C' and resid 3774 through 3787 removed outlier: 4.296A 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 3826 through 3839 Processing helix chain 'C' and resid 3843 through 3857 removed outlier: 3.656A pdb=" N GLU C3854 " --> pdb=" O GLN C3850 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C3855 " --> pdb=" O ASN C3851 " (cutoff:3.500A) Processing helix chain 'C' and resid 3877 through 3893 removed outlier: 3.549A 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: 3.614A pdb=" N TYR C3937 " --> pdb=" O PHE C3933 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLY C3939 " --> pdb=" O TRP C3935 " (cutoff:3.500A) Processing helix chain 'C' and resid 3944 through 3970 removed outlier: 3.636A 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: 3.958A pdb=" N ALA C3988 " --> pdb=" O ARG C3984 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS C3998 " --> pdb=" O HIS C3994 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN C4005 " --> pdb=" O MET C4001 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP C4006 " --> pdb=" O LYS C4002 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER C4007 " --> pdb=" O LEU C4003 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4032 Processing helix chain 'C' and resid 4038 through 4052 Processing helix chain 'C' and resid 4053 through 4072 removed outlier: 3.748A pdb=" N MET C4064 " --> pdb=" O LYS C4060 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE C4065 " --> pdb=" O PHE C4061 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C4068 " --> pdb=" O MET C4064 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP C4070 " --> pdb=" O LEU C4066 " (cutoff:3.500A) Processing helix chain 'C' and resid 4074 through 4082 removed outlier: 3.853A pdb=" N TYR C4080 " --> pdb=" O ALA C4076 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N THR C4082 " --> pdb=" O GLN C4078 " (cutoff:3.500A) Processing helix chain 'C' and resid 4089 through 4101 removed outlier: 4.154A pdb=" N ASP C4098 " --> pdb=" O GLN C4094 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N SER C4099 " --> pdb=" O LYS C4095 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN C4100 " --> pdb=" O ALA C4096 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS C4101 " --> pdb=" O MET C4097 " (cutoff:3.500A) Processing helix chain 'C' and resid 4104 through 4116 removed outlier: 5.495A pdb=" N GLU C4116 " --> pdb=" O LEU C4112 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4155 removed outlier: 4.192A pdb=" N PHE C4128 " --> pdb=" O ASN C4124 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA C4129 " --> pdb=" O PHE C4125 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASN C4130 " --> pdb=" O GLU C4126 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N PHE C4132 " --> pdb=" O PHE C4128 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN C4133 " --> pdb=" O ALA C4129 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLU C4134 " --> pdb=" O ASN C4130 " (cutoff:3.500A) Proline residue: C4135 - end of helix removed outlier: 4.215A pdb=" N ASP C4138 " --> pdb=" O GLU C4134 " (cutoff:3.500A) removed outlier: 3.796A 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: 3.580A pdb=" N ASN C4162 " --> pdb=" O PRO C4158 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE C4163 " --> pdb=" O ARG C4159 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU C4164 " --> pdb=" O LEU C4160 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU C4165 " --> pdb=" O ARG C4161 " (cutoff:3.500A) Processing helix chain 'C' and resid 4169 through 4175 Processing helix chain 'C' and resid 4198 through 4208 Proline residue: C4208 - end of helix Processing helix chain 'C' and resid 4209 through 4224 Processing helix chain 'C' and resid 4226 through 4252 removed outlier: 4.500A pdb=" N MET C4231 " --> pdb=" O GLU C4227 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLU C4232 " --> pdb=" O ALA C4228 " (cutoff:3.500A) Processing helix chain 'C' and resid 4542 through 4559 Processing helix chain 'C' and resid 4560 through 4580 removed outlier: 3.919A pdb=" N LEU C4567 " --> pdb=" O ARG C4563 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE C4579 " --> pdb=" O PHE C4575 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TYR C4580 " --> pdb=" O ILE C4576 " (cutoff:3.500A) Processing helix chain 'C' and resid 4640 through 4683 removed outlier: 4.035A 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 4709 removed outlier: 3.601A pdb=" N ARG C4703 " --> pdb=" O GLY C4699 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU C4704 " --> pdb=" O GLN C4700 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL C4705 " --> pdb=" O TRP C4701 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU C4706 " --> pdb=" O ASP C4702 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASN C4707 " --> pdb=" O ARG C4703 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR C4708 " --> pdb=" O LEU C4704 " (cutoff:3.500A) Proline residue: C4709 - end of helix 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 4749 Processing helix chain 'C' and resid 4772 through 4786 removed outlier: 3.508A pdb=" N ASP C4786 " --> pdb=" O VAL C4782 " (cutoff:3.500A) Processing helix chain 'C' and resid 4787 through 4805 removed outlier: 4.008A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4808 through 4820 removed outlier: 5.096A pdb=" N HIS C4812 " --> pdb=" O PHE C4808 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU C4813 " --> pdb=" O PHE C4809 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU C4814 " --> pdb=" O ALA C4810 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP C4815 " --> pdb=" O ALA C4811 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE C4816 " --> pdb=" O HIS C4812 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ALA C4817 " --> pdb=" O LEU C4813 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET C4818 " --> pdb=" O LEU C4814 " (cutoff:3.500A) Processing helix chain 'C' and resid 4821 through 4832 removed outlier: 3.962A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 4.149A 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 4878 through 4893 removed outlier: 3.703A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) Processing helix chain 'C' and resid 4896 through 4901 removed outlier: 4.302A 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: 4.056A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (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: 3.812A pdb=" N HIS C5003 " --> pdb=" O ASP C4999 " (cutoff:3.500A) removed outlier: 6.154A 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 255 removed outlier: 4.317A pdb=" N CYS C 253 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR C 254 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS C 255 " --> pdb=" O VAL C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 255' Processing helix chain 'C' and resid 3296 through 3302 removed outlier: 4.251A pdb=" N ALA C3300 " --> pdb=" O PRO C3297 " (cutoff:3.500A) Proline residue: C3301 - end of helix Processing helix chain 'C' and resid 3152 through 3157 removed outlier: 4.112A 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: 3.753A pdb=" N CYS D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 303 through 308 removed outlier: 3.702A pdb=" N ALA D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N HIS D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 303 through 308' Processing helix chain 'D' and resid 364 through 370 Processing helix chain 'D' and resid 394 through 423 removed outlier: 4.510A pdb=" N ARG D 402 " --> pdb=" O SER D 398 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N MET D 403 " --> pdb=" O GLN D 399 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLY D 423 " --> pdb=" O ASP D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 453 removed outlier: 3.513A pdb=" N GLY D 450 " --> pdb=" O GLN D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 482 removed outlier: 3.654A pdb=" N GLN D 465 " --> pdb=" O HIS D 461 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SER D 466 " --> pdb=" O GLU D 462 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS D 467 " --> pdb=" O GLU D 463 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 497 removed outlier: 3.707A pdb=" N VAL D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR D 497 " --> pdb=" O ARG D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.683A pdb=" N TYR D 506 " --> pdb=" O HIS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 531 removed outlier: 3.720A pdb=" N GLU D 513 " --> pdb=" O GLU D 509 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER D 514 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN D 520 " --> pdb=" O LYS D 516 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR D 523 " --> pdb=" O VAL D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 541 removed outlier: 4.021A pdb=" N LEU D 539 " --> pdb=" O ALA D 535 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N PHE D 540 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER D 541 " --> pdb=" O CYS D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 552 removed outlier: 3.547A pdb=" N VAL D 547 " --> pdb=" O ASN D 543 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS D 550 " --> pdb=" O TRP D 546 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU D 551 " --> pdb=" O VAL D 547 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASP D 552 " --> pdb=" O VAL D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 571 removed outlier: 3.933A pdb=" N ILE D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU D 570 " --> pdb=" O CYS D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 578 removed outlier: 3.956A pdb=" N ASN D 576 " --> pdb=" O PRO D 572 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE D 577 " --> pdb=" O GLU D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 593 removed outlier: 3.800A pdb=" N LEU D 590 " --> pdb=" O ILE D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 609 removed outlier: 3.936A pdb=" N LEU D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL D 608 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N CYS D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 629 removed outlier: 3.633A 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: 4.622A pdb=" N ALA D 814 " --> pdb=" O PRO D 810 " (cutoff:3.500A) removed outlier: 4.564A 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: 3.832A pdb=" N PHE D 851 " --> pdb=" O SER D 847 " (cutoff:3.500A) removed outlier: 3.736A 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: 3.561A pdb=" N ILE D 870 " --> pdb=" O HIS D 866 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLU D 872 " --> pdb=" O GLU D 868 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS D 873 " --> pdb=" O ARG D 869 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU D 874 " --> pdb=" O ILE D 870 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA D 875 " --> pdb=" O ARG D 871 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE D 878 " --> pdb=" O LEU D 874 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU D 880 " --> pdb=" O GLU D 876 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU D 881 " --> pdb=" O ASN D 877 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N TRP D 882 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ALA D 883 " --> pdb=" O HIS D 879 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR D 885 " --> pdb=" O LEU D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 909 through 914 removed outlier: 3.788A 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: 3.928A pdb=" N ASN D 949 " --> pdb=" O LYS D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 1004 removed outlier: 3.507A pdb=" N VAL D 995 " --> pdb=" O ASN D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1030 through 1048 removed outlier: 4.096A pdb=" N SER D1038 " --> pdb=" O SER D1034 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU D1039 " --> pdb=" O ASN D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1067 through 1073 removed outlier: 3.984A pdb=" N ARG D1071 " --> pdb=" O SER D1067 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL D1072 " --> pdb=" O ARG D1068 " (cutoff:3.500A) removed outlier: 4.937A 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: 6.592A pdb=" N GLU D1221 " --> pdb=" O CYS D1217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1423 through 1430 removed outlier: 3.532A pdb=" N LEU D1428 " --> pdb=" O PRO D1424 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASN D1429 " --> pdb=" O GLU D1425 " (cutoff:3.500A) Processing helix chain 'D' and resid 1444 through 1449 removed outlier: 4.046A pdb=" N VAL D1448 " --> pdb=" O GLU D1444 " (cutoff:3.500A) removed outlier: 5.495A 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: 4.740A pdb=" N PHE D1500 " --> pdb=" O TRP D1496 " (cutoff:3.500A) removed outlier: 4.449A 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: 3.845A pdb=" N ALA D1578 " --> pdb=" O PRO D1574 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE D1580 " --> pdb=" O SER D1576 " (cutoff:3.500A) Processing helix chain 'D' and resid 1649 through 1657 removed outlier: 4.455A pdb=" N LEU D1653 " --> pdb=" O ASP D1649 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER D1654 " --> pdb=" O ILE D1650 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLU D1655 " --> pdb=" O LEU D1651 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU D1657 " --> pdb=" O LEU D1653 " (cutoff:3.500A) Processing helix chain 'D' and resid 1658 through 1675 removed outlier: 3.927A pdb=" N PHE D1662 " --> pdb=" O ASP D1658 " (cutoff:3.500A) Processing helix chain 'D' and resid 1678 through 1689 removed outlier: 3.921A pdb=" N ALA D1684 " --> pdb=" O ARG D1680 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N CYS D1686 " --> pdb=" O ALA D1682 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER D1687 " --> pdb=" O HIS D1683 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS D1688 " --> pdb=" O ALA D1684 " (cutoff:3.500A) Processing helix chain 'D' and resid 1690 through 1700 removed outlier: 3.720A 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 1721 through 1734 removed outlier: 3.670A pdb=" N SER D1726 " --> pdb=" O SER D1722 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER D1732 " --> pdb=" O ARG D1728 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU D1733 " --> pdb=" O SER D1729 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR D1734 " --> pdb=" O MET D1730 " (cutoff:3.500A) Processing helix chain 'D' and resid 1739 through 1745 removed outlier: 3.676A pdb=" N ILE D1745 " --> pdb=" O GLU D1741 " (cutoff:3.500A) Processing helix chain 'D' and resid 1803 through 1825 removed outlier: 3.694A pdb=" N ASP D1809 " --> pdb=" O GLU D1805 " (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 1925 through 1930 removed outlier: 4.155A pdb=" N MET D1929 " --> pdb=" O GLY D1925 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LYS D1930 " --> pdb=" O LEU D1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1925 through 1930' Processing helix chain 'D' and resid 1934 through 1987 removed outlier: 3.706A pdb=" N GLN D1938 " --> pdb=" O SER D1934 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP D1967 " --> pdb=" O GLU D1963 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS D1968 " --> pdb=" O ARG D1964 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE D1984 " --> pdb=" O LEU D1980 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR D1985 " --> pdb=" O MET D1981 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N MET D1986 " --> pdb=" O ARG D1982 " (cutoff:3.500A) Processing helix chain 'D' and resid 1990 through 2001 removed outlier: 4.398A pdb=" N ARG D1994 " --> pdb=" O GLU D1990 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU D1997 " --> pdb=" O ARG D1993 " (cutoff:3.500A) removed outlier: 4.758A 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: 3.680A pdb=" N ASN D2007 " --> pdb=" O GLN D2003 " (cutoff:3.500A) Processing helix chain 'D' and resid 2017 through 2022 removed outlier: 4.429A 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 removed outlier: 3.835A pdb=" N LEU D2039 " --> pdb=" O HIS D2035 " (cutoff:3.500A) Processing helix chain 'D' and resid 2093 through 2109 removed outlier: 3.769A pdb=" N SER D2099 " --> pdb=" O GLN D2095 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP D2109 " --> pdb=" O TRP D2105 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2130 removed outlier: 3.975A pdb=" N GLY D2130 " --> pdb=" O ARG D2126 " (cutoff:3.500A) Processing helix chain 'D' and resid 2131 through 2142 Proline residue: D2139 - end of helix removed outlier: 5.411A pdb=" N TYR D2142 " --> pdb=" O LEU D2138 " (cutoff:3.500A) Processing helix chain 'D' and resid 2145 through 2169 removed outlier: 4.274A pdb=" N VAL D2149 " --> pdb=" O SER D2145 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLU D2150 " --> pdb=" O PRO D2146 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ASP D2151 " --> pdb=" O SER D2147 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N CYS D2158 " --> pdb=" O SER D2154 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE D2167 " --> pdb=" O ARG D2163 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL D2168 " --> pdb=" O SER D2164 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLN D2169 " --> pdb=" O LEU D2165 " (cutoff:3.500A) Processing helix chain 'D' and resid 2171 through 2189 removed outlier: 3.693A pdb=" N GLN D2180 " --> pdb=" O ASN D2176 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER D2181 " --> pdb=" O LEU D2177 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN D2188 " --> pdb=" O ASN D2184 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS D2189 " --> pdb=" O ILE D2185 " (cutoff:3.500A) Processing helix chain 'D' and resid 2194 through 2202 Processing helix chain 'D' and resid 2203 through 2219 removed outlier: 5.000A pdb=" N GLY D2218 " --> pdb=" O VAL D2214 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU D2219 " --> pdb=" O LEU D2215 " (cutoff:3.500A) Processing helix chain 'D' and resid 2225 through 2244 removed outlier: 3.582A pdb=" N SER D2231 " --> pdb=" O LYS D2227 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG D2241 " --> pdb=" O CYS D2237 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE D2242 " --> pdb=" O TYR D2238 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER D2243 " --> pdb=" O PHE D2239 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ARG D2244 " --> pdb=" O CYS D2240 " (cutoff:3.500A) Processing helix chain 'D' and resid 2245 through 2255 removed outlier: 4.029A pdb=" N HIS D2253 " --> pdb=" O SER D2249 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D2254 " --> pdb=" O MET D2250 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N SER D2255 " --> pdb=" O PHE D2251 " (cutoff:3.500A) Processing helix chain 'D' and resid 2256 through 2264 removed outlier: 3.788A pdb=" N ASN D2260 " --> pdb=" O TYR D2256 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE D2263 " --> pdb=" O GLU D2259 " (cutoff:3.500A) Processing helix chain 'D' and resid 2271 through 2281 removed outlier: 3.714A pdb=" N VAL D2275 " --> pdb=" O THR D2271 " (cutoff:3.500A) Processing helix chain 'D' and resid 2283 through 2290 Processing helix chain 'D' and resid 2291 through 2309 removed outlier: 3.594A pdb=" N LEU D2295 " --> pdb=" O GLN D2291 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS D2297 " --> pdb=" O GLN D2293 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL D2298 " --> pdb=" O ASP D2294 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU D2307 " --> pdb=" O ALA D2303 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN D2308 " --> pdb=" O GLY D2304 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER D2309 " --> pdb=" O CYS D2305 " (cutoff:3.500A) Processing helix chain 'D' and resid 2310 through 2317 removed outlier: 3.523A pdb=" N GLY D2317 " --> pdb=" O LEU D2313 " (cutoff:3.500A) Processing helix chain 'D' and resid 2324 through 2340 removed outlier: 3.559A pdb=" N GLY D2328 " --> pdb=" O ASN D2324 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE D2334 " --> pdb=" O ARG D2330 " (cutoff:3.500A) Processing helix chain 'D' and resid 2346 through 2361 Proline residue: D2361 - end of helix Processing helix chain 'D' and resid 2375 through 2390 removed outlier: 3.571A pdb=" N ALA D2379 " --> pdb=" O GLY D2375 " (cutoff:3.500A) removed outlier: 3.925A 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: 3.836A pdb=" N MET D2423 " --> pdb=" O GLY D2419 " (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: 4.143A pdb=" N LYS D2499 " --> pdb=" O VAL D2495 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D2504 " --> pdb=" O ALA D2500 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE D2505 " --> pdb=" O SER D2501 " (cutoff:3.500A) Processing helix chain 'D' and resid 2514 through 2525 removed outlier: 3.509A pdb=" N VAL D2521 " --> pdb=" O PHE D2517 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL D2524 " --> pdb=" O HIS D2520 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY D2525 " --> pdb=" O VAL D2521 " (cutoff:3.500A) Processing helix chain 'D' and resid 2526 through 2538 removed outlier: 3.785A pdb=" N MET D2530 " --> pdb=" O PHE D2526 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N THR D2538 " --> pdb=" O ALA D2534 " (cutoff:3.500A) Processing helix chain 'D' and resid 2544 through 2566 removed outlier: 3.574A pdb=" N LEU D2548 " --> pdb=" O THR D2544 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA D2549 " --> pdb=" O GLU D2545 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU D2559 " --> pdb=" O CYS D2555 " (cutoff:3.500A) Proline residue: D2560 - end of helix Processing helix chain 'D' and resid 2567 through 2573 removed outlier: 5.394A pdb=" N GLY D2571 " --> pdb=" O PRO D2567 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N THR D2572 " --> pdb=" O LEU D2568 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLU D2573 " --> pdb=" O PHE D2569 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2567 through 2573' Processing helix chain 'D' and resid 2575 through 2592 Processing helix chain 'D' and resid 2596 through 2614 Processing helix chain 'D' and resid 2615 through 2630 removed outlier: 4.397A pdb=" N LEU D2619 " --> pdb=" O ARG D2615 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLN D2620 " --> pdb=" O PRO D2616 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N HIS D2621 " --> pdb=" O SER D2617 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU D2622 " --> pdb=" O MET D2618 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE D2628 " --> pdb=" O ARG D2624 " (cutoff:3.500A) Processing helix chain 'D' and resid 2634 through 2652 removed outlier: 3.833A pdb=" N LYS D2638 " --> pdb=" O ASN D2634 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N MET D2639 " --> pdb=" O GLU D2635 " (cutoff:3.500A) Proline residue: D2640 - end of helix Processing helix chain 'D' and resid 2669 through 2689 removed outlier: 4.645A pdb=" N HIS D2673 " --> pdb=" O GLU D2669 " (cutoff:3.500A) Processing helix chain 'D' and resid 2693 through 2711 removed outlier: 3.659A pdb=" N ARG D2697 " --> pdb=" O GLN D2693 " (cutoff:3.500A) Proline residue: D2701 - end of helix Proline residue: D2711 - end of helix Processing helix chain 'D' and resid 2751 through 2774 removed outlier: 3.885A pdb=" N LYS D2757 " --> pdb=" O SER D2753 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N HIS D2763 " --> pdb=" O ALA D2759 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN D2774 " --> pdb=" O LYS D2770 " (cutoff:3.500A) Processing helix chain 'D' and resid 2799 through 2819 removed outlier: 3.802A pdb=" N GLU D2803 " --> pdb=" O GLU D2799 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE D2804 " --> pdb=" O LYS D2800 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG D2806 " --> pdb=" O LYS D2802 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N TRP D2807 " --> pdb=" O GLU D2803 " (cutoff:3.500A) Proline residue: D2808 - end of helix removed outlier: 4.109A pdb=" N TRP D2819 " --> pdb=" O ALA D2815 " (cutoff:3.500A) Processing helix chain 'D' and resid 2868 through 2895 removed outlier: 3.592A pdb=" N THR D2885 " --> pdb=" O ASN D2881 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU D2893 " --> pdb=" O LYS D2889 " (cutoff:3.500A) Processing helix chain 'D' and resid 2912 through 2934 removed outlier: 5.561A pdb=" N ARG D2918 " --> pdb=" O LYS D2914 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ASP D2919 " --> pdb=" O GLU D2915 " (cutoff:3.500A) Processing helix chain 'D' and resid 2949 through 2954 removed outlier: 3.622A pdb=" N ARG D2954 " --> pdb=" O SER D2950 " (cutoff:3.500A) Processing helix chain 'D' and resid 2955 through 2983 removed outlier: 3.927A pdb=" N ILE D2969 " --> pdb=" O ARG D2965 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU D2972 " --> pdb=" O ASP D2968 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE D2973 " --> pdb=" O ILE D2969 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE D2974 " --> pdb=" O SER D2970 " (cutoff:3.500A) Processing helix chain 'D' and resid 2991 through 3014 removed outlier: 3.784A pdb=" N LEU D3002 " --> pdb=" O PHE D2998 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU D3003 " --> pdb=" O ALA D2999 " (cutoff:3.500A) Proline residue: D3004 - end of helix removed outlier: 3.547A pdb=" N THR D3011 " --> pdb=" O ASN D3007 " (cutoff:3.500A) Processing helix chain 'D' and resid 3032 through 3051 removed outlier: 3.505A pdb=" N ALA D3048 " --> pdb=" O CYS D3044 " (cutoff:3.500A) Processing helix 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 Processing helix chain 'D' and resid 3085 through 3112 removed outlier: 3.933A pdb=" N GLU D3108 " --> pdb=" O GLU D3104 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN D3109 " --> pdb=" O LYS D3105 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU D3112 " --> pdb=" O GLU D3108 " (cutoff:3.500A) Processing helix chain 'D' and resid 3123 through 3151 removed outlier: 3.758A pdb=" N GLN D3127 " --> pdb=" O LYS D3123 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LEU D3137 " --> pdb=" O THR D3133 " (cutoff:3.500A) Proline residue: D3138 - end of helix removed outlier: 3.617A pdb=" N HIS D3150 " --> pdb=" O HIS D3146 " (cutoff:3.500A) Processing helix chain 'D' and resid 3159 through 3176 removed outlier: 4.256A pdb=" N VAL D3163 " --> pdb=" O ASP D3159 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER D3174 " --> pdb=" O CYS D3170 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU D3175 " --> pdb=" O SER D3171 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLY D3176 " --> pdb=" O ILE D3172 " (cutoff:3.500A) Processing helix chain 'D' and resid 3180 through 3201 Proline residue: D3188 - end of helix removed outlier: 3.624A pdb=" N ALA D3200 " --> pdb=" O ARG D3196 " (cutoff:3.500A) Processing helix chain 'D' and resid 3207 through 3212 removed outlier: 4.491A pdb=" N GLU D3212 " --> pdb=" O PRO D3208 " (cutoff:3.500A) Processing helix chain 'D' and resid 3217 through 3222 Processing helix chain 'D' and resid 3226 through 3231 removed outlier: 7.367A pdb=" N LEU D3230 " --> pdb=" O GLU D3226 " (cutoff:3.500A) removed outlier: 5.917A 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 3240 removed outlier: 3.658A pdb=" N MET D3239 " --> pdb=" O SER D3235 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N CYS D3240 " --> pdb=" O VAL D3236 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3235 through 3240' Processing helix chain 'D' and resid 3245 through 3260 removed outlier: 3.538A pdb=" N LEU D3249 " --> pdb=" O VAL D3245 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY D3260 " --> pdb=" O LEU D3256 " (cutoff:3.500A) Processing helix chain 'D' and resid 3262 through 3267 Proline residue: D3267 - end of helix Processing helix chain 'D' and resid 3268 through 3285 removed outlier: 4.427A pdb=" N LEU D3274 " --> pdb=" O ILE D3270 " (cutoff:3.500A) Proline residue: D3275 - end of helix Proline residue: D3282 - end of helix Processing helix chain 'D' and resid 3308 through 3328 removed outlier: 3.926A pdb=" N LEU D3312 " --> pdb=" O THR D3308 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU D3327 " --> pdb=" O ILE D3323 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLY D3328 " --> pdb=" O VAL D3324 " (cutoff:3.500A) Processing helix chain 'D' and resid 3332 through 3347 removed outlier: 5.303A pdb=" N LYS D3336 " --> pdb=" O ALA D3332 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ARG D3337 " --> pdb=" O THR D3333 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL D3340 " --> pdb=" O LYS D3336 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE D3341 " --> pdb=" O ARG D3337 " (cutoff:3.500A) Proline residue: D3344 - end of helix removed outlier: 5.121A pdb=" N SER D3347 " --> pdb=" O GLN D3343 " (cutoff:3.500A) Processing helix chain 'D' and resid 3350 through 3383 removed outlier: 4.818A pdb=" N LEU D3354 " --> pdb=" O ARG D3350 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N HIS D3355 " --> pdb=" O PRO D3351 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE D3359 " --> pdb=" O HIS D3355 " (cutoff:3.500A) Proline residue: D3360 - end of helix removed outlier: 3.679A pdb=" N GLU D3382 " --> pdb=" O GLN D3378 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA D3383 " --> pdb=" O LEU D3379 " (cutoff:3.500A) Processing helix chain 'D' and resid 3389 through 3413 removed outlier: 6.670A pdb=" N LEU D3393 " --> pdb=" O GLU D3389 " (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 3449 removed outlier: 3.749A pdb=" N GLU D3433 " --> pdb=" O ALA D3429 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU D3434 " --> pdb=" O ASN D3430 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N HIS D3449 " --> pdb=" O TRP D3445 " (cutoff:3.500A) Processing helix chain 'D' and resid 3450 through 3463 removed outlier: 3.649A pdb=" N GLN D3456 " --> pdb=" O LYS D3452 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN D3457 " --> pdb=" O ARG D3453 " (cutoff:3.500A) Processing helix chain 'D' and resid 3465 through 3478 removed outlier: 6.738A pdb=" N PHE D3469 " --> pdb=" O ASN D3465 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU D3470 " --> pdb=" O ASN D3466 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASP D3473 " --> pdb=" O PHE D3469 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N SER D3474 " --> pdb=" O LEU D3470 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET D3478 " --> pdb=" O SER D3474 " (cutoff:3.500A) Processing helix chain 'D' and resid 3508 through 3526 removed outlier: 3.744A pdb=" N MET D3517 " --> pdb=" O THR D3513 " (cutoff:3.500A) Proline residue: D3519 - end of helix removed outlier: 3.628A pdb=" N CYS D3525 " --> pdb=" O GLY D3521 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA D3526 " --> pdb=" O LEU D3522 " (cutoff:3.500A) Processing helix chain 'D' and resid 3529 through 3543 Processing helix chain 'D' and resid 3545 through 3557 removed outlier: 3.558A pdb=" N ARG D3550 " --> pdb=" O ASP D3546 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU D3551 " --> pdb=" O GLU D3547 " (cutoff:3.500A) Processing helix chain 'D' and resid 3562 through 3567 removed outlier: 4.113A pdb=" N SER D3566 " --> pdb=" O LYS D3562 " (cutoff:3.500A) Proline residue: D3567 - end of helix No H-bonds generated for 'chain 'D' and resid 3562 through 3567' Processing helix chain 'D' and resid 3568 through 3579 Processing helix chain 'D' and resid 3588 through 3612 removed outlier: 3.585A pdb=" N VAL D3593 " --> pdb=" O PRO D3589 " (cutoff:3.500A) Proline residue: D3612 - end of helix Processing helix chain 'D' and resid 3628 through 3638 removed outlier: 4.503A pdb=" N VAL D3632 " --> pdb=" O ARG D3628 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL D3633 " --> pdb=" O ARG D3629 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE D3636 " --> pdb=" O VAL D3632 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARG D3637 " --> pdb=" O VAL D3633 " (cutoff:3.500A) Processing helix chain 'D' and resid 3640 through 3645 removed outlier: 3.749A pdb=" N LEU D3644 " --> pdb=" O PRO D3640 " (cutoff:3.500A) Proline residue: D3645 - end of helix No H-bonds generated for 'chain 'D' and resid 3640 through 3645' Processing helix chain 'D' and resid 3646 through 3665 removed outlier: 3.628A pdb=" N GLU D3655 " --> pdb=" O ASN D3651 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU D3663 " --> pdb=" O ALA D3659 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N THR D3664 " --> pdb=" O ALA D3660 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU D3665 " --> pdb=" O TRP D3661 " (cutoff:3.500A) Processing helix chain 'D' and resid 3669 through 3679 removed outlier: 3.644A pdb=" N LYS D3679 " --> pdb=" O ASP D3675 " (cutoff:3.500A) Processing helix chain 'D' and resid 3696 through 3711 Processing helix chain 'D' and resid 3719 through 3735 removed outlier: 3.830A pdb=" N CYS D3733 " --> pdb=" O MET D3729 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N HIS D3734 " --> pdb=" O ALA D3730 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU D3735 " --> pdb=" O LYS D3731 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3772 removed outlier: 3.686A pdb=" N LYS D3756 " --> pdb=" O SER D3752 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU D3757 " --> pdb=" O PHE D3753 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET D3758 " --> pdb=" O GLU D3754 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN D3761 " --> pdb=" O GLU D3757 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D3770 " --> pdb=" O GLN D3766 " (cutoff:3.500A) Processing helix chain 'D' and resid 3774 through 3787 removed outlier: 4.296A 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 3826 through 3839 Processing helix chain 'D' and resid 3843 through 3857 removed outlier: 3.656A pdb=" N GLU D3854 " --> pdb=" O GLN D3850 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY D3855 " --> pdb=" O ASN D3851 " (cutoff:3.500A) Processing helix chain 'D' and resid 3877 through 3893 removed outlier: 3.549A 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: 3.615A pdb=" N TYR D3937 " --> pdb=" O PHE D3933 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLY D3939 " --> pdb=" O TRP D3935 " (cutoff:3.500A) Processing helix chain 'D' and resid 3944 through 3970 removed outlier: 3.636A 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: 3.958A pdb=" N ALA D3988 " --> pdb=" O ARG D3984 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS D3998 " --> pdb=" O HIS D3994 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN D4005 " --> pdb=" O MET D4001 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP D4006 " --> pdb=" O LYS D4002 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N SER D4007 " --> pdb=" O LEU D4003 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4032 Processing helix chain 'D' and resid 4038 through 4052 Processing helix chain 'D' and resid 4053 through 4072 removed outlier: 3.748A pdb=" N MET D4064 " --> pdb=" O LYS D4060 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE D4065 " --> pdb=" O PHE D4061 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU D4068 " --> pdb=" O MET D4064 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP D4070 " --> pdb=" O LEU D4066 " (cutoff:3.500A) Processing helix chain 'D' and resid 4074 through 4082 removed outlier: 3.853A pdb=" N TYR D4080 " --> pdb=" O ALA D4076 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N THR D4082 " --> pdb=" O GLN D4078 " (cutoff:3.500A) Processing helix chain 'D' and resid 4089 through 4101 removed outlier: 4.154A pdb=" N ASP D4098 " --> pdb=" O GLN D4094 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N SER D4099 " --> pdb=" O LYS D4095 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN D4100 " --> pdb=" O ALA D4096 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS D4101 " --> pdb=" O MET D4097 " (cutoff:3.500A) Processing helix chain 'D' and resid 4104 through 4116 removed outlier: 5.495A pdb=" N GLU D4116 " --> pdb=" O LEU D4112 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4155 removed outlier: 4.191A pdb=" N PHE D4128 " --> pdb=" O ASN D4124 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA D4129 " --> pdb=" O PHE D4125 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASN D4130 " --> pdb=" O GLU D4126 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N PHE D4132 " --> pdb=" O PHE D4128 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN D4133 " --> pdb=" O ALA D4129 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLU D4134 " --> pdb=" O ASN D4130 " (cutoff:3.500A) Proline residue: D4135 - end of helix removed outlier: 4.215A pdb=" N ASP D4138 " --> pdb=" O GLU D4134 " (cutoff:3.500A) removed outlier: 3.796A 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: 3.581A pdb=" N ASN D4162 " --> pdb=" O PRO D4158 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE D4163 " --> pdb=" O ARG D4159 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU D4164 " --> pdb=" O LEU D4160 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU D4165 " --> pdb=" O ARG D4161 " (cutoff:3.500A) Processing helix chain 'D' and resid 4169 through 4175 Processing helix chain 'D' and resid 4198 through 4208 Proline residue: D4208 - end of helix Processing helix chain 'D' and resid 4209 through 4224 Processing helix chain 'D' and resid 4226 through 4252 removed outlier: 4.500A pdb=" N MET D4231 " --> pdb=" O GLU D4227 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLU D4232 " --> pdb=" O ALA D4228 " (cutoff:3.500A) Processing helix chain 'D' and resid 4542 through 4559 Processing helix chain 'D' and resid 4560 through 4580 removed outlier: 3.919A pdb=" N LEU D4567 " --> pdb=" O ARG D4563 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE D4579 " --> pdb=" O PHE D4575 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N TYR D4580 " --> pdb=" O ILE D4576 " (cutoff:3.500A) Processing helix chain 'D' and resid 4640 through 4683 removed outlier: 4.035A 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 4709 removed outlier: 3.601A pdb=" N ARG D4703 " --> pdb=" O GLY D4699 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU D4704 " --> pdb=" O GLN D4700 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL D4705 " --> pdb=" O TRP D4701 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU D4706 " --> pdb=" O ASP D4702 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASN D4707 " --> pdb=" O ARG D4703 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR D4708 " --> pdb=" O LEU D4704 " (cutoff:3.500A) Proline residue: D4709 - end of helix 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 4749 Processing helix chain 'D' and resid 4772 through 4786 removed outlier: 3.507A pdb=" N ASP D4786 " --> pdb=" O VAL D4782 " (cutoff:3.500A) Processing helix chain 'D' and resid 4787 through 4805 removed outlier: 4.008A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4808 through 4820 removed outlier: 5.096A pdb=" N HIS D4812 " --> pdb=" O PHE D4808 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU D4813 " --> pdb=" O PHE D4809 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU D4814 " --> pdb=" O ALA D4810 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP D4815 " --> pdb=" O ALA D4811 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE D4816 " --> pdb=" O HIS D4812 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ALA D4817 " --> pdb=" O LEU D4813 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N MET D4818 " --> pdb=" O LEU D4814 " (cutoff:3.500A) Processing helix chain 'D' and resid 4821 through 4832 removed outlier: 3.962A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 4.149A 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 4878 through 4893 removed outlier: 3.703A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) Processing helix chain 'D' and resid 4896 through 4901 removed outlier: 4.301A 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: 4.056A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (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: 3.812A pdb=" N HIS D5003 " --> pdb=" O ASP D4999 " (cutoff:3.500A) removed outlier: 6.153A 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 255 removed outlier: 4.317A pdb=" N CYS D 253 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR D 254 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS D 255 " --> pdb=" O VAL D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 250 through 255' Processing helix chain 'D' and resid 3296 through 3302 removed outlier: 4.250A pdb=" N ALA D3300 " --> pdb=" O PRO D3297 " (cutoff:3.500A) Proline residue: D3301 - end of helix Processing helix chain 'D' and resid 3152 through 3157 removed outlier: 4.111A 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: 5.407A pdb=" N ARG E 42 " --> pdb=" O SER E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 66 removed outlier: 3.790A pdb=" N ALA E 64 " --> pdb=" O GLU E 60 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET E 66 " --> pdb=" O GLY E 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 43 removed outlier: 5.407A pdb=" N ARG F 42 " --> pdb=" O SER F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 66 removed outlier: 3.790A pdb=" N ALA F 64 " --> pdb=" O GLU F 60 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN F 65 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET F 66 " --> pdb=" O GLY F 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 43 removed outlier: 5.407A pdb=" N ARG G 42 " --> pdb=" O SER G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 66 removed outlier: 3.790A pdb=" N ALA G 64 " --> pdb=" O GLU G 60 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET G 66 " --> pdb=" O GLY G 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 43 removed outlier: 5.407A pdb=" N ARG H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 66 removed outlier: 3.790A pdb=" N ALA H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN H 65 " --> pdb=" O GLU H 61 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET H 66 " --> pdb=" O GLY H 62 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 49 through 52 removed outlier: 6.668A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 28 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 35 " --> pdb=" O CYS A 24 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.505A pdb=" N LEU A 108 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU A 109 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 4.282A 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: 3.644A pdb=" N ALA A 153 " --> pdb=" O ASP A 168 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N ASP A 168 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 220 through 224 Processing sheet with id= 5, first strand: chain 'A' and resid 245 through 248 removed outlier: 5.158A pdb=" N VAL A 245 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS A 374 " --> pdb=" O TYR A 247 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 260 through 264 removed outlier: 3.517A pdb=" N ARG A 283 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 14.730A pdb=" N LEU A 280 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 10.592A pdb=" N LEU A 293 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE A 282 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 289 " --> pdb=" O HIS A 284 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 314 through 317 removed outlier: 3.517A pdb=" N CYS A 315 " --> pdb=" O GLN A 349 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN A 349 " --> pdb=" O CYS A 315 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 681 through 686 removed outlier: 3.584A pdb=" N ARG A1646 " --> pdb=" O ILE A1641 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 753 through 759 removed outlier: 4.598A pdb=" N ASP A 742 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 668 " --> pdb=" O ASP A 742 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS A 788 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP A1626 " --> pdb=" O PHE A 791 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 765 through 769 removed outlier: 5.512A pdb=" N GLN A 765 " --> pdb=" O GLY A1477 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY A1477 " --> pdb=" O GLN A 765 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 838 through 841 removed outlier: 4.047A pdb=" N GLN A1198 " --> pdb=" O GLY A 841 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL A1199 " --> pdb=" O VAL A1095 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N GLY A1086 " --> pdb=" O LEU A1155 " (cutoff:3.500A) removed outlier: 3.706A 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 1074 through 1078 removed outlier: 4.889A pdb=" N ILE A1074 " --> pdb=" O SER A1239 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR A1235 " --> pdb=" O GLU A1078 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N THR A1236 " --> pdb=" O MET A1608 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 1134 through 1137 removed outlier: 3.563A pdb=" N VAL A1123 " --> pdb=" O TRP A1132 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU A1120 " --> pdb=" O ARG A1106 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET A1100 " --> pdb=" O GLY A1126 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLU A1099 " --> pdb=" O GLY A1195 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A1101 " --> pdb=" O SER A1193 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 1267 through 1273 removed outlier: 4.077A pdb=" N LEU A1566 " --> pdb=" O PRO A1268 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A1562 " --> pdb=" O LEU A1272 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL A1561 " --> pdb=" O PHE A1440 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLY A1567 " --> pdb=" O TYR A1434 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TYR A1434 " --> pdb=" O GLY A1567 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A1519 " --> pdb=" O THR A1528 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A1526 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLY A1525 " --> pdb=" O VAL A1542 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 1294 through 1298 removed outlier: 4.280A pdb=" N THR A1546 " --> pdb=" O PHE A1297 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A1289 " --> pdb=" O VAL A1552 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N PHE A1288 " --> pdb=" O LEU A1600 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU A1596 " --> pdb=" O SER A1292 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 4177 through 4184 removed outlier: 5.188A pdb=" N TYR A4177 " --> pdb=" O ILE A4197 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 4581 through 4584 Processing sheet with id= 19, first strand: chain 'B' and resid 49 through 52 removed outlier: 6.668A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 28 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU B 35 " --> pdb=" O CYS B 24 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.506A pdb=" N LEU B 108 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU B 109 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET B 116 " --> pdb=" O HIS B 111 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 148 through 153 removed outlier: 3.644A pdb=" N ALA B 153 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N ASP B 168 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 220 through 224 Processing sheet with id= 23, first strand: chain 'B' and resid 245 through 248 removed outlier: 5.159A pdb=" N VAL B 245 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS B 374 " --> pdb=" O TYR B 247 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 260 through 264 removed outlier: 3.516A pdb=" N ARG B 283 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 14.731A pdb=" N LEU B 280 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 10.592A pdb=" N LEU B 293 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE B 282 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG B 289 " --> pdb=" O HIS B 284 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 314 through 317 removed outlier: 3.518A pdb=" N CYS B 315 " --> pdb=" O GLN B 349 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN B 349 " --> pdb=" O CYS B 315 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 681 through 686 removed outlier: 3.584A pdb=" N ARG B1646 " --> pdb=" O ILE B1641 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'B' and resid 753 through 759 removed outlier: 4.599A pdb=" N ASP B 742 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 668 " --> pdb=" O ASP B 742 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS B 788 " --> pdb=" O ASP B 669 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP B1626 " --> pdb=" O PHE B 791 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 765 through 769 removed outlier: 5.511A pdb=" N GLN B 765 " --> pdb=" O GLY B1477 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY B1477 " --> pdb=" O GLN B 765 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 838 through 841 removed outlier: 4.046A pdb=" N GLN B1198 " --> pdb=" O GLY B 841 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B1199 " --> pdb=" O VAL B1095 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLY B1086 " --> pdb=" O LEU B1155 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE B1161 " --> pdb=" O MET B1152 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 937 through 941 No H-bonds generated for sheet with id= 30 Processing sheet with id= 31, first strand: chain 'B' and resid 1074 through 1078 removed outlier: 4.888A pdb=" N ILE B1074 " --> pdb=" O SER B1239 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR B1235 " --> pdb=" O GLU B1078 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N THR B1236 " --> pdb=" O MET B1608 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 1134 through 1137 removed outlier: 3.563A pdb=" N VAL B1123 " --> pdb=" O TRP B1132 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU B1120 " --> pdb=" O ARG B1106 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET B1100 " --> pdb=" O GLY B1126 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLU B1099 " --> pdb=" O GLY B1195 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG B1101 " --> pdb=" O SER B1193 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 1267 through 1273 removed outlier: 4.076A pdb=" N LEU B1566 " --> pdb=" O PRO B1268 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B1562 " --> pdb=" O LEU B1272 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL B1561 " --> pdb=" O PHE B1440 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY B1567 " --> pdb=" O TYR B1434 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR B1434 " --> pdb=" O GLY B1567 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B1519 " --> pdb=" O THR B1528 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B1526 " --> pdb=" O ASP B1521 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLY B1525 " --> pdb=" O VAL B1542 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'B' and resid 1294 through 1298 removed outlier: 4.280A pdb=" N THR B1546 " --> pdb=" O PHE B1297 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B1289 " --> pdb=" O VAL B1552 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N PHE B1288 " --> pdb=" O LEU B1600 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU B1596 " --> pdb=" O SER B1292 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'B' and resid 4177 through 4184 removed outlier: 5.188A pdb=" N TYR B4177 " --> pdb=" O ILE B4197 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 4581 through 4584 Processing sheet with id= 37, first strand: chain 'C' and resid 49 through 52 removed outlier: 6.667A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 28 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU C 35 " --> pdb=" O CYS C 24 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.506A pdb=" N LEU C 108 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU C 109 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET C 116 " --> pdb=" O HIS C 111 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'C' and resid 148 through 153 removed outlier: 3.643A pdb=" N ALA C 153 " --> pdb=" O ASP C 168 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N ASP C 168 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'C' and resid 220 through 224 Processing sheet with id= 41, first strand: chain 'C' and resid 245 through 248 removed outlier: 5.159A pdb=" N VAL C 245 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS C 374 " --> pdb=" O TYR C 247 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'C' and resid 260 through 264 removed outlier: 3.515A pdb=" N ARG C 283 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 14.731A pdb=" N LEU C 280 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 10.592A pdb=" N LEU C 293 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE C 282 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 289 " --> pdb=" O HIS C 284 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 314 through 317 removed outlier: 3.518A pdb=" N CYS C 315 " --> pdb=" O GLN C 349 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN C 349 " --> pdb=" O CYS C 315 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C' and resid 681 through 686 removed outlier: 3.584A pdb=" N ARG C1646 " --> pdb=" O ILE C1641 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'C' and resid 753 through 759 removed outlier: 4.599A pdb=" N ASP C 742 " --> pdb=" O VAL C 668 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 668 " --> pdb=" O ASP C 742 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS C 788 " --> pdb=" O ASP C 669 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP C1626 " --> pdb=" O PHE C 791 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'C' and resid 765 through 769 removed outlier: 5.512A pdb=" N GLN C 765 " --> pdb=" O GLY C1477 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY C1477 " --> pdb=" O GLN C 765 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'C' and resid 838 through 841 removed outlier: 4.046A pdb=" N GLN C1198 " --> pdb=" O GLY C 841 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL C1199 " --> pdb=" O VAL C1095 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLY C1086 " --> pdb=" O LEU C1155 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE C1161 " --> pdb=" O MET C1152 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'C' and resid 937 through 941 No H-bonds generated for sheet with id= 48 Processing sheet with id= 49, first strand: chain 'C' and resid 1074 through 1078 removed outlier: 4.888A pdb=" N ILE C1074 " --> pdb=" O SER C1239 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR C1235 " --> pdb=" O GLU C1078 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N THR C1236 " --> pdb=" O MET C1608 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 1134 through 1137 removed outlier: 3.562A pdb=" N VAL C1123 " --> pdb=" O TRP C1132 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU C1120 " --> pdb=" O ARG C1106 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET C1100 " --> pdb=" O GLY C1126 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLU C1099 " --> pdb=" O GLY C1195 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG C1101 " --> pdb=" O SER C1193 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 1267 through 1273 removed outlier: 4.076A pdb=" N LEU C1566 " --> pdb=" O PRO C1268 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE C1562 " --> pdb=" O LEU C1272 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL C1561 " --> pdb=" O PHE C1440 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLY C1567 " --> pdb=" O TYR C1434 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR C1434 " --> pdb=" O GLY C1567 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C1519 " --> pdb=" O THR C1528 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU C1526 " --> pdb=" O ASP C1521 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLY C1525 " --> pdb=" O VAL C1542 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 1294 through 1298 removed outlier: 4.281A pdb=" N THR C1546 " --> pdb=" O PHE C1297 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C1289 " --> pdb=" O VAL C1552 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N PHE C1288 " --> pdb=" O LEU C1600 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU C1596 " --> pdb=" O SER C1292 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 4177 through 4184 removed outlier: 5.189A pdb=" N TYR C4177 " --> pdb=" O ILE C4197 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 4581 through 4584 Processing sheet with id= 55, first strand: chain 'D' and resid 49 through 52 removed outlier: 6.667A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 28 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU D 35 " --> pdb=" O CYS D 24 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.506A pdb=" N LEU D 108 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU D 109 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET D 116 " --> pdb=" O HIS D 111 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'D' and resid 148 through 153 removed outlier: 3.644A pdb=" N ALA D 153 " --> pdb=" O ASP D 168 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N ASP D 168 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'D' and resid 220 through 224 Processing sheet with id= 59, first strand: chain 'D' and resid 245 through 248 removed outlier: 5.159A pdb=" N VAL D 245 " --> pdb=" O ALA D 376 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS D 374 " --> pdb=" O TYR D 247 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'D' and resid 260 through 264 removed outlier: 3.515A pdb=" N ARG D 283 " --> pdb=" O ARG D 261 " (cutoff:3.500A) removed outlier: 14.731A pdb=" N LEU D 280 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 10.592A pdb=" N LEU D 293 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE D 282 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG D 289 " --> pdb=" O HIS D 284 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'D' and resid 314 through 317 removed outlier: 3.518A pdb=" N CYS D 315 " --> pdb=" O GLN D 349 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN D 349 " --> pdb=" O CYS D 315 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'D' and resid 681 through 686 removed outlier: 3.584A pdb=" N ARG D1646 " --> pdb=" O ILE D1641 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'D' and resid 753 through 759 removed outlier: 4.599A pdb=" N ASP D 742 " --> pdb=" O VAL D 668 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL D 668 " --> pdb=" O ASP D 742 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS D 788 " --> pdb=" O ASP D 669 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP D1626 " --> pdb=" O PHE D 791 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'D' and resid 765 through 769 removed outlier: 5.512A pdb=" N GLN D 765 " --> pdb=" O GLY D1477 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY D1477 " --> pdb=" O GLN D 765 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'D' and resid 838 through 841 removed outlier: 4.046A pdb=" N GLN D1198 " --> pdb=" O GLY D 841 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL D1199 " --> pdb=" O VAL D1095 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLY D1086 " --> pdb=" O LEU D1155 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE D1161 " --> pdb=" O MET D1152 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'D' and resid 937 through 941 No H-bonds generated for sheet with id= 66 Processing sheet with id= 67, first strand: chain 'D' and resid 1074 through 1078 removed outlier: 4.888A pdb=" N ILE D1074 " --> pdb=" O SER D1239 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR D1235 " --> pdb=" O GLU D1078 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N THR D1236 " --> pdb=" O MET D1608 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'D' and resid 1134 through 1137 removed outlier: 3.563A pdb=" N VAL D1123 " --> pdb=" O TRP D1132 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU D1120 " --> pdb=" O ARG D1106 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET D1100 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLU D1099 " --> pdb=" O GLY D1195 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG D1101 " --> pdb=" O SER D1193 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'D' and resid 1267 through 1273 removed outlier: 4.076A pdb=" N LEU D1566 " --> pdb=" O PRO D1268 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE D1562 " --> pdb=" O LEU D1272 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL D1561 " --> pdb=" O PHE D1440 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY D1567 " --> pdb=" O TYR D1434 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR D1434 " --> pdb=" O GLY D1567 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D1519 " --> pdb=" O THR D1528 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D1526 " --> pdb=" O ASP D1521 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLY D1525 " --> pdb=" O VAL D1542 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'D' and resid 1294 through 1298 removed outlier: 4.281A pdb=" N THR D1546 " --> pdb=" O PHE D1297 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D1289 " --> pdb=" O VAL D1552 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N PHE D1288 " --> pdb=" O LEU D1600 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU D1596 " --> pdb=" O SER D1292 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'D' and resid 4177 through 4184 removed outlier: 5.189A pdb=" N TYR D4177 " --> pdb=" O ILE D4197 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'D' and resid 4581 through 4584 Processing sheet with id= 73, first strand: chain 'E' and resid 1 through 7 removed outlier: 7.873A pdb=" N GLY E 1 " --> pdb=" O THR E 77 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR E 77 " --> pdb=" O GLY E 1 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU E 3 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR E 75 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG E 71 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR E 27 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLN E 20 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'F' and resid 1 through 7 removed outlier: 7.873A pdb=" N GLY F 1 " --> pdb=" O THR F 77 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR F 77 " --> pdb=" O GLY F 1 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU F 3 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR F 75 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG F 71 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR F 27 " --> pdb=" O ASP F 100 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLN F 20 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'G' and resid 1 through 7 removed outlier: 7.873A pdb=" N GLY G 1 " --> pdb=" O THR G 77 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR G 77 " --> pdb=" O GLY G 1 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU G 3 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR G 75 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG G 71 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR G 27 " --> pdb=" O ASP G 100 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLN G 20 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'H' and resid 1 through 7 removed outlier: 7.873A pdb=" N GLY H 1 " --> pdb=" O THR H 77 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR H 77 " --> pdb=" O GLY H 1 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU H 3 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR H 75 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG H 71 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR H 27 " --> pdb=" O ASP H 100 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLN H 20 " --> pdb=" O ILE H 50 " (cutoff:3.500A) 6807 hydrogen bonds defined for protein. 20333 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: 96.51 Time building geometry restraints manager: 44.39 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: 46490 1.34 - 1.47: 33575 1.47 - 1.59: 64623 1.59 - 1.71: 4 1.71 - 1.84: 1512 Bond restraints: 146204 Sorted by residual: bond pdb=" C HIS A 904 " pdb=" N PRO A 905 " ideal model delta sigma weight residual 1.334 1.422 -0.088 2.34e-02 1.83e+03 1.42e+01 bond pdb=" C HIS B 904 " pdb=" N PRO B 905 " ideal model delta sigma weight residual 1.334 1.422 -0.088 2.34e-02 1.83e+03 1.41e+01 bond pdb=" C HIS D 904 " pdb=" N PRO D 905 " ideal model delta sigma weight residual 1.334 1.422 -0.088 2.34e-02 1.83e+03 1.41e+01 bond pdb=" C HIS C 904 " pdb=" N PRO C 905 " ideal model delta sigma weight residual 1.334 1.422 -0.088 2.34e-02 1.83e+03 1.41e+01 bond pdb=" C VAL A4666 " pdb=" N PRO A4667 " ideal model delta sigma weight residual 1.335 1.371 -0.035 1.36e-02 5.41e+03 6.81e+00 ... (remaining 146199 not shown) Histogram of bond angle deviations from ideal: 90.72 - 99.76: 144 99.76 - 108.81: 10452 108.81 - 117.85: 97926 117.85 - 126.89: 87393 126.89 - 135.93: 2129 Bond angle restraints: 198044 Sorted by residual: angle pdb=" CA GLU C4196 " pdb=" CB GLU C4196 " pdb=" CG GLU C4196 " ideal model delta sigma weight residual 114.10 127.95 -13.85 2.00e+00 2.50e-01 4.79e+01 angle pdb=" CA GLU D4196 " pdb=" CB GLU D4196 " pdb=" CG GLU D4196 " ideal model delta sigma weight residual 114.10 127.95 -13.85 2.00e+00 2.50e-01 4.79e+01 angle pdb=" CA GLU B4196 " pdb=" CB GLU B4196 " pdb=" CG GLU B4196 " ideal model delta sigma weight residual 114.10 127.95 -13.85 2.00e+00 2.50e-01 4.79e+01 angle pdb=" CA GLU A4196 " pdb=" CB GLU A4196 " pdb=" CG GLU A4196 " ideal model delta sigma weight residual 114.10 127.92 -13.82 2.00e+00 2.50e-01 4.78e+01 angle pdb=" CA PRO D3085 " pdb=" N PRO D3085 " pdb=" CD PRO D3085 " ideal model delta sigma weight residual 112.00 103.23 8.77 1.40e+00 5.10e-01 3.93e+01 ... (remaining 198039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.71: 84787 30.71 - 61.43: 3293 61.43 - 92.14: 220 92.14 - 122.85: 0 122.85 - 153.56: 4 Dihedral angle restraints: 88304 sinusoidal: 36136 harmonic: 52168 Sorted by residual: dihedral pdb=" C2' AMP D5101 " pdb=" C1' AMP D5101 " pdb=" N9 AMP D5101 " pdb=" C4 AMP D5101 " ideal model delta sinusoidal sigma weight residual 91.55 -62.01 153.56 1 2.00e+01 2.50e-03 4.55e+01 dihedral pdb=" C2' AMP A5101 " pdb=" C1' AMP A5101 " pdb=" N9 AMP A5101 " pdb=" C4 AMP A5101 " ideal model delta sinusoidal sigma weight residual 91.55 -61.97 153.53 1 2.00e+01 2.50e-03 4.55e+01 dihedral pdb=" C2' AMP C5101 " pdb=" C1' AMP C5101 " pdb=" N9 AMP C5101 " pdb=" C4 AMP C5101 " ideal model delta sinusoidal sigma weight residual 91.55 -61.96 153.51 1 2.00e+01 2.50e-03 4.55e+01 ... (remaining 88301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 17359 0.072 - 0.143: 3850 0.143 - 0.215: 509 0.215 - 0.287: 42 0.287 - 0.358: 16 Chirality restraints: 21776 Sorted by residual: chirality pdb=" CB ILE A1562 " pdb=" CA ILE A1562 " pdb=" CG1 ILE A1562 " pdb=" CG2 ILE A1562 " 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 D1562 " pdb=" CA ILE D1562 " pdb=" CG1 ILE D1562 " pdb=" CG2 ILE D1562 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CB ILE B1562 " pdb=" CA ILE B1562 " pdb=" CG1 ILE B1562 " pdb=" CG2 ILE B1562 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 21773 not shown) Planarity restraints: 25752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A3132 " 0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C THR A3132 " -0.071 2.00e-02 2.50e+03 pdb=" O THR A3132 " 0.027 2.00e-02 2.50e+03 pdb=" N THR A3133 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B3132 " -0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C THR B3132 " 0.071 2.00e-02 2.50e+03 pdb=" O THR B3132 " -0.027 2.00e-02 2.50e+03 pdb=" N THR B3133 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C3132 " -0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C THR C3132 " 0.071 2.00e-02 2.50e+03 pdb=" O THR C3132 " -0.027 2.00e-02 2.50e+03 pdb=" N THR C3133 " -0.024 2.00e-02 2.50e+03 ... (remaining 25749 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 7557 2.73 - 3.27: 144829 3.27 - 3.82: 243659 3.82 - 4.36: 293076 4.36 - 4.90: 486952 Nonbonded interactions: 1176073 Sorted by model distance: nonbonded pdb=" OG1 THR C 978 " pdb=" OE1 GLN C 981 " model vdw 2.188 2.440 nonbonded pdb=" OG1 THR A 978 " pdb=" OE1 GLN A 981 " model vdw 2.188 2.440 nonbonded pdb=" OG1 THR D 978 " pdb=" OE1 GLN D 981 " model vdw 2.188 2.440 nonbonded pdb=" OG1 THR B 978 " pdb=" OE1 GLN B 981 " model vdw 2.189 2.440 nonbonded pdb=" OG SER B2309 " pdb=" O ILE B2321 " model vdw 2.223 2.440 ... (remaining 1176068 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: 3.030 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: 0.200 Extract box with map and model: 18.280 Check model and map are aligned: 1.580 Set scattering table: 1.010 Process input model: 450.360 Find NCS groups from input model: 7.910 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:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 485.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 0.097 146204 Z= 0.384 Angle : 1.063 15.377 198044 Z= 0.574 Chirality : 0.060 0.358 21776 Planarity : 0.008 0.081 25752 Dihedral : 15.010 153.565 54596 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.41 % Favored : 96.48 % Rotamer: Outliers : 3.28 % Allowed : 2.29 % Favored : 94.43 % Cbeta Deviations : 0.02 % 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: -0.61 (0.06), residues: 17832 helix: 0.00 (0.05), residues: 8804 sheet: -0.73 (0.13), residues: 1580 loop : -0.66 (0.07), residues: 7448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP A3285 HIS 0.016 0.002 HIS B 181 PHE 0.039 0.003 PHE B3951 TYR 0.040 0.003 TYR A4715 ARG 0.012 0.001 ARG B1725 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1688 residues out of total 15540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 487 poor density : 1201 time to evaluate : 12.306 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.7606 (mtp) cc_final: 0.7209 (mtp) REVERT: A 413 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8713 (tm-30) REVERT: A 457 GLU cc_start: 0.9395 (tp30) cc_final: 0.9090 (tm-30) REVERT: A 604 CYS cc_start: 0.8499 (t) cc_final: 0.8104 (m) REVERT: A 961 MET cc_start: 0.6378 (pmm) cc_final: 0.5734 (pmm) REVERT: A 999 ASP cc_start: 0.9338 (m-30) cc_final: 0.9039 (t70) REVERT: A 1072 VAL cc_start: 0.8255 (OUTLIER) cc_final: 0.7694 (p) REVERT: A 1152 MET cc_start: 0.8203 (mmm) cc_final: 0.7815 (mmm) REVERT: A 1186 ASP cc_start: 0.8776 (m-30) cc_final: 0.8393 (m-30) REVERT: A 1573 MET cc_start: 0.8564 (tpt) cc_final: 0.8254 (tpt) REVERT: A 1601 MET cc_start: 0.8727 (mmt) cc_final: 0.8213 (mmt) REVERT: A 1982 ARG cc_start: 0.8335 (mmt90) cc_final: 0.7663 (ptp90) REVERT: A 2178 MET cc_start: 0.8868 (ppp) cc_final: 0.8642 (ppp) REVERT: A 2203 MET cc_start: 0.8662 (mtm) cc_final: 0.8383 (mtm) REVERT: A 2208 MET cc_start: 0.9244 (tpp) cc_final: 0.9007 (mmm) REVERT: A 3673 MET cc_start: 0.9362 (tpp) cc_final: 0.8783 (tpp) REVERT: A 3758 MET cc_start: 0.9285 (tmm) cc_final: 0.8952 (tmm) REVERT: A 4047 MET cc_start: 0.8850 (tmm) cc_final: 0.8425 (tmm) REVERT: A 4172 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8815 (mm-30) REVERT: A 4180 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8812 (ptp90) REVERT: A 4244 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8936 (mm-30) REVERT: A 4543 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7665 (pm20) REVERT: A 4635 SER cc_start: 0.9098 (OUTLIER) cc_final: 0.8634 (p) REVERT: A 4648 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8862 (tp) REVERT: A 4680 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9208 (mtpt) REVERT: A 4686 LEU cc_start: 0.8659 (tp) cc_final: 0.7827 (tp) REVERT: A 4773 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8791 (m) REVERT: A 4798 MET cc_start: 0.9031 (mmm) cc_final: 0.8792 (mmm) REVERT: A 4824 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8126 (mtm-85) REVERT: A 4933 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7837 (mt0) REVERT: A 4954 MET cc_start: 0.8965 (mmm) cc_final: 0.8465 (mmm) REVERT: A 4957 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8515 (mtpp) REVERT: A 4980 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9248 (tp) REVERT: A 5016 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8694 (mp0) REVERT: A 5032 TYR cc_start: 0.8538 (m-80) cc_final: 0.7409 (m-80) REVERT: B 196 MET cc_start: 0.8902 (mpp) cc_final: 0.8679 (mpp) REVERT: B 380 GLN cc_start: 0.9202 (tp40) cc_final: 0.8912 (mm-40) REVERT: B 383 HIS cc_start: 0.8316 (m90) cc_final: 0.7996 (m90) REVERT: B 457 GLU cc_start: 0.9434 (tp30) cc_final: 0.9129 (tm-30) REVERT: B 604 CYS cc_start: 0.8649 (t) cc_final: 0.8336 (m) REVERT: B 961 MET cc_start: 0.6707 (pmm) cc_final: 0.6320 (pmm) REVERT: B 999 ASP cc_start: 0.9285 (m-30) cc_final: 0.9015 (t0) REVERT: B 1072 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7699 (p) REVERT: B 1152 MET cc_start: 0.8385 (mmm) cc_final: 0.7961 (mmm) REVERT: B 1181 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8880 (mp0) REVERT: B 1186 ASP cc_start: 0.8543 (m-30) cc_final: 0.8164 (m-30) REVERT: B 1599 MET cc_start: 0.8512 (ppp) cc_final: 0.8299 (ppp) REVERT: B 1982 ARG cc_start: 0.8394 (mmt90) cc_final: 0.7909 (ptp90) REVERT: B 2178 MET cc_start: 0.8815 (ppp) cc_final: 0.8561 (ppp) REVERT: B 2203 MET cc_start: 0.8561 (mtm) cc_final: 0.8307 (mtm) REVERT: B 3467 MET cc_start: 0.5486 (tmm) cc_final: 0.5281 (tmm) REVERT: B 3652 MET cc_start: 0.8794 (mmt) cc_final: 0.8539 (mmm) REVERT: B 3673 MET cc_start: 0.9301 (tpp) cc_final: 0.8764 (tpp) REVERT: B 3758 MET cc_start: 0.9218 (tmm) cc_final: 0.8716 (tmm) REVERT: B 4044 MET cc_start: 0.9560 (tpp) cc_final: 0.9247 (tpt) REVERT: B 4047 MET cc_start: 0.8900 (tmm) cc_final: 0.8558 (tmm) REVERT: B 4048 LEU cc_start: 0.9593 (mt) cc_final: 0.9392 (mt) REVERT: B 4064 MET cc_start: 0.9075 (ppp) cc_final: 0.8841 (ppp) REVERT: B 4180 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8735 (ptp90) REVERT: B 4581 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8068 (tptm) REVERT: B 4583 SER cc_start: 0.7138 (OUTLIER) cc_final: 0.6896 (t) REVERT: B 4686 LEU cc_start: 0.8656 (tp) cc_final: 0.7811 (tp) REVERT: B 4773 VAL cc_start: 0.9309 (OUTLIER) cc_final: 0.8919 (t) REVERT: B 4774 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8954 (mptt) REVERT: B 4777 ILE cc_start: 0.9501 (OUTLIER) cc_final: 0.9239 (mm) REVERT: B 4933 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7729 (mt0) REVERT: B 4957 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8636 (mtpp) REVERT: B 4980 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9205 (tp) REVERT: B 5032 TYR cc_start: 0.8482 (m-80) cc_final: 0.7450 (m-80) REVERT: B 5034 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8496 (p0) REVERT: C 196 MET cc_start: 0.8904 (mpp) cc_final: 0.8682 (mpp) REVERT: C 380 GLN cc_start: 0.9203 (tp40) cc_final: 0.8911 (mm-40) REVERT: C 383 HIS cc_start: 0.8315 (m90) cc_final: 0.7998 (m90) REVERT: C 457 GLU cc_start: 0.9433 (tp30) cc_final: 0.9129 (tm-30) REVERT: C 604 CYS cc_start: 0.8647 (t) cc_final: 0.8336 (m) REVERT: C 961 MET cc_start: 0.6707 (pmm) cc_final: 0.6322 (pmm) REVERT: C 999 ASP cc_start: 0.9286 (m-30) cc_final: 0.9015 (t0) REVERT: C 1072 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7701 (p) REVERT: C 1152 MET cc_start: 0.8383 (mmm) cc_final: 0.7961 (mmm) REVERT: C 1181 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8878 (mp0) REVERT: C 1186 ASP cc_start: 0.8542 (m-30) cc_final: 0.8163 (m-30) REVERT: C 1599 MET cc_start: 0.8512 (ppp) cc_final: 0.8298 (ppp) REVERT: C 1982 ARG cc_start: 0.8394 (mmt90) cc_final: 0.7909 (ptp90) REVERT: C 2178 MET cc_start: 0.8813 (ppp) cc_final: 0.8565 (ppp) REVERT: C 2203 MET cc_start: 0.8560 (mtm) cc_final: 0.8310 (mtm) REVERT: C 3467 MET cc_start: 0.5487 (tmm) cc_final: 0.5283 (tmm) REVERT: C 3652 MET cc_start: 0.8795 (mmt) cc_final: 0.8539 (mmm) REVERT: C 3673 MET cc_start: 0.9300 (tpp) cc_final: 0.8762 (tpp) REVERT: C 3758 MET cc_start: 0.9220 (tmm) cc_final: 0.8717 (tmm) REVERT: C 4044 MET cc_start: 0.9560 (tpp) cc_final: 0.9247 (tpt) REVERT: C 4047 MET cc_start: 0.8899 (tmm) cc_final: 0.8555 (tmm) REVERT: C 4048 LEU cc_start: 0.9593 (mt) cc_final: 0.9392 (mt) REVERT: C 4064 MET cc_start: 0.9076 (ppp) cc_final: 0.8842 (ppp) REVERT: C 4180 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8735 (ptp90) REVERT: C 4581 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8069 (tptm) REVERT: C 4583 SER cc_start: 0.7137 (OUTLIER) cc_final: 0.6896 (t) REVERT: C 4686 LEU cc_start: 0.8654 (tp) cc_final: 0.7812 (tp) REVERT: C 4773 VAL cc_start: 0.9309 (OUTLIER) cc_final: 0.8920 (t) REVERT: C 4774 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8955 (mptt) REVERT: C 4777 ILE cc_start: 0.9500 (OUTLIER) cc_final: 0.9238 (mm) REVERT: C 4933 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7718 (mt0) REVERT: C 4957 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8637 (mtpp) REVERT: C 4980 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9205 (tp) REVERT: C 5032 TYR cc_start: 0.8483 (m-80) cc_final: 0.7447 (m-80) REVERT: C 5034 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8497 (p0) REVERT: D 196 MET cc_start: 0.8902 (mpp) cc_final: 0.8690 (mpp) REVERT: D 380 GLN cc_start: 0.9203 (tp40) cc_final: 0.8912 (mm-40) REVERT: D 383 HIS cc_start: 0.8317 (m90) cc_final: 0.7998 (m90) REVERT: D 457 GLU cc_start: 0.9433 (tp30) cc_final: 0.9129 (tm-30) REVERT: D 604 CYS cc_start: 0.8647 (t) cc_final: 0.8338 (m) REVERT: D 961 MET cc_start: 0.6706 (pmm) cc_final: 0.6322 (pmm) REVERT: D 999 ASP cc_start: 0.9285 (m-30) cc_final: 0.9015 (t0) REVERT: D 1072 VAL cc_start: 0.8194 (OUTLIER) cc_final: 0.7701 (p) REVERT: D 1152 MET cc_start: 0.8386 (mmm) cc_final: 0.7964 (mmm) REVERT: D 1181 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8879 (mp0) REVERT: D 1186 ASP cc_start: 0.8542 (m-30) cc_final: 0.8163 (m-30) REVERT: D 1599 MET cc_start: 0.8509 (ppp) cc_final: 0.8298 (ppp) REVERT: D 1982 ARG cc_start: 0.8393 (mmt90) cc_final: 0.7909 (ptp90) REVERT: D 2178 MET cc_start: 0.8813 (ppp) cc_final: 0.8558 (ppp) REVERT: D 2203 MET cc_start: 0.8560 (mtm) cc_final: 0.8309 (mtm) REVERT: D 3467 MET cc_start: 0.5483 (tmm) cc_final: 0.5278 (tmm) REVERT: D 3652 MET cc_start: 0.8793 (mmt) cc_final: 0.8539 (mmm) REVERT: D 3673 MET cc_start: 0.9300 (tpp) cc_final: 0.8761 (tpp) REVERT: D 3758 MET cc_start: 0.9220 (tmm) cc_final: 0.8717 (tmm) REVERT: D 4044 MET cc_start: 0.9559 (tpp) cc_final: 0.9246 (tpt) REVERT: D 4047 MET cc_start: 0.8897 (tmm) cc_final: 0.8554 (tmm) REVERT: D 4048 LEU cc_start: 0.9593 (mt) cc_final: 0.9391 (mt) REVERT: D 4064 MET cc_start: 0.9077 (ppp) cc_final: 0.8845 (ppp) REVERT: D 4180 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8735 (ptp90) REVERT: D 4581 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7967 (tptm) REVERT: D 4583 SER cc_start: 0.7144 (OUTLIER) cc_final: 0.6901 (t) REVERT: D 4686 LEU cc_start: 0.8656 (tp) cc_final: 0.7812 (tp) REVERT: D 4773 VAL cc_start: 0.9311 (OUTLIER) cc_final: 0.8921 (t) REVERT: D 4774 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8955 (mptt) REVERT: D 4777 ILE cc_start: 0.9502 (OUTLIER) cc_final: 0.9237 (mm) REVERT: D 4933 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7761 (mt0) REVERT: D 4957 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8638 (mtpp) REVERT: D 4980 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9206 (tp) REVERT: D 5032 TYR cc_start: 0.8483 (m-80) cc_final: 0.7442 (m-80) REVERT: D 5034 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8495 (p0) outliers start: 487 outliers final: 63 residues processed: 1607 average time/residue: 1.2465 time to fit residues: 3519.3142 Evaluate side-chains 961 residues out of total 15540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 852 time to evaluate : 12.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 4180 ARG Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4244 GLU Chi-restraints excluded: chain A residue 4543 GLU Chi-restraints excluded: chain A residue 4555 LEU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4578 LEU Chi-restraints excluded: chain A residue 4584 ASP Chi-restraints excluded: chain A residue 4628 VAL Chi-restraints excluded: chain A residue 4635 SER Chi-restraints excluded: chain A residue 4639 MET Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4680 LYS Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4706 LEU Chi-restraints excluded: chain A residue 4716 TRP Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4773 VAL Chi-restraints excluded: chain A residue 4818 MET Chi-restraints excluded: chain A residue 4824 ARG Chi-restraints excluded: chain A residue 4932 ILE Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4957 LYS Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 4981 GLU Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5004 THR Chi-restraints excluded: chain A residue 5016 GLU Chi-restraints excluded: chain B residue 1072 VAL Chi-restraints excluded: chain B residue 4180 ARG Chi-restraints excluded: chain B residue 4221 VAL Chi-restraints excluded: chain B residue 4555 LEU Chi-restraints excluded: chain B residue 4578 LEU Chi-restraints excluded: chain B residue 4581 LYS Chi-restraints excluded: chain B residue 4583 SER Chi-restraints excluded: chain B residue 4584 ASP Chi-restraints excluded: chain B residue 4628 VAL Chi-restraints excluded: chain B residue 4634 GLU Chi-restraints excluded: chain B residue 4639 MET Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4706 LEU Chi-restraints excluded: chain B residue 4716 TRP Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4773 VAL Chi-restraints excluded: chain B residue 4774 LYS Chi-restraints excluded: chain B residue 4777 ILE Chi-restraints excluded: chain B residue 4818 MET Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4957 LYS Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 4981 GLU Chi-restraints excluded: chain B residue 5004 THR Chi-restraints excluded: chain B residue 5034 ASP Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 4180 ARG Chi-restraints excluded: chain C residue 4221 VAL Chi-restraints excluded: chain C residue 4555 LEU Chi-restraints excluded: chain C residue 4578 LEU Chi-restraints excluded: chain C residue 4581 LYS Chi-restraints excluded: chain C residue 4583 SER Chi-restraints excluded: chain C residue 4584 ASP Chi-restraints excluded: chain C residue 4628 VAL Chi-restraints excluded: chain C residue 4634 GLU Chi-restraints excluded: chain C residue 4639 MET Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4706 LEU Chi-restraints excluded: chain C residue 4716 TRP Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4773 VAL Chi-restraints excluded: chain C residue 4774 LYS Chi-restraints excluded: chain C residue 4777 ILE Chi-restraints excluded: chain C residue 4818 MET Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4957 LYS Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 4981 GLU Chi-restraints excluded: chain C residue 5004 THR Chi-restraints excluded: chain C residue 5034 ASP Chi-restraints excluded: chain D residue 1072 VAL Chi-restraints excluded: chain D residue 4180 ARG Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4555 LEU Chi-restraints excluded: chain D residue 4578 LEU Chi-restraints excluded: chain D residue 4581 LYS Chi-restraints excluded: chain D residue 4583 SER Chi-restraints excluded: chain D residue 4584 ASP Chi-restraints excluded: chain D residue 4628 VAL Chi-restraints excluded: chain D residue 4634 GLU Chi-restraints excluded: chain D residue 4639 MET Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4706 LEU Chi-restraints excluded: chain D residue 4716 TRP Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4773 VAL Chi-restraints excluded: chain D residue 4774 LYS Chi-restraints excluded: chain D residue 4777 ILE Chi-restraints excluded: chain D residue 4818 MET Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4957 LYS Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 4981 GLU Chi-restraints excluded: chain D residue 5004 THR Chi-restraints excluded: chain D residue 5034 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1509 optimal weight: 0.0370 chunk 1355 optimal weight: 10.0000 chunk 751 optimal weight: 20.0000 chunk 462 optimal weight: 8.9990 chunk 914 optimal weight: 9.9990 chunk 724 optimal weight: 30.0000 chunk 1401 optimal weight: 7.9990 chunk 542 optimal weight: 2.9990 chunk 852 optimal weight: 6.9990 chunk 1043 optimal weight: 2.9990 chunk 1623 optimal weight: 5.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS A 624 ASN A 877 ASN A1003 GLN A1563 GLN A2003 GLN A2127 GLN A2498 HIS A2574 HIS A2877 GLN ** A2962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4133 GLN A4223 ASN ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4886 HIS A4997 ASN ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A5006 GLN A5015 GLN A5031 GLN ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 HIS B 624 ASN B 877 ASN ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 GLN B1484 HIS B1563 GLN B2003 GLN B2127 GLN B2498 HIS B2574 HIS B2877 GLN ** B2962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4133 GLN B4223 ASN ** B4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4886 HIS ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5006 GLN B5015 GLN ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 HIS C 624 ASN C 877 ASN C1003 GLN C1563 GLN C2003 GLN C2127 GLN C2574 HIS ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4133 GLN C4223 ASN ** C4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4886 HIS ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C5006 GLN C5015 GLN ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 597 HIS D 624 ASN D 877 ASN D1003 GLN D1484 HIS D1563 GLN D2003 GLN D2127 GLN D2877 GLN ** D2962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4133 GLN D4223 ASN ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4886 HIS D5003 HIS D5006 GLN D5015 GLN ** D5031 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** Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 146204 Z= 0.268 Angle : 0.672 14.815 198044 Z= 0.340 Chirality : 0.042 0.363 21776 Planarity : 0.005 0.067 25752 Dihedral : 6.169 153.114 19841 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.38 % Allowed : 7.62 % Favored : 91.00 % 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: 0.06 (0.06), residues: 17832 helix: 0.84 (0.06), residues: 8736 sheet: -0.82 (0.13), residues: 1592 loop : -0.62 (0.07), residues: 7504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A4778 HIS 0.010 0.001 HIS A2498 PHE 0.043 0.002 PHE A3753 TYR 0.026 0.002 TYR B 959 ARG 0.011 0.001 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 15540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 880 time to evaluate : 12.303 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: A 457 GLU cc_start: 0.9474 (tp30) cc_final: 0.9079 (tm-30) REVERT: A 604 CYS cc_start: 0.8483 (t) cc_final: 0.8272 (m) REVERT: A 891 TRP cc_start: 0.8779 (m-10) cc_final: 0.8493 (m-10) REVERT: A 961 MET cc_start: 0.6110 (pmm) cc_final: 0.5623 (pmm) REVERT: A 1152 MET cc_start: 0.8500 (mmm) cc_final: 0.8208 (mmm) REVERT: A 1494 MET cc_start: 0.7296 (mmm) cc_final: 0.6570 (mmt) REVERT: A 1573 MET cc_start: 0.8747 (tpt) cc_final: 0.8416 (tpt) REVERT: A 1648 MET cc_start: 0.7620 (ppp) cc_final: 0.7121 (ppp) REVERT: A 2178 MET cc_start: 0.8746 (ppp) cc_final: 0.8475 (ppp) REVERT: A 3201 MET cc_start: 0.7217 (ttm) cc_final: 0.6571 (ptm) REVERT: A 3437 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.7891 (mpp) REVERT: A 3638 MET cc_start: 0.5981 (mtt) cc_final: 0.5649 (tmm) REVERT: A 3673 MET cc_start: 0.9396 (tpp) cc_final: 0.8671 (tpp) REVERT: A 3758 MET cc_start: 0.9204 (tmm) cc_final: 0.8790 (tmm) REVERT: A 4047 MET cc_start: 0.8806 (tmm) cc_final: 0.8290 (tmm) REVERT: A 4093 PHE cc_start: 0.3940 (m-10) cc_final: 0.3558 (m-10) REVERT: A 4223 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8162 (t0) REVERT: A 4224 GLU cc_start: 0.8197 (mp0) cc_final: 0.7429 (mp0) REVERT: A 4244 GLU cc_start: 0.9263 (OUTLIER) cc_final: 0.9055 (mm-30) REVERT: A 4543 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7721 (pm20) REVERT: A 4580 TYR cc_start: 0.7322 (OUTLIER) cc_final: 0.5688 (t80) REVERT: A 4732 PHE cc_start: 0.7775 (m-80) cc_final: 0.7495 (m-80) REVERT: A 4798 MET cc_start: 0.9030 (mmm) cc_final: 0.8762 (mmm) REVERT: A 4806 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8289 (t0) REVERT: A 4824 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8149 (mtm-85) REVERT: A 4879 MET cc_start: 0.8396 (tpp) cc_final: 0.7835 (tpp) REVERT: A 4954 MET cc_start: 0.8896 (mmm) cc_final: 0.8552 (mmm) REVERT: A 4980 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9133 (tt) REVERT: A 4989 MET cc_start: 0.8895 (tmm) cc_final: 0.8672 (tpt) REVERT: A 5013 MET cc_start: 0.8614 (mtp) cc_final: 0.8140 (mmm) REVERT: A 5032 TYR cc_start: 0.8491 (m-80) cc_final: 0.7568 (m-80) REVERT: B 196 MET cc_start: 0.8805 (mpp) cc_final: 0.8488 (mpp) REVERT: B 457 GLU cc_start: 0.9482 (tp30) cc_final: 0.9090 (tm-30) REVERT: B 891 TRP cc_start: 0.8528 (m-10) cc_final: 0.8322 (m100) REVERT: B 961 MET cc_start: 0.6631 (pmm) cc_final: 0.6234 (pmm) REVERT: B 1152 MET cc_start: 0.8515 (mmm) cc_final: 0.8167 (mmm) REVERT: B 1181 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8870 (mp0) REVERT: B 1648 MET cc_start: 0.7739 (ppp) cc_final: 0.7491 (ppp) REVERT: B 2178 MET cc_start: 0.8635 (ppp) cc_final: 0.8392 (ppp) REVERT: B 2208 MET cc_start: 0.9389 (mmm) cc_final: 0.9127 (mmm) REVERT: B 3201 MET cc_start: 0.7537 (ttm) cc_final: 0.7027 (ptm) REVERT: B 3437 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8326 (mpp) REVERT: B 3673 MET cc_start: 0.9365 (tpp) cc_final: 0.8702 (tpp) REVERT: B 3758 MET cc_start: 0.9162 (tmm) cc_final: 0.8707 (tmm) REVERT: B 4047 MET cc_start: 0.8878 (tmm) cc_final: 0.8385 (tmm) REVERT: B 4093 PHE cc_start: 0.3976 (m-10) cc_final: 0.3556 (m-10) REVERT: B 4157 ASP cc_start: 0.9235 (t0) cc_final: 0.8749 (t0) REVERT: B 4223 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8268 (t0) REVERT: B 4580 TYR cc_start: 0.7478 (OUTLIER) cc_final: 0.5835 (t80) REVERT: B 4798 MET cc_start: 0.8866 (mmm) cc_final: 0.8611 (mmm) REVERT: B 4806 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8428 (t0) REVERT: B 4954 MET cc_start: 0.8645 (tpp) cc_final: 0.8063 (mmm) REVERT: B 4980 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9090 (tt) REVERT: B 4998 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7890 (tttm) REVERT: B 5013 MET cc_start: 0.8493 (mtp) cc_final: 0.8229 (mmm) REVERT: B 5020 ASP cc_start: 0.8941 (m-30) cc_final: 0.8706 (m-30) REVERT: B 5032 TYR cc_start: 0.8538 (m-80) cc_final: 0.7831 (m-80) REVERT: B 5034 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8474 (p0) REVERT: C 196 MET cc_start: 0.8818 (mpp) cc_final: 0.8496 (mpp) REVERT: C 457 GLU cc_start: 0.9481 (tp30) cc_final: 0.9090 (tm-30) REVERT: C 891 TRP cc_start: 0.8528 (m-10) cc_final: 0.8322 (m100) REVERT: C 961 MET cc_start: 0.6633 (pmm) cc_final: 0.6236 (pmm) REVERT: C 1152 MET cc_start: 0.8513 (mmm) cc_final: 0.8163 (mmm) REVERT: C 1181 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8877 (mp0) REVERT: C 1648 MET cc_start: 0.7740 (ppp) cc_final: 0.7490 (ppp) REVERT: C 2178 MET cc_start: 0.8682 (ppp) cc_final: 0.8447 (ppp) REVERT: C 3201 MET cc_start: 0.7539 (ttm) cc_final: 0.7029 (ptm) REVERT: C 3437 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8326 (mpp) REVERT: C 3673 MET cc_start: 0.9364 (tpp) cc_final: 0.8688 (tpp) REVERT: C 3758 MET cc_start: 0.9161 (tmm) cc_final: 0.8707 (tmm) REVERT: C 4023 MET cc_start: 0.9039 (tmm) cc_final: 0.8837 (ttt) REVERT: C 4047 MET cc_start: 0.8877 (tmm) cc_final: 0.8384 (tmm) REVERT: C 4093 PHE cc_start: 0.3980 (m-10) cc_final: 0.3561 (m-10) REVERT: C 4157 ASP cc_start: 0.9235 (t0) cc_final: 0.8748 (t0) REVERT: C 4223 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8273 (t0) REVERT: C 4580 TYR cc_start: 0.7478 (OUTLIER) cc_final: 0.5836 (t80) REVERT: C 4798 MET cc_start: 0.8867 (mmm) cc_final: 0.8614 (mmm) REVERT: C 4806 ASN cc_start: 0.8796 (OUTLIER) cc_final: 0.8427 (t0) REVERT: C 4954 MET cc_start: 0.8642 (tpp) cc_final: 0.8062 (mmm) REVERT: C 4980 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9091 (tt) REVERT: C 4998 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7887 (tttm) REVERT: C 5013 MET cc_start: 0.8495 (mtp) cc_final: 0.8227 (mmm) REVERT: C 5020 ASP cc_start: 0.8938 (m-30) cc_final: 0.8706 (m-30) REVERT: C 5032 TYR cc_start: 0.8541 (m-80) cc_final: 0.7827 (m-80) REVERT: C 5034 ASP cc_start: 0.9101 (OUTLIER) cc_final: 0.8473 (p0) REVERT: D 196 MET cc_start: 0.8804 (mpp) cc_final: 0.8488 (mpp) REVERT: D 457 GLU cc_start: 0.9481 (tp30) cc_final: 0.9090 (tm-30) REVERT: D 891 TRP cc_start: 0.8527 (m-10) cc_final: 0.8320 (m100) REVERT: D 961 MET cc_start: 0.6634 (pmm) cc_final: 0.6237 (pmm) REVERT: D 1152 MET cc_start: 0.8512 (mmm) cc_final: 0.8165 (mmm) REVERT: D 1181 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8869 (mp0) REVERT: D 1648 MET cc_start: 0.7739 (ppp) cc_final: 0.7488 (ppp) REVERT: D 2178 MET cc_start: 0.8635 (ppp) cc_final: 0.8391 (ppp) REVERT: D 2208 MET cc_start: 0.9390 (mmm) cc_final: 0.9126 (mmm) REVERT: D 3201 MET cc_start: 0.7540 (ttm) cc_final: 0.7029 (ptm) REVERT: D 3437 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8326 (mpp) REVERT: D 3673 MET cc_start: 0.9365 (tpp) cc_final: 0.8701 (tpp) REVERT: D 3758 MET cc_start: 0.9165 (tmm) cc_final: 0.8710 (tmm) REVERT: D 4023 MET cc_start: 0.9043 (tmm) cc_final: 0.8836 (ttt) REVERT: D 4047 MET cc_start: 0.8876 (tmm) cc_final: 0.8382 (tmm) REVERT: D 4093 PHE cc_start: 0.3975 (m-10) cc_final: 0.3556 (m-10) REVERT: D 4157 ASP cc_start: 0.9235 (t0) cc_final: 0.8748 (t0) REVERT: D 4223 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8268 (t0) REVERT: D 4580 TYR cc_start: 0.7528 (OUTLIER) cc_final: 0.5864 (t80) REVERT: D 4798 MET cc_start: 0.8872 (mmm) cc_final: 0.8619 (mmm) REVERT: D 4806 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8402 (t0) REVERT: D 4954 MET cc_start: 0.8642 (tpp) cc_final: 0.8062 (mmm) REVERT: D 4980 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9089 (tt) REVERT: D 4998 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7829 (tttm) REVERT: D 5013 MET cc_start: 0.8493 (mtp) cc_final: 0.8229 (mmm) REVERT: D 5020 ASP cc_start: 0.8937 (m-30) cc_final: 0.8707 (m-30) REVERT: D 5032 TYR cc_start: 0.8536 (m-80) cc_final: 0.7827 (m-80) REVERT: D 5034 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8474 (p0) outliers start: 191 outliers final: 87 residues processed: 1013 average time/residue: 1.1769 time to fit residues: 2132.3873 Evaluate side-chains 897 residues out of total 15540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 781 time to evaluate : 12.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 920 TYR Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2307 LEU Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 3304 CYS Chi-restraints excluded: chain A residue 3437 MET Chi-restraints excluded: chain A residue 4050 GLU Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4209 GLN Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4223 ASN Chi-restraints excluded: chain A residue 4244 GLU Chi-restraints excluded: chain A residue 4543 GLU Chi-restraints excluded: chain A residue 4555 LEU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4584 ASP Chi-restraints excluded: chain A residue 4639 MET Chi-restraints excluded: chain A residue 4649 LEU Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4716 TRP Chi-restraints excluded: chain A residue 4806 ASN Chi-restraints excluded: chain A residue 4818 MET Chi-restraints excluded: chain A residue 4824 ARG Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5004 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2307 LEU Chi-restraints excluded: chain B residue 2463 LEU Chi-restraints excluded: chain B residue 3304 CYS Chi-restraints excluded: chain B residue 3437 MET Chi-restraints excluded: chain B residue 4050 GLU Chi-restraints excluded: chain B residue 4209 GLN Chi-restraints excluded: chain B residue 4223 ASN Chi-restraints excluded: chain B residue 4555 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4584 ASP Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4649 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4716 TRP Chi-restraints excluded: chain B residue 4806 ASN Chi-restraints excluded: chain B residue 4818 MET Chi-restraints excluded: chain B residue 4861 LYS Chi-restraints excluded: chain B residue 4955 GLU Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 4998 LYS Chi-restraints excluded: chain B residue 5004 THR Chi-restraints excluded: chain B residue 5034 ASP Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2307 LEU Chi-restraints excluded: chain C residue 2463 LEU Chi-restraints excluded: chain C residue 3304 CYS Chi-restraints excluded: chain C residue 3437 MET Chi-restraints excluded: chain C residue 4050 GLU Chi-restraints excluded: chain C residue 4209 GLN Chi-restraints excluded: chain C residue 4223 ASN Chi-restraints excluded: chain C residue 4555 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4584 ASP Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4716 TRP Chi-restraints excluded: chain C residue 4806 ASN Chi-restraints excluded: chain C residue 4818 MET Chi-restraints excluded: chain C residue 4861 LYS Chi-restraints excluded: chain C residue 4955 GLU Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 4998 LYS Chi-restraints excluded: chain C residue 5004 THR Chi-restraints excluded: chain C residue 5034 ASP Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2307 LEU Chi-restraints excluded: chain D residue 2463 LEU Chi-restraints excluded: chain D residue 3304 CYS Chi-restraints excluded: chain D residue 3437 MET Chi-restraints excluded: chain D residue 4050 GLU Chi-restraints excluded: chain D residue 4209 GLN Chi-restraints excluded: chain D residue 4223 ASN Chi-restraints excluded: chain D residue 4555 LEU Chi-restraints excluded: chain D residue 4578 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4584 ASP Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4649 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4716 TRP Chi-restraints excluded: chain D residue 4806 ASN Chi-restraints excluded: chain D residue 4818 MET Chi-restraints excluded: chain D residue 4861 LYS Chi-restraints excluded: chain D residue 4955 GLU Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 4998 LYS Chi-restraints excluded: chain D residue 5004 THR Chi-restraints excluded: chain D residue 5034 ASP Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain H residue 79 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 902 optimal weight: 20.0000 chunk 503 optimal weight: 6.9990 chunk 1351 optimal weight: 6.9990 chunk 1105 optimal weight: 4.9990 chunk 447 optimal weight: 0.9990 chunk 1626 optimal weight: 30.0000 chunk 1757 optimal weight: 3.9990 chunk 1448 optimal weight: 50.0000 chunk 1613 optimal weight: 4.9990 chunk 554 optimal weight: 20.0000 chunk 1304 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1003 GLN A1569 GLN ** A2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3419 ASN A4120 ASN A4223 ASN A4997 ASN ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1569 GLN ** B2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3419 ASN B4120 ASN B4223 ASN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 ASN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1569 GLN C2877 GLN ** C2962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3419 ASN C4120 ASN C4223 ASN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1569 GLN D2574 HIS ** D2962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3419 ASN D4120 ASN D4223 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 146204 Z= 0.231 Angle : 0.623 12.366 198044 Z= 0.313 Chirality : 0.041 0.326 21776 Planarity : 0.004 0.061 25752 Dihedral : 5.516 152.832 19684 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.19 % Allowed : 9.63 % Favored : 89.19 % 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: 0.23 (0.06), residues: 17832 helix: 1.03 (0.06), residues: 8780 sheet: -0.88 (0.13), residues: 1632 loop : -0.58 (0.07), residues: 7420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C2661 HIS 0.009 0.001 HIS C2498 PHE 0.038 0.002 PHE A3096 TYR 0.022 0.001 TYR B 959 ARG 0.006 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 15540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 808 time to evaluate : 12.379 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: A 457 GLU cc_start: 0.9420 (tp30) cc_final: 0.9054 (tm-30) REVERT: A 891 TRP cc_start: 0.8782 (m-10) cc_final: 0.8492 (m-10) REVERT: A 961 MET cc_start: 0.6142 (pmm) cc_final: 0.5713 (pmm) REVERT: A 1152 MET cc_start: 0.8401 (mmm) cc_final: 0.7828 (mmm) REVERT: A 1648 MET cc_start: 0.7681 (ppp) cc_final: 0.7131 (ppp) REVERT: A 2153 MET cc_start: 0.9351 (mmp) cc_final: 0.9143 (mmp) REVERT: A 2178 MET cc_start: 0.8761 (ppp) cc_final: 0.8408 (ppp) REVERT: A 3437 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7996 (mpp) REVERT: A 3638 MET cc_start: 0.5916 (mtt) cc_final: 0.5715 (tmm) REVERT: A 3673 MET cc_start: 0.9435 (tpp) cc_final: 0.8678 (tpp) REVERT: A 3758 MET cc_start: 0.9188 (tmm) cc_final: 0.8759 (tmm) REVERT: A 4047 MET cc_start: 0.8726 (tmm) cc_final: 0.8304 (tmm) REVERT: A 4093 PHE cc_start: 0.3951 (m-10) cc_final: 0.3602 (m-10) REVERT: A 4157 ASP cc_start: 0.9212 (t0) cc_final: 0.8709 (t0) REVERT: A 4223 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8484 (t0) REVERT: A 4244 GLU cc_start: 0.9289 (mm-30) cc_final: 0.9007 (mm-30) REVERT: A 4543 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7696 (pm20) REVERT: A 4580 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.5764 (t80) REVERT: A 4798 MET cc_start: 0.8975 (mmm) cc_final: 0.8684 (mmm) REVERT: A 4806 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8247 (t0) REVERT: A 4818 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7222 (mmt) REVERT: A 4879 MET cc_start: 0.8428 (tpp) cc_final: 0.8117 (tpp) REVERT: A 4954 MET cc_start: 0.8949 (mmm) cc_final: 0.8468 (mmm) REVERT: A 4980 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9018 (tt) REVERT: A 4989 MET cc_start: 0.8893 (tmm) cc_final: 0.8655 (tpt) REVERT: A 5013 MET cc_start: 0.8597 (mtp) cc_final: 0.8317 (mmm) REVERT: A 5032 TYR cc_start: 0.8547 (m-80) cc_final: 0.7681 (m-80) REVERT: B 196 MET cc_start: 0.8789 (mpp) cc_final: 0.8418 (mpp) REVERT: B 457 GLU cc_start: 0.9437 (tp30) cc_final: 0.9082 (tm-30) REVERT: B 891 TRP cc_start: 0.8482 (m-10) cc_final: 0.8217 (m100) REVERT: B 961 MET cc_start: 0.6618 (pmm) cc_final: 0.6232 (pmm) REVERT: B 1152 MET cc_start: 0.8478 (mmm) cc_final: 0.7920 (mmm) REVERT: B 1573 MET cc_start: 0.8222 (tpp) cc_final: 0.7887 (tpp) REVERT: B 1648 MET cc_start: 0.7788 (ppp) cc_final: 0.7226 (ppp) REVERT: B 2178 MET cc_start: 0.8647 (ppp) cc_final: 0.8358 (ppp) REVERT: B 2198 MET cc_start: 0.8703 (mmp) cc_final: 0.8500 (mmp) REVERT: B 3201 MET cc_start: 0.7299 (ttm) cc_final: 0.6682 (ptm) REVERT: B 3437 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8263 (mpp) REVERT: B 3638 MET cc_start: 0.5701 (mtt) cc_final: 0.5366 (tmm) REVERT: B 3673 MET cc_start: 0.9402 (tpp) cc_final: 0.8713 (tpp) REVERT: B 3758 MET cc_start: 0.9138 (tmm) cc_final: 0.8850 (tmm) REVERT: B 4047 MET cc_start: 0.8735 (tmm) cc_final: 0.8333 (tmm) REVERT: B 4093 PHE cc_start: 0.3997 (m-10) cc_final: 0.3598 (m-10) REVERT: B 4157 ASP cc_start: 0.9169 (t0) cc_final: 0.8663 (t0) REVERT: B 4580 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.5700 (t80) REVERT: B 4806 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8356 (t0) REVERT: B 4818 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7276 (mmt) REVERT: B 4879 MET cc_start: 0.8508 (tpp) cc_final: 0.8202 (tpp) REVERT: B 4954 MET cc_start: 0.8664 (tpp) cc_final: 0.8063 (mmm) REVERT: B 4980 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9013 (tt) REVERT: B 4998 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7906 (tttm) REVERT: B 5013 MET cc_start: 0.8506 (mtp) cc_final: 0.8193 (mmm) REVERT: B 5020 ASP cc_start: 0.8919 (m-30) cc_final: 0.8709 (m-30) REVERT: B 5032 TYR cc_start: 0.8581 (m-80) cc_final: 0.7927 (m-80) REVERT: C 196 MET cc_start: 0.8788 (mpp) cc_final: 0.8417 (mpp) REVERT: C 457 GLU cc_start: 0.9436 (tp30) cc_final: 0.9082 (tm-30) REVERT: C 891 TRP cc_start: 0.8481 (m-10) cc_final: 0.8216 (m100) REVERT: C 961 MET cc_start: 0.6617 (pmm) cc_final: 0.6235 (pmm) REVERT: C 1152 MET cc_start: 0.8478 (mmm) cc_final: 0.7918 (mmm) REVERT: C 1573 MET cc_start: 0.8220 (tpp) cc_final: 0.7886 (tpp) REVERT: C 1648 MET cc_start: 0.7784 (ppp) cc_final: 0.7226 (ppp) REVERT: C 2198 MET cc_start: 0.8700 (mmp) cc_final: 0.8494 (mmp) REVERT: C 3201 MET cc_start: 0.7303 (ttm) cc_final: 0.6686 (ptm) REVERT: C 3437 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8263 (mpp) REVERT: C 3638 MET cc_start: 0.5702 (mtt) cc_final: 0.5366 (tmm) REVERT: C 3673 MET cc_start: 0.9401 (tpp) cc_final: 0.8713 (tpp) REVERT: C 3758 MET cc_start: 0.9139 (tmm) cc_final: 0.8850 (tmm) REVERT: C 4047 MET cc_start: 0.8793 (tmm) cc_final: 0.8318 (tmm) REVERT: C 4093 PHE cc_start: 0.4002 (m-10) cc_final: 0.3599 (m-10) REVERT: C 4157 ASP cc_start: 0.9169 (t0) cc_final: 0.8662 (t0) REVERT: C 4580 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.5701 (t80) REVERT: C 4806 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8377 (t0) REVERT: C 4818 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7276 (mmt) REVERT: C 4879 MET cc_start: 0.8500 (tpp) cc_final: 0.8198 (tpp) REVERT: C 4954 MET cc_start: 0.8664 (tpp) cc_final: 0.8062 (mmm) REVERT: C 4980 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.8995 (tt) REVERT: C 4998 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7901 (tttm) REVERT: C 5013 MET cc_start: 0.8509 (mtp) cc_final: 0.8171 (mmm) REVERT: C 5020 ASP cc_start: 0.8917 (m-30) cc_final: 0.8707 (m-30) REVERT: C 5032 TYR cc_start: 0.8584 (m-80) cc_final: 0.7926 (m-80) REVERT: D 196 MET cc_start: 0.8788 (mpp) cc_final: 0.8418 (mpp) REVERT: D 457 GLU cc_start: 0.9436 (tp30) cc_final: 0.9081 (tm-30) REVERT: D 891 TRP cc_start: 0.8481 (m-10) cc_final: 0.8215 (m100) REVERT: D 961 MET cc_start: 0.6618 (pmm) cc_final: 0.6237 (pmm) REVERT: D 1152 MET cc_start: 0.8477 (mmm) cc_final: 0.7917 (mmm) REVERT: D 1573 MET cc_start: 0.8220 (tpp) cc_final: 0.7886 (tpp) REVERT: D 1648 MET cc_start: 0.7785 (ppp) cc_final: 0.7226 (ppp) REVERT: D 2178 MET cc_start: 0.8648 (ppp) cc_final: 0.8358 (ppp) REVERT: D 2198 MET cc_start: 0.8700 (mmp) cc_final: 0.8495 (mmp) REVERT: D 3201 MET cc_start: 0.7299 (ttm) cc_final: 0.6681 (ptm) REVERT: D 3437 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8263 (mpp) REVERT: D 3638 MET cc_start: 0.5692 (mtt) cc_final: 0.5361 (tmm) REVERT: D 3673 MET cc_start: 0.9401 (tpp) cc_final: 0.8712 (tpp) REVERT: D 3758 MET cc_start: 0.9140 (tmm) cc_final: 0.8852 (tmm) REVERT: D 4047 MET cc_start: 0.8790 (tmm) cc_final: 0.8316 (tmm) REVERT: D 4093 PHE cc_start: 0.3998 (m-10) cc_final: 0.3594 (m-10) REVERT: D 4157 ASP cc_start: 0.9168 (t0) cc_final: 0.8661 (t0) REVERT: D 4580 TYR cc_start: 0.7587 (OUTLIER) cc_final: 0.5758 (t80) REVERT: D 4639 MET cc_start: 0.8027 (mmm) cc_final: 0.7575 (mmm) REVERT: D 4806 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8345 (t0) REVERT: D 4818 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7277 (mmt) REVERT: D 4879 MET cc_start: 0.8502 (tpp) cc_final: 0.8198 (tpp) REVERT: D 4954 MET cc_start: 0.8665 (tpp) cc_final: 0.8063 (mmm) REVERT: D 4980 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9013 (tt) REVERT: D 4998 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7850 (tttm) REVERT: D 5013 MET cc_start: 0.8510 (mtp) cc_final: 0.8196 (mmm) REVERT: D 5020 ASP cc_start: 0.8916 (m-30) cc_final: 0.8707 (m-30) REVERT: D 5032 TYR cc_start: 0.8579 (m-80) cc_final: 0.7969 (m-80) REVERT: E 13 ARG cc_start: 0.9065 (ptp90) cc_final: 0.8859 (ptp90) REVERT: F 13 ARG cc_start: 0.9064 (ptp90) cc_final: 0.8858 (ptp90) REVERT: G 13 ARG cc_start: 0.9065 (ptp90) cc_final: 0.8859 (ptp90) REVERT: H 13 ARG cc_start: 0.9065 (ptp90) cc_final: 0.8859 (ptp90) outliers start: 161 outliers final: 94 residues processed: 927 average time/residue: 1.1872 time to fit residues: 1972.1089 Evaluate side-chains 896 residues out of total 15540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 777 time to evaluate : 12.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 1608 MET Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2307 LEU Chi-restraints excluded: chain A residue 2423 MET Chi-restraints excluded: chain A residue 3304 CYS Chi-restraints excluded: chain A residue 3437 MET Chi-restraints excluded: chain A residue 3468 SER Chi-restraints excluded: chain A residue 4045 VAL Chi-restraints excluded: chain A residue 4050 GLU Chi-restraints excluded: chain A residue 4057 MET Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4209 GLN Chi-restraints excluded: chain A residue 4223 ASN Chi-restraints excluded: chain A residue 4543 GLU Chi-restraints excluded: chain A residue 4555 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4584 ASP Chi-restraints excluded: chain A residue 4639 MET Chi-restraints excluded: chain A residue 4649 LEU Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4716 TRP Chi-restraints excluded: chain A residue 4800 LEU Chi-restraints excluded: chain A residue 4806 ASN Chi-restraints excluded: chain A residue 4818 MET Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 1608 MET Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2307 LEU Chi-restraints excluded: chain B residue 2423 MET Chi-restraints excluded: chain B residue 3304 CYS Chi-restraints excluded: chain B residue 3437 MET Chi-restraints excluded: chain B residue 4045 VAL Chi-restraints excluded: chain B residue 4050 GLU Chi-restraints excluded: chain B residue 4057 MET Chi-restraints excluded: chain B residue 4209 GLN Chi-restraints excluded: chain B residue 4555 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4584 ASP Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4649 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4716 TRP Chi-restraints excluded: chain B residue 4800 LEU Chi-restraints excluded: chain B residue 4806 ASN Chi-restraints excluded: chain B residue 4818 MET Chi-restraints excluded: chain B residue 4861 LYS Chi-restraints excluded: chain B residue 4955 GLU Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 4998 LYS Chi-restraints excluded: chain B residue 5034 ASP Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 1608 MET Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2307 LEU Chi-restraints excluded: chain C residue 3304 CYS Chi-restraints excluded: chain C residue 3437 MET Chi-restraints excluded: chain C residue 4045 VAL Chi-restraints excluded: chain C residue 4050 GLU Chi-restraints excluded: chain C residue 4057 MET Chi-restraints excluded: chain C residue 4209 GLN Chi-restraints excluded: chain C residue 4555 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4584 ASP Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4649 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4716 TRP Chi-restraints excluded: chain C residue 4800 LEU Chi-restraints excluded: chain C residue 4806 ASN Chi-restraints excluded: chain C residue 4818 MET Chi-restraints excluded: chain C residue 4861 LYS Chi-restraints excluded: chain C residue 4955 GLU Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 4998 LYS Chi-restraints excluded: chain C residue 5034 ASP Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 1608 MET Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2307 LEU Chi-restraints excluded: chain D residue 3304 CYS Chi-restraints excluded: chain D residue 3437 MET Chi-restraints excluded: chain D residue 4045 VAL Chi-restraints excluded: chain D residue 4050 GLU Chi-restraints excluded: chain D residue 4057 MET Chi-restraints excluded: chain D residue 4209 GLN Chi-restraints excluded: chain D residue 4555 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4584 ASP Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4649 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4716 TRP Chi-restraints excluded: chain D residue 4800 LEU Chi-restraints excluded: chain D residue 4806 ASN Chi-restraints excluded: chain D residue 4818 MET Chi-restraints excluded: chain D residue 4861 LYS Chi-restraints excluded: chain D residue 4955 GLU Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 4998 LYS Chi-restraints excluded: chain D residue 5034 ASP Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 94 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1607 optimal weight: 3.9990 chunk 1222 optimal weight: 5.9990 chunk 844 optimal weight: 0.0070 chunk 180 optimal weight: 4.9990 chunk 776 optimal weight: 0.8980 chunk 1092 optimal weight: 20.0000 chunk 1632 optimal weight: 6.9990 chunk 1728 optimal weight: 0.8980 chunk 852 optimal weight: 6.9990 chunk 1547 optimal weight: 30.0000 chunk 465 optimal weight: 7.9990 overall best weight: 2.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1003 GLN A1563 GLN ** A2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4223 ASN A4997 ASN ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1563 GLN ** B2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4223 ASN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1563 GLN ** C2962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4223 ASN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1563 GLN ** D2962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4223 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 146204 Z= 0.186 Angle : 0.589 12.445 198044 Z= 0.293 Chirality : 0.040 0.292 21776 Planarity : 0.004 0.059 25752 Dihedral : 5.293 152.215 19669 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.09 % Allowed : 10.59 % Favored : 88.32 % 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: 0.38 (0.06), residues: 17832 helix: 1.20 (0.06), residues: 8812 sheet: -0.86 (0.13), residues: 1672 loop : -0.56 (0.07), residues: 7348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C2680 HIS 0.008 0.001 HIS C2498 PHE 0.034 0.001 PHE A3096 TYR 0.017 0.001 TYR B 959 ARG 0.010 0.000 ARG A4736 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 15540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 808 time to evaluate : 12.335 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: symmetry clash REVERT: A 116 MET cc_start: 0.8601 (mpp) cc_final: 0.7809 (mpp) REVERT: A 457 GLU cc_start: 0.9430 (tp30) cc_final: 0.9070 (tm-30) REVERT: A 891 TRP cc_start: 0.8650 (m-10) cc_final: 0.8328 (m-10) REVERT: A 961 MET cc_start: 0.6201 (pmm) cc_final: 0.5801 (pmm) REVERT: A 1152 MET cc_start: 0.8218 (mmm) cc_final: 0.7636 (mmm) REVERT: A 1260 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7800 (pmm) REVERT: A 1648 MET cc_start: 0.7696 (ppp) cc_final: 0.7299 (ppp) REVERT: A 2153 MET cc_start: 0.9355 (mmp) cc_final: 0.9104 (mmp) REVERT: A 3250 MET cc_start: 0.7846 (mmm) cc_final: 0.7520 (ptm) REVERT: A 3437 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7989 (mpp) REVERT: A 3673 MET cc_start: 0.9452 (tpp) cc_final: 0.8673 (tpp) REVERT: A 3758 MET cc_start: 0.9136 (tmm) cc_final: 0.8759 (tmm) REVERT: A 4047 MET cc_start: 0.8635 (tmm) cc_final: 0.8212 (tmm) REVERT: A 4093 PHE cc_start: 0.4061 (m-10) cc_final: 0.3723 (m-10) REVERT: A 4157 ASP cc_start: 0.9159 (t0) cc_final: 0.8658 (t0) REVERT: A 4172 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8905 (mm-30) REVERT: A 4244 GLU cc_start: 0.9300 (mm-30) cc_final: 0.8995 (mm-30) REVERT: A 4580 TYR cc_start: 0.7485 (OUTLIER) cc_final: 0.5567 (t80) REVERT: A 4818 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7212 (mmt) REVERT: A 4954 MET cc_start: 0.8935 (mmm) cc_final: 0.8533 (mmm) REVERT: A 4980 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.8791 (tt) REVERT: A 4989 MET cc_start: 0.8864 (tmm) cc_final: 0.8646 (tpt) REVERT: A 5013 MET cc_start: 0.8636 (mtp) cc_final: 0.8378 (mmm) REVERT: B 116 MET cc_start: 0.8627 (mpp) cc_final: 0.7756 (mpp) REVERT: B 196 MET cc_start: 0.8796 (mpp) cc_final: 0.8419 (mpp) REVERT: B 457 GLU cc_start: 0.9435 (tp30) cc_final: 0.9081 (tm-30) REVERT: B 891 TRP cc_start: 0.8445 (m-10) cc_final: 0.8177 (m100) REVERT: B 961 MET cc_start: 0.6606 (pmm) cc_final: 0.6185 (pmm) REVERT: B 1260 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7813 (pmm) REVERT: B 1573 MET cc_start: 0.8457 (tpp) cc_final: 0.8098 (tpp) REVERT: B 1648 MET cc_start: 0.7839 (ppp) cc_final: 0.7417 (ppp) REVERT: B 3201 MET cc_start: 0.7305 (ttm) cc_final: 0.6665 (ptm) REVERT: B 3250 MET cc_start: 0.7963 (mmm) cc_final: 0.7641 (ptm) REVERT: B 3437 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8305 (mpp) REVERT: B 3573 MET cc_start: 0.8629 (mmt) cc_final: 0.8234 (mmp) REVERT: B 3638 MET cc_start: 0.5654 (mtt) cc_final: 0.5386 (tmm) REVERT: B 3673 MET cc_start: 0.9414 (tpp) cc_final: 0.8687 (tpp) REVERT: B 3758 MET cc_start: 0.9082 (tmm) cc_final: 0.8848 (tmm) REVERT: B 4047 MET cc_start: 0.8646 (tmm) cc_final: 0.8252 (tmm) REVERT: B 4093 PHE cc_start: 0.4134 (m-10) cc_final: 0.3730 (m-10) REVERT: B 4157 ASP cc_start: 0.9127 (t0) cc_final: 0.8619 (t0) REVERT: B 4223 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8372 (t0) REVERT: B 4580 TYR cc_start: 0.7564 (OUTLIER) cc_final: 0.5712 (t80) REVERT: B 4818 MET cc_start: 0.7849 (mmt) cc_final: 0.7488 (mpp) REVERT: B 4879 MET cc_start: 0.8512 (tpp) cc_final: 0.8243 (tpp) REVERT: B 4954 MET cc_start: 0.8648 (tpp) cc_final: 0.8083 (mmm) REVERT: B 4980 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.8920 (tt) REVERT: B 4998 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7919 (tttm) REVERT: B 5032 TYR cc_start: 0.8594 (m-80) cc_final: 0.7959 (m-80) REVERT: C 116 MET cc_start: 0.8627 (mpp) cc_final: 0.7755 (mpp) REVERT: C 196 MET cc_start: 0.8799 (mpp) cc_final: 0.8423 (mpp) REVERT: C 457 GLU cc_start: 0.9435 (tp30) cc_final: 0.9081 (tm-30) REVERT: C 891 TRP cc_start: 0.8445 (m-10) cc_final: 0.8177 (m100) REVERT: C 961 MET cc_start: 0.6608 (pmm) cc_final: 0.6185 (pmm) REVERT: C 1260 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7815 (pmm) REVERT: C 1573 MET cc_start: 0.8455 (tpp) cc_final: 0.8096 (tpp) REVERT: C 1648 MET cc_start: 0.7844 (ppp) cc_final: 0.7418 (ppp) REVERT: C 2178 MET cc_start: 0.8660 (ppp) cc_final: 0.8433 (ppp) REVERT: C 3201 MET cc_start: 0.7311 (ttm) cc_final: 0.6671 (ptm) REVERT: C 3250 MET cc_start: 0.7961 (mmm) cc_final: 0.7640 (ptm) REVERT: C 3437 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8304 (mpp) REVERT: C 3573 MET cc_start: 0.8631 (mmt) cc_final: 0.8237 (mmp) REVERT: C 3638 MET cc_start: 0.5652 (mtt) cc_final: 0.5384 (tmm) REVERT: C 3673 MET cc_start: 0.9423 (tpp) cc_final: 0.8710 (tpp) REVERT: C 3758 MET cc_start: 0.9083 (tmm) cc_final: 0.8849 (tmm) REVERT: C 4047 MET cc_start: 0.8699 (tmm) cc_final: 0.8286 (tmm) REVERT: C 4093 PHE cc_start: 0.4133 (m-10) cc_final: 0.3728 (m-10) REVERT: C 4157 ASP cc_start: 0.9128 (t0) cc_final: 0.8620 (t0) REVERT: C 4223 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8375 (t0) REVERT: C 4580 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.5713 (t80) REVERT: C 4732 PHE cc_start: 0.7862 (m-80) cc_final: 0.7620 (m-80) REVERT: C 4818 MET cc_start: 0.7848 (mmt) cc_final: 0.7490 (mpp) REVERT: C 4879 MET cc_start: 0.8489 (tpp) cc_final: 0.8227 (tpp) REVERT: C 4954 MET cc_start: 0.8648 (tpp) cc_final: 0.8082 (mmm) REVERT: C 4980 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.8922 (tt) REVERT: C 4998 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7917 (tttm) REVERT: C 5032 TYR cc_start: 0.8596 (m-80) cc_final: 0.7953 (m-80) REVERT: D 116 MET cc_start: 0.8625 (mpp) cc_final: 0.7755 (mpp) REVERT: D 196 MET cc_start: 0.8795 (mpp) cc_final: 0.8417 (mpp) REVERT: D 457 GLU cc_start: 0.9435 (tp30) cc_final: 0.9081 (tm-30) REVERT: D 891 TRP cc_start: 0.8444 (m-10) cc_final: 0.8176 (m100) REVERT: D 961 MET cc_start: 0.6610 (pmm) cc_final: 0.6186 (pmm) REVERT: D 1260 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7813 (pmm) REVERT: D 1573 MET cc_start: 0.8457 (tpp) cc_final: 0.8098 (tpp) REVERT: D 1648 MET cc_start: 0.7841 (ppp) cc_final: 0.7416 (ppp) REVERT: D 3201 MET cc_start: 0.7307 (ttm) cc_final: 0.6668 (ptm) REVERT: D 3250 MET cc_start: 0.7963 (mmm) cc_final: 0.7641 (ptm) REVERT: D 3437 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8304 (mpp) REVERT: D 3638 MET cc_start: 0.5651 (mtt) cc_final: 0.5379 (tmm) REVERT: D 3673 MET cc_start: 0.9423 (tpp) cc_final: 0.8707 (tpp) REVERT: D 3758 MET cc_start: 0.9077 (tmm) cc_final: 0.8847 (tmm) REVERT: D 4047 MET cc_start: 0.8696 (tmm) cc_final: 0.8257 (tmm) REVERT: D 4093 PHE cc_start: 0.4131 (m-10) cc_final: 0.3726 (m-10) REVERT: D 4157 ASP cc_start: 0.9128 (t0) cc_final: 0.8618 (t0) REVERT: D 4223 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8371 (t0) REVERT: D 4580 TYR cc_start: 0.7613 (OUTLIER) cc_final: 0.5724 (t80) REVERT: D 4581 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7524 (mtpp) REVERT: D 4732 PHE cc_start: 0.7856 (m-80) cc_final: 0.7613 (m-80) REVERT: D 4818 MET cc_start: 0.7848 (mmt) cc_final: 0.7488 (mpp) REVERT: D 4879 MET cc_start: 0.8492 (tpp) cc_final: 0.8226 (tpp) REVERT: D 4954 MET cc_start: 0.8648 (tpp) cc_final: 0.8085 (mmm) REVERT: D 4980 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.8920 (tt) REVERT: D 4998 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7868 (tttm) REVERT: D 5032 TYR cc_start: 0.8589 (m-80) cc_final: 0.7951 (m-80) outliers start: 146 outliers final: 89 residues processed: 903 average time/residue: 1.2501 time to fit residues: 2027.2672 Evaluate side-chains 883 residues out of total 15540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 770 time to evaluate : 12.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 1003 GLN Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1608 MET Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2307 LEU Chi-restraints excluded: chain A residue 2423 MET Chi-restraints excluded: chain A residue 2816 MET Chi-restraints excluded: chain A residue 3304 CYS Chi-restraints excluded: chain A residue 3437 MET Chi-restraints excluded: chain A residue 3468 SER Chi-restraints excluded: chain A residue 4050 GLU Chi-restraints excluded: chain A residue 4057 MET Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4223 ASN Chi-restraints excluded: chain A residue 4555 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4584 ASP Chi-restraints excluded: chain A residue 4639 MET Chi-restraints excluded: chain A residue 4649 LEU Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4716 TRP Chi-restraints excluded: chain A residue 4800 LEU Chi-restraints excluded: chain A residue 4818 MET Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 1260 MET Chi-restraints excluded: chain B residue 1608 MET Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2307 LEU Chi-restraints excluded: chain B residue 2423 MET Chi-restraints excluded: chain B residue 2816 MET Chi-restraints excluded: chain B residue 3304 CYS Chi-restraints excluded: chain B residue 3437 MET Chi-restraints excluded: chain B residue 4050 GLU Chi-restraints excluded: chain B residue 4057 MET Chi-restraints excluded: chain B residue 4223 ASN Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4581 LYS Chi-restraints excluded: chain B residue 4584 ASP Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4649 LEU Chi-restraints excluded: chain B residue 4716 TRP Chi-restraints excluded: chain B residue 4800 LEU Chi-restraints excluded: chain B residue 4861 LYS Chi-restraints excluded: chain B residue 4932 ILE Chi-restraints excluded: chain B residue 4955 GLU Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 4998 LYS Chi-restraints excluded: chain B residue 5034 ASP Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 897 ARG Chi-restraints excluded: chain C residue 1260 MET Chi-restraints excluded: chain C residue 1608 MET Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2307 LEU Chi-restraints excluded: chain C residue 2816 MET Chi-restraints excluded: chain C residue 3304 CYS Chi-restraints excluded: chain C residue 3437 MET Chi-restraints excluded: chain C residue 4050 GLU Chi-restraints excluded: chain C residue 4057 MET Chi-restraints excluded: chain C residue 4209 GLN Chi-restraints excluded: chain C residue 4223 ASN Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4581 LYS Chi-restraints excluded: chain C residue 4584 ASP Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4649 LEU Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4716 TRP Chi-restraints excluded: chain C residue 4800 LEU Chi-restraints excluded: chain C residue 4861 LYS Chi-restraints excluded: chain C residue 4932 ILE Chi-restraints excluded: chain C residue 4955 GLU Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 4998 LYS Chi-restraints excluded: chain C residue 5034 ASP Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 897 ARG Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1608 MET Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2307 LEU Chi-restraints excluded: chain D residue 2816 MET Chi-restraints excluded: chain D residue 3304 CYS Chi-restraints excluded: chain D residue 3437 MET Chi-restraints excluded: chain D residue 4050 GLU Chi-restraints excluded: chain D residue 4057 MET Chi-restraints excluded: chain D residue 4223 ASN Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4581 LYS Chi-restraints excluded: chain D residue 4584 ASP Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4649 LEU Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4716 TRP Chi-restraints excluded: chain D residue 4800 LEU Chi-restraints excluded: chain D residue 4861 LYS Chi-restraints excluded: chain D residue 4932 ILE Chi-restraints excluded: chain D residue 4955 GLU Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 4998 LYS Chi-restraints excluded: chain D residue 5034 ASP Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain H residue 79 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1439 optimal weight: 0.0670 chunk 981 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 1286 optimal weight: 5.9990 chunk 713 optimal weight: 30.0000 chunk 1474 optimal weight: 9.9990 chunk 1194 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 882 optimal weight: 20.0000 chunk 1551 optimal weight: 20.0000 chunk 436 optimal weight: 0.7980 overall best weight: 4.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A5015 GLN ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 974 HIS ** B1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4223 ASN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 974 HIS ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4223 ASN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 974 HIS ** D1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4223 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 146204 Z= 0.275 Angle : 0.627 12.714 198044 Z= 0.313 Chirality : 0.041 0.284 21776 Planarity : 0.004 0.058 25752 Dihedral : 5.210 152.832 19646 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.44 % Allowed : 11.14 % Favored : 87.42 % 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: 0.32 (0.06), residues: 17832 helix: 1.19 (0.06), residues: 8784 sheet: -0.96 (0.13), residues: 1652 loop : -0.63 (0.07), residues: 7396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C2680 HIS 0.008 0.001 HIS D4812 PHE 0.031 0.002 PHE A3096 TYR 0.016 0.001 TYR A4851 ARG 0.006 0.000 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 15540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 780 time to evaluate : 12.272 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: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.8506 (mpp) cc_final: 0.8191 (mpp) REVERT: A 457 GLU cc_start: 0.9424 (tp30) cc_final: 0.9075 (tm-30) REVERT: A 891 TRP cc_start: 0.8680 (m-10) cc_final: 0.8374 (m-10) REVERT: A 961 MET cc_start: 0.6290 (pmm) cc_final: 0.5913 (pmm) REVERT: A 1260 MET cc_start: 0.8533 (pmm) cc_final: 0.8033 (pmm) REVERT: A 1573 MET cc_start: 0.8062 (tpp) cc_final: 0.7713 (tpp) REVERT: A 1648 MET cc_start: 0.7790 (ppp) cc_final: 0.7377 (ppp) REVERT: A 2153 MET cc_start: 0.9332 (mmp) cc_final: 0.9044 (mmp) REVERT: A 2178 MET cc_start: 0.8770 (ppp) cc_final: 0.8480 (ppp) REVERT: A 2250 MET cc_start: 0.9324 (tpp) cc_final: 0.9110 (tpp) REVERT: A 3201 MET cc_start: 0.6924 (ptm) cc_final: 0.6331 (ptm) REVERT: A 3250 MET cc_start: 0.7925 (mmm) cc_final: 0.7602 (ptm) REVERT: A 3673 MET cc_start: 0.9471 (tpp) cc_final: 0.8668 (tpp) REVERT: A 3758 MET cc_start: 0.9111 (tmm) cc_final: 0.8772 (tmm) REVERT: A 3999 MET cc_start: 0.8972 (mmm) cc_final: 0.8585 (mmm) REVERT: A 4047 MET cc_start: 0.8609 (tmm) cc_final: 0.8176 (tmm) REVERT: A 4093 PHE cc_start: 0.4371 (m-10) cc_final: 0.3959 (m-10) REVERT: A 4157 ASP cc_start: 0.9181 (t0) cc_final: 0.8679 (t0) REVERT: A 4244 GLU cc_start: 0.9324 (mm-30) cc_final: 0.9031 (mm-30) REVERT: A 4580 TYR cc_start: 0.7536 (OUTLIER) cc_final: 0.5796 (t80) REVERT: A 4806 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8219 (t0) REVERT: A 4954 MET cc_start: 0.8913 (mmm) cc_final: 0.8541 (mmm) REVERT: A 4980 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9033 (tp) REVERT: A 4989 MET cc_start: 0.8874 (tmm) cc_final: 0.8215 (tmm) REVERT: A 4998 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7957 (tttm) REVERT: A 5013 MET cc_start: 0.8722 (mtp) cc_final: 0.8490 (mmm) REVERT: B 116 MET cc_start: 0.8599 (mpp) cc_final: 0.8178 (mpp) REVERT: B 196 MET cc_start: 0.8762 (mpp) cc_final: 0.8376 (mpp) REVERT: B 457 GLU cc_start: 0.9445 (tp30) cc_final: 0.9095 (tm-30) REVERT: B 891 TRP cc_start: 0.8481 (m-10) cc_final: 0.8236 (m100) REVERT: B 961 MET cc_start: 0.6755 (pmm) cc_final: 0.6366 (pmm) REVERT: B 1152 MET cc_start: 0.8686 (mmm) cc_final: 0.7823 (mmm) REVERT: B 1260 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7839 (pmm) REVERT: B 2178 MET cc_start: 0.8715 (ppp) cc_final: 0.8425 (ppp) REVERT: B 3201 MET cc_start: 0.7346 (ttm) cc_final: 0.6737 (ptm) REVERT: B 3250 MET cc_start: 0.7948 (mmm) cc_final: 0.7645 (ptm) REVERT: B 3437 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8307 (mpp) REVERT: B 3673 MET cc_start: 0.9455 (tpp) cc_final: 0.8679 (tpp) REVERT: B 3758 MET cc_start: 0.9078 (tmm) cc_final: 0.8855 (tmm) REVERT: B 3999 MET cc_start: 0.8977 (mmm) cc_final: 0.8513 (mmm) REVERT: B 4047 MET cc_start: 0.8640 (tmm) cc_final: 0.8224 (tmm) REVERT: B 4093 PHE cc_start: 0.4313 (m-10) cc_final: 0.3892 (m-10) REVERT: B 4157 ASP cc_start: 0.9179 (t0) cc_final: 0.8688 (t0) REVERT: B 4580 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.5839 (t80) REVERT: B 4806 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8300 (t0) REVERT: B 4818 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7356 (mmt) REVERT: B 4980 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9112 (tp) REVERT: B 5013 MET cc_start: 0.8772 (mmm) cc_final: 0.8280 (mmm) REVERT: B 5032 TYR cc_start: 0.8612 (m-80) cc_final: 0.7965 (m-80) REVERT: C 116 MET cc_start: 0.8599 (mpp) cc_final: 0.8177 (mpp) REVERT: C 196 MET cc_start: 0.8688 (mpp) cc_final: 0.8340 (mpp) REVERT: C 457 GLU cc_start: 0.9445 (tp30) cc_final: 0.9095 (tm-30) REVERT: C 891 TRP cc_start: 0.8481 (m-10) cc_final: 0.8236 (m100) REVERT: C 961 MET cc_start: 0.6758 (pmm) cc_final: 0.6364 (pmm) REVERT: C 1152 MET cc_start: 0.8684 (mmm) cc_final: 0.7822 (mmm) REVERT: C 1260 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7838 (pmm) REVERT: C 2178 MET cc_start: 0.8699 (ppp) cc_final: 0.8388 (ppp) REVERT: C 3201 MET cc_start: 0.7352 (ttm) cc_final: 0.6740 (ptm) REVERT: C 3250 MET cc_start: 0.7949 (mmm) cc_final: 0.7646 (ptm) REVERT: C 3437 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8308 (mpp) REVERT: C 3673 MET cc_start: 0.9453 (tpp) cc_final: 0.8677 (tpp) REVERT: C 3758 MET cc_start: 0.9079 (tmm) cc_final: 0.8855 (tmm) REVERT: C 3999 MET cc_start: 0.8975 (mmm) cc_final: 0.8516 (mmm) REVERT: C 4047 MET cc_start: 0.8664 (tmm) cc_final: 0.8233 (tmm) REVERT: C 4093 PHE cc_start: 0.4311 (m-10) cc_final: 0.3891 (m-10) REVERT: C 4157 ASP cc_start: 0.9179 (t0) cc_final: 0.8688 (t0) REVERT: C 4580 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.5839 (t80) REVERT: C 4806 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8300 (t0) REVERT: C 4818 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7352 (mmt) REVERT: C 4980 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9115 (tp) REVERT: C 5013 MET cc_start: 0.8772 (mmm) cc_final: 0.8282 (mmm) REVERT: C 5032 TYR cc_start: 0.8612 (m-80) cc_final: 0.7958 (m-80) REVERT: D 116 MET cc_start: 0.8595 (mpp) cc_final: 0.8176 (mpp) REVERT: D 196 MET cc_start: 0.8762 (mpp) cc_final: 0.8376 (mpp) REVERT: D 457 GLU cc_start: 0.9445 (tp30) cc_final: 0.9095 (tm-30) REVERT: D 891 TRP cc_start: 0.8479 (m-10) cc_final: 0.8235 (m100) REVERT: D 961 MET cc_start: 0.6758 (pmm) cc_final: 0.6366 (pmm) REVERT: D 1152 MET cc_start: 0.8684 (mmm) cc_final: 0.7822 (mmm) REVERT: D 1260 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7839 (pmm) REVERT: D 2178 MET cc_start: 0.8716 (ppp) cc_final: 0.8413 (ppp) REVERT: D 3201 MET cc_start: 0.7350 (ttm) cc_final: 0.6738 (ptm) REVERT: D 3250 MET cc_start: 0.7949 (mmm) cc_final: 0.7643 (ptm) REVERT: D 3437 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8307 (mpp) REVERT: D 3673 MET cc_start: 0.9453 (tpp) cc_final: 0.8707 (tpp) REVERT: D 3758 MET cc_start: 0.9080 (tmm) cc_final: 0.8859 (tmm) REVERT: D 3999 MET cc_start: 0.8976 (mmm) cc_final: 0.8515 (mmm) REVERT: D 4047 MET cc_start: 0.8664 (tmm) cc_final: 0.8231 (tmm) REVERT: D 4093 PHE cc_start: 0.4308 (m-10) cc_final: 0.3887 (m-10) REVERT: D 4157 ASP cc_start: 0.9178 (t0) cc_final: 0.8688 (t0) REVERT: D 4580 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.5887 (t80) REVERT: D 4806 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8289 (t0) REVERT: D 4818 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7358 (mmt) REVERT: D 4980 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9112 (tp) REVERT: D 5013 MET cc_start: 0.8772 (mmm) cc_final: 0.8282 (mmm) REVERT: D 5032 TYR cc_start: 0.8606 (m-80) cc_final: 0.7957 (m-80) outliers start: 201 outliers final: 122 residues processed: 935 average time/residue: 1.1784 time to fit residues: 1982.0623 Evaluate side-chains 911 residues out of total 15540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 767 time to evaluate : 13.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 1608 MET Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2307 LEU Chi-restraints excluded: chain A residue 2423 MET Chi-restraints excluded: chain A residue 2585 THR Chi-restraints excluded: chain A residue 2816 MET Chi-restraints excluded: chain A residue 3304 CYS Chi-restraints excluded: chain A residue 3468 SER Chi-restraints excluded: chain A residue 3511 VAL Chi-restraints excluded: chain A residue 4050 GLU Chi-restraints excluded: chain A residue 4057 MET Chi-restraints excluded: chain A residue 4070 ASP Chi-restraints excluded: chain A residue 4097 MET Chi-restraints excluded: chain A residue 4223 ASN Chi-restraints excluded: chain A residue 4555 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4584 ASP Chi-restraints excluded: chain A residue 4649 LEU Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4716 TRP Chi-restraints excluded: chain A residue 4800 LEU Chi-restraints excluded: chain A residue 4806 ASN Chi-restraints excluded: chain A residue 4876 CYS Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 4998 LYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 974 HIS Chi-restraints excluded: chain B residue 1260 MET Chi-restraints excluded: chain B residue 1608 MET Chi-restraints excluded: chain B residue 2209 GLU Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2307 LEU Chi-restraints excluded: chain B residue 2423 MET Chi-restraints excluded: chain B residue 2816 MET Chi-restraints excluded: chain B residue 3304 CYS Chi-restraints excluded: chain B residue 3437 MET Chi-restraints excluded: chain B residue 3511 VAL Chi-restraints excluded: chain B residue 3529 ASP Chi-restraints excluded: chain B residue 3546 ASP Chi-restraints excluded: chain B residue 4050 GLU Chi-restraints excluded: chain B residue 4057 MET Chi-restraints excluded: chain B residue 4209 GLN Chi-restraints excluded: chain B residue 4555 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4581 LYS Chi-restraints excluded: chain B residue 4584 ASP Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4649 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4716 TRP Chi-restraints excluded: chain B residue 4800 LEU Chi-restraints excluded: chain B residue 4806 ASN Chi-restraints excluded: chain B residue 4818 MET Chi-restraints excluded: chain B residue 4861 LYS Chi-restraints excluded: chain B residue 4932 ILE Chi-restraints excluded: chain B residue 4955 GLU Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 974 HIS Chi-restraints excluded: chain C residue 1260 MET Chi-restraints excluded: chain C residue 1608 MET Chi-restraints excluded: chain C residue 2209 GLU Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2307 LEU Chi-restraints excluded: chain C residue 2816 MET Chi-restraints excluded: chain C residue 3304 CYS Chi-restraints excluded: chain C residue 3437 MET Chi-restraints excluded: chain C residue 3511 VAL Chi-restraints excluded: chain C residue 3529 ASP Chi-restraints excluded: chain C residue 3546 ASP Chi-restraints excluded: chain C residue 4050 GLU Chi-restraints excluded: chain C residue 4057 MET Chi-restraints excluded: chain C residue 4209 GLN Chi-restraints excluded: chain C residue 4555 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4581 LYS Chi-restraints excluded: chain C residue 4584 ASP Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4649 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4716 TRP Chi-restraints excluded: chain C residue 4800 LEU Chi-restraints excluded: chain C residue 4806 ASN Chi-restraints excluded: chain C residue 4818 MET Chi-restraints excluded: chain C residue 4861 LYS Chi-restraints excluded: chain C residue 4932 ILE Chi-restraints excluded: chain C residue 4955 GLU Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 974 HIS Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1608 MET Chi-restraints excluded: chain D residue 2209 GLU Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2307 LEU Chi-restraints excluded: chain D residue 2816 MET Chi-restraints excluded: chain D residue 3304 CYS Chi-restraints excluded: chain D residue 3437 MET Chi-restraints excluded: chain D residue 3511 VAL Chi-restraints excluded: chain D residue 3529 ASP Chi-restraints excluded: chain D residue 3546 ASP Chi-restraints excluded: chain D residue 4050 GLU Chi-restraints excluded: chain D residue 4057 MET Chi-restraints excluded: chain D residue 4209 GLN Chi-restraints excluded: chain D residue 4555 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4584 ASP Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4649 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4716 TRP Chi-restraints excluded: chain D residue 4800 LEU Chi-restraints excluded: chain D residue 4806 ASN Chi-restraints excluded: chain D residue 4818 MET Chi-restraints excluded: chain D residue 4861 LYS Chi-restraints excluded: chain D residue 4932 ILE Chi-restraints excluded: chain D residue 4955 GLU Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 94 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 581 optimal weight: 0.3980 chunk 1556 optimal weight: 8.9990 chunk 341 optimal weight: 8.9990 chunk 1014 optimal weight: 20.0000 chunk 426 optimal weight: 0.9990 chunk 1729 optimal weight: 1.9990 chunk 1436 optimal weight: 9.9990 chunk 800 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 chunk 572 optimal weight: 8.9990 chunk 908 optimal weight: 30.0000 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A5015 GLN ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 974 HIS ** B1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4223 ASN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 974 HIS ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4223 ASN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 974 HIS ** D1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4054 ASN D4223 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 146204 Z= 0.276 Angle : 0.633 13.704 198044 Z= 0.313 Chirality : 0.041 0.278 21776 Planarity : 0.004 0.058 25752 Dihedral : 5.160 152.383 19634 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.39 % Allowed : 11.84 % Favored : 86.77 % 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: 0.31 (0.06), residues: 17832 helix: 1.17 (0.06), residues: 8820 sheet: -0.99 (0.13), residues: 1620 loop : -0.62 (0.07), residues: 7392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C2680 HIS 0.021 0.001 HIS B 974 PHE 0.032 0.002 PHE A3096 TYR 0.017 0.001 TYR A 565 ARG 0.006 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 15540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 767 time to evaluate : 12.301 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.8513 (mpp) cc_final: 0.8136 (mpp) REVERT: A 457 GLU cc_start: 0.9420 (tp30) cc_final: 0.9074 (tm-30) REVERT: A 891 TRP cc_start: 0.8671 (m-10) cc_final: 0.8310 (m-10) REVERT: A 903 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6743 (pp) REVERT: A 961 MET cc_start: 0.6412 (pmm) cc_final: 0.6106 (pmm) REVERT: A 1152 MET cc_start: 0.8522 (mmm) cc_final: 0.7656 (mmm) REVERT: A 1260 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7799 (pmm) REVERT: A 1981 MET cc_start: 0.7880 (mmp) cc_final: 0.7678 (mmp) REVERT: A 2153 MET cc_start: 0.9329 (mmp) cc_final: 0.9024 (mmp) REVERT: A 2178 MET cc_start: 0.8789 (ppp) cc_final: 0.8536 (ppp) REVERT: A 3201 MET cc_start: 0.6838 (ptm) cc_final: 0.6247 (ptm) REVERT: A 3467 MET cc_start: 0.5292 (tmm) cc_final: 0.5079 (tmm) REVERT: A 3528 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8242 (t) REVERT: A 3673 MET cc_start: 0.9476 (tpp) cc_final: 0.8650 (tpp) REVERT: A 3758 MET cc_start: 0.9085 (tmm) cc_final: 0.8872 (tmm) REVERT: A 3999 MET cc_start: 0.8969 (mmm) cc_final: 0.8587 (mmm) REVERT: A 4047 MET cc_start: 0.8584 (tmm) cc_final: 0.8119 (tmm) REVERT: A 4093 PHE cc_start: 0.4385 (m-10) cc_final: 0.3903 (m-10) REVERT: A 4157 ASP cc_start: 0.9184 (t0) cc_final: 0.8696 (t0) REVERT: A 4244 GLU cc_start: 0.9326 (mm-30) cc_final: 0.9042 (mm-30) REVERT: A 4580 TYR cc_start: 0.7622 (OUTLIER) cc_final: 0.5718 (t80) REVERT: A 4806 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8238 (t0) REVERT: A 4954 MET cc_start: 0.8879 (mmm) cc_final: 0.8503 (mmm) REVERT: A 4989 MET cc_start: 0.8880 (tmm) cc_final: 0.8225 (tmm) REVERT: A 4998 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7957 (tttm) REVERT: A 5013 MET cc_start: 0.8742 (mtp) cc_final: 0.8522 (mmm) REVERT: B 116 MET cc_start: 0.8593 (mpp) cc_final: 0.8145 (mpp) REVERT: B 457 GLU cc_start: 0.9437 (tp30) cc_final: 0.9092 (tm-30) REVERT: B 891 TRP cc_start: 0.8498 (m-10) cc_final: 0.8268 (m100) REVERT: B 903 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6608 (pp) REVERT: B 961 MET cc_start: 0.6806 (pmm) cc_final: 0.6417 (pmm) REVERT: B 1152 MET cc_start: 0.8790 (mmm) cc_final: 0.7910 (mmm) REVERT: B 1260 MET cc_start: 0.8402 (pmm) cc_final: 0.8096 (pmm) REVERT: B 1981 MET cc_start: 0.8291 (mmm) cc_final: 0.7962 (mmp) REVERT: B 2178 MET cc_start: 0.8684 (ppp) cc_final: 0.8385 (ppp) REVERT: B 3201 MET cc_start: 0.7343 (ttm) cc_final: 0.6735 (ptm) REVERT: B 3437 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8304 (mpp) REVERT: B 3673 MET cc_start: 0.9460 (tpp) cc_final: 0.8694 (tpp) REVERT: B 3758 MET cc_start: 0.9061 (tmm) cc_final: 0.8849 (tmm) REVERT: B 3999 MET cc_start: 0.8971 (mmm) cc_final: 0.8593 (mmm) REVERT: B 4047 MET cc_start: 0.8595 (tmm) cc_final: 0.8132 (tmm) REVERT: B 4093 PHE cc_start: 0.4522 (m-10) cc_final: 0.4096 (m-10) REVERT: B 4157 ASP cc_start: 0.9177 (t0) cc_final: 0.8680 (t0) REVERT: B 4580 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.5989 (t80) REVERT: B 4806 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8335 (t0) REVERT: B 4818 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7361 (mmt) REVERT: B 5015 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8677 (mp10) REVERT: B 5032 TYR cc_start: 0.8580 (m-80) cc_final: 0.7909 (m-80) REVERT: C 116 MET cc_start: 0.8594 (mpp) cc_final: 0.8144 (mpp) REVERT: C 196 MET cc_start: 0.8682 (mpp) cc_final: 0.8328 (mpp) REVERT: C 457 GLU cc_start: 0.9437 (tp30) cc_final: 0.9092 (tm-30) REVERT: C 891 TRP cc_start: 0.8499 (m-10) cc_final: 0.8269 (m100) REVERT: C 903 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6604 (pp) REVERT: C 961 MET cc_start: 0.6809 (pmm) cc_final: 0.6417 (pmm) REVERT: C 1152 MET cc_start: 0.8787 (mmm) cc_final: 0.7908 (mmm) REVERT: C 1260 MET cc_start: 0.8405 (pmm) cc_final: 0.8097 (pmm) REVERT: C 1981 MET cc_start: 0.8291 (mmm) cc_final: 0.7962 (mmp) REVERT: C 2178 MET cc_start: 0.8692 (ppp) cc_final: 0.8382 (ppp) REVERT: C 3201 MET cc_start: 0.7347 (ttm) cc_final: 0.6738 (ptm) REVERT: C 3437 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8305 (mpp) REVERT: C 3673 MET cc_start: 0.9459 (tpp) cc_final: 0.8694 (tpp) REVERT: C 3758 MET cc_start: 0.9062 (tmm) cc_final: 0.8848 (tmm) REVERT: C 3999 MET cc_start: 0.8971 (mmm) cc_final: 0.8593 (mmm) REVERT: C 4047 MET cc_start: 0.8638 (tmm) cc_final: 0.8205 (tmm) REVERT: C 4093 PHE cc_start: 0.4517 (m-10) cc_final: 0.4093 (m-10) REVERT: C 4157 ASP cc_start: 0.9176 (t0) cc_final: 0.8680 (t0) REVERT: C 4580 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.5986 (t80) REVERT: C 4806 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8333 (t0) REVERT: C 4818 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7362 (mmt) REVERT: C 5015 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8678 (mp10) REVERT: C 5032 TYR cc_start: 0.8580 (m-80) cc_final: 0.7902 (m-80) REVERT: D 116 MET cc_start: 0.8592 (mpp) cc_final: 0.8144 (mpp) REVERT: D 457 GLU cc_start: 0.9437 (tp30) cc_final: 0.9091 (tm-30) REVERT: D 891 TRP cc_start: 0.8498 (m-10) cc_final: 0.8269 (m100) REVERT: D 903 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6604 (pp) REVERT: D 961 MET cc_start: 0.6811 (pmm) cc_final: 0.6419 (pmm) REVERT: D 1152 MET cc_start: 0.8789 (mmm) cc_final: 0.7910 (mmm) REVERT: D 1260 MET cc_start: 0.8405 (pmm) cc_final: 0.8098 (pmm) REVERT: D 2178 MET cc_start: 0.8685 (ppp) cc_final: 0.8382 (ppp) REVERT: D 3201 MET cc_start: 0.7345 (ttm) cc_final: 0.6737 (ptm) REVERT: D 3437 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8305 (mpp) REVERT: D 3673 MET cc_start: 0.9459 (tpp) cc_final: 0.8694 (tpp) REVERT: D 3758 MET cc_start: 0.9065 (tmm) cc_final: 0.8854 (tmm) REVERT: D 3999 MET cc_start: 0.8972 (mmm) cc_final: 0.8595 (mmm) REVERT: D 4047 MET cc_start: 0.8649 (tmm) cc_final: 0.8203 (tmm) REVERT: D 4093 PHE cc_start: 0.4515 (m-10) cc_final: 0.4091 (m-10) REVERT: D 4157 ASP cc_start: 0.9176 (t0) cc_final: 0.8679 (t0) REVERT: D 4580 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.5967 (t80) REVERT: D 4806 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8313 (t0) REVERT: D 4818 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7365 (mmt) REVERT: D 5015 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8679 (mp10) REVERT: D 5032 TYR cc_start: 0.8577 (m-80) cc_final: 0.7903 (m-80) outliers start: 193 outliers final: 126 residues processed: 915 average time/residue: 1.1612 time to fit residues: 1918.8789 Evaluate side-chains 908 residues out of total 15540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 758 time to evaluate : 12.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1608 MET Chi-restraints excluded: chain A residue 1769 THR Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2307 LEU Chi-restraints excluded: chain A residue 2423 MET Chi-restraints excluded: chain A residue 2585 THR Chi-restraints excluded: chain A residue 2816 MET Chi-restraints excluded: chain A residue 3304 CYS Chi-restraints excluded: chain A residue 3468 SER Chi-restraints excluded: chain A residue 3511 VAL Chi-restraints excluded: chain A residue 3528 THR Chi-restraints excluded: chain A residue 3529 ASP Chi-restraints excluded: chain A residue 3546 ASP Chi-restraints excluded: chain A residue 4050 GLU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4070 ASP Chi-restraints excluded: chain A residue 4088 ILE Chi-restraints excluded: chain A residue 4555 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4584 ASP Chi-restraints excluded: chain A residue 4628 VAL Chi-restraints excluded: chain A residue 4649 LEU Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4716 TRP Chi-restraints excluded: chain A residue 4800 LEU Chi-restraints excluded: chain A residue 4806 ASN Chi-restraints excluded: chain A residue 4876 CYS Chi-restraints excluded: chain A residue 4998 LYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 1608 MET Chi-restraints excluded: chain B residue 1769 THR Chi-restraints excluded: chain B residue 2209 GLU Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2307 LEU Chi-restraints excluded: chain B residue 2423 MET Chi-restraints excluded: chain B residue 2816 MET Chi-restraints excluded: chain B residue 3304 CYS Chi-restraints excluded: chain B residue 3437 MET Chi-restraints excluded: chain B residue 3511 VAL Chi-restraints excluded: chain B residue 3529 ASP Chi-restraints excluded: chain B residue 3546 ASP Chi-restraints excluded: chain B residue 4050 GLU Chi-restraints excluded: chain B residue 4057 MET Chi-restraints excluded: chain B residue 4070 ASP Chi-restraints excluded: chain B residue 4088 ILE Chi-restraints excluded: chain B residue 4209 GLN Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4581 LYS Chi-restraints excluded: chain B residue 4584 ASP Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4649 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4716 TRP Chi-restraints excluded: chain B residue 4800 LEU Chi-restraints excluded: chain B residue 4806 ASN Chi-restraints excluded: chain B residue 4818 MET Chi-restraints excluded: chain B residue 4861 LYS Chi-restraints excluded: chain B residue 4932 ILE Chi-restraints excluded: chain B residue 4955 GLU Chi-restraints excluded: chain B residue 5015 GLN Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 1608 MET Chi-restraints excluded: chain C residue 1769 THR Chi-restraints excluded: chain C residue 2209 GLU Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2307 LEU Chi-restraints excluded: chain C residue 2816 MET Chi-restraints excluded: chain C residue 3304 CYS Chi-restraints excluded: chain C residue 3437 MET Chi-restraints excluded: chain C residue 3511 VAL Chi-restraints excluded: chain C residue 3529 ASP Chi-restraints excluded: chain C residue 3546 ASP Chi-restraints excluded: chain C residue 4050 GLU Chi-restraints excluded: chain C residue 4057 MET Chi-restraints excluded: chain C residue 4070 ASP Chi-restraints excluded: chain C residue 4088 ILE Chi-restraints excluded: chain C residue 4209 GLN Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4581 LYS Chi-restraints excluded: chain C residue 4584 ASP Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4649 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4716 TRP Chi-restraints excluded: chain C residue 4800 LEU Chi-restraints excluded: chain C residue 4806 ASN Chi-restraints excluded: chain C residue 4818 MET Chi-restraints excluded: chain C residue 4861 LYS Chi-restraints excluded: chain C residue 4932 ILE Chi-restraints excluded: chain C residue 4955 GLU Chi-restraints excluded: chain C residue 5015 GLN Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1608 MET Chi-restraints excluded: chain D residue 1769 THR Chi-restraints excluded: chain D residue 2209 GLU Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2307 LEU Chi-restraints excluded: chain D residue 2816 MET Chi-restraints excluded: chain D residue 3304 CYS Chi-restraints excluded: chain D residue 3437 MET Chi-restraints excluded: chain D residue 3511 VAL Chi-restraints excluded: chain D residue 3529 ASP Chi-restraints excluded: chain D residue 3546 ASP Chi-restraints excluded: chain D residue 4050 GLU Chi-restraints excluded: chain D residue 4057 MET Chi-restraints excluded: chain D residue 4070 ASP Chi-restraints excluded: chain D residue 4088 ILE Chi-restraints excluded: chain D residue 4209 GLN Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4581 LYS Chi-restraints excluded: chain D residue 4584 ASP Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4649 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4716 TRP Chi-restraints excluded: chain D residue 4800 LEU Chi-restraints excluded: chain D residue 4806 ASN Chi-restraints excluded: chain D residue 4818 MET Chi-restraints excluded: chain D residue 4861 LYS Chi-restraints excluded: chain D residue 4932 ILE Chi-restraints excluded: chain D residue 4955 GLU Chi-restraints excluded: chain D residue 5015 GLN Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 94 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1667 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 985 optimal weight: 10.0000 chunk 1263 optimal weight: 7.9990 chunk 978 optimal weight: 20.0000 chunk 1456 optimal weight: 10.0000 chunk 966 optimal weight: 30.0000 chunk 1723 optimal weight: 4.9990 chunk 1078 optimal weight: 10.0000 chunk 1050 optimal weight: 5.9990 chunk 795 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3960 GLN ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A5015 GLN ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1158 ASN ** B2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2976 HIS B3960 GLN B4223 ASN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1158 ASN ** C2961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2976 HIS C3960 GLN C4054 ASN C4223 ASN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1158 ASN ** D2961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2976 HIS D3960 GLN D4223 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 146204 Z= 0.319 Angle : 0.676 13.404 198044 Z= 0.335 Chirality : 0.042 0.282 21776 Planarity : 0.004 0.058 25752 Dihedral : 5.243 152.392 19626 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.35 % Allowed : 12.30 % Favored : 86.34 % 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: 17832 helix: 1.07 (0.06), residues: 8852 sheet: -1.05 (0.13), residues: 1604 loop : -0.63 (0.07), residues: 7376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A2680 HIS 0.010 0.001 HIS D2498 PHE 0.033 0.002 PHE B3096 TYR 0.019 0.002 TYR A4851 ARG 0.006 0.001 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 15540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 773 time to evaluate : 12.304 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: symmetry clash REVERT: A 22 LEU cc_start: 0.9017 (mt) cc_final: 0.8751 (tp) REVERT: A 31 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7283 (pm20) REVERT: A 116 MET cc_start: 0.8540 (mpp) cc_final: 0.7941 (mpp) REVERT: A 202 MET cc_start: 0.8994 (tpt) cc_final: 0.8742 (tpt) REVERT: A 457 GLU cc_start: 0.9411 (tp30) cc_final: 0.9052 (tm-30) REVERT: A 891 TRP cc_start: 0.8607 (m-10) cc_final: 0.8234 (m-10) REVERT: A 903 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6570 (pp) REVERT: A 961 MET cc_start: 0.6752 (pmm) cc_final: 0.6488 (pmm) REVERT: A 1152 MET cc_start: 0.8758 (mmm) cc_final: 0.7927 (mmm) REVERT: A 1573 MET cc_start: 0.8124 (tpp) cc_final: 0.7718 (tpp) REVERT: A 1636 MET cc_start: 0.7846 (tmm) cc_final: 0.7629 (tmm) REVERT: A 2153 MET cc_start: 0.9336 (mmp) cc_final: 0.9005 (mmp) REVERT: A 2178 MET cc_start: 0.8851 (ppp) cc_final: 0.8579 (ppp) REVERT: A 2186 MET cc_start: 0.8733 (mmt) cc_final: 0.8492 (mmt) REVERT: A 2530 MET cc_start: 0.6756 (ppp) cc_final: 0.5623 (ppp) REVERT: A 3201 MET cc_start: 0.6823 (ptm) cc_final: 0.6256 (ptm) REVERT: A 3250 MET cc_start: 0.7960 (mmm) cc_final: 0.7671 (ptp) REVERT: A 3528 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8154 (t) REVERT: A 3673 MET cc_start: 0.9490 (tpp) cc_final: 0.8641 (tpp) REVERT: A 3757 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7328 (mt-10) REVERT: A 3999 MET cc_start: 0.9020 (mmm) cc_final: 0.8623 (mmm) REVERT: A 4047 MET cc_start: 0.8577 (tmm) cc_final: 0.8101 (tmm) REVERT: A 4093 PHE cc_start: 0.4788 (m-10) cc_final: 0.4360 (m-10) REVERT: A 4157 ASP cc_start: 0.9189 (t0) cc_final: 0.8700 (t0) REVERT: A 4580 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.5950 (t80) REVERT: A 4806 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8308 (t0) REVERT: A 4989 MET cc_start: 0.8933 (tmm) cc_final: 0.8241 (tmm) REVERT: A 4998 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7956 (tttm) REVERT: A 5013 MET cc_start: 0.8845 (mtp) cc_final: 0.8632 (mmm) REVERT: B 22 LEU cc_start: 0.9039 (mt) cc_final: 0.8774 (tp) REVERT: B 31 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7138 (pm20) REVERT: B 116 MET cc_start: 0.8552 (mpp) cc_final: 0.7928 (mpp) REVERT: B 202 MET cc_start: 0.8974 (tpt) cc_final: 0.8741 (tpt) REVERT: B 457 GLU cc_start: 0.9422 (tp30) cc_final: 0.9064 (tm-30) REVERT: B 891 TRP cc_start: 0.8473 (m-10) cc_final: 0.8114 (m-10) REVERT: B 903 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6391 (pp) REVERT: B 961 MET cc_start: 0.6991 (pmm) cc_final: 0.6671 (pmm) REVERT: B 1260 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7619 (pmm) REVERT: B 1981 MET cc_start: 0.8398 (mmm) cc_final: 0.8003 (mmp) REVERT: B 2178 MET cc_start: 0.8756 (ppp) cc_final: 0.8455 (ppp) REVERT: B 2186 MET cc_start: 0.8741 (mmt) cc_final: 0.8497 (mmt) REVERT: B 2208 MET cc_start: 0.9241 (ttp) cc_final: 0.8975 (ttm) REVERT: B 3250 MET cc_start: 0.7954 (mmm) cc_final: 0.7702 (ptp) REVERT: B 3573 MET cc_start: 0.8598 (mmt) cc_final: 0.8183 (mmp) REVERT: B 3673 MET cc_start: 0.9478 (tpp) cc_final: 0.8677 (tpp) REVERT: B 3999 MET cc_start: 0.9039 (mmm) cc_final: 0.8593 (mmm) REVERT: B 4047 MET cc_start: 0.8627 (tmm) cc_final: 0.8209 (tmm) REVERT: B 4048 LEU cc_start: 0.9519 (mt) cc_final: 0.9276 (mt) REVERT: B 4093 PHE cc_start: 0.4809 (m-10) cc_final: 0.4366 (m-10) REVERT: B 4157 ASP cc_start: 0.9180 (t0) cc_final: 0.8690 (t0) REVERT: B 4580 TYR cc_start: 0.7781 (OUTLIER) cc_final: 0.5964 (t80) REVERT: B 4806 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8310 (t0) REVERT: B 4818 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7450 (mmt) REVERT: B 5013 MET cc_start: 0.8748 (mmm) cc_final: 0.8466 (mmm) REVERT: B 5015 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8654 (mp10) REVERT: C 22 LEU cc_start: 0.9042 (mt) cc_final: 0.8777 (tp) REVERT: C 31 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7136 (pm20) REVERT: C 116 MET cc_start: 0.8554 (mpp) cc_final: 0.7929 (mpp) REVERT: C 202 MET cc_start: 0.8971 (tpt) cc_final: 0.8738 (tpt) REVERT: C 457 GLU cc_start: 0.9422 (tp30) cc_final: 0.9065 (tm-30) REVERT: C 891 TRP cc_start: 0.8472 (m-10) cc_final: 0.8113 (m-10) REVERT: C 903 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6391 (pp) REVERT: C 961 MET cc_start: 0.6991 (pmm) cc_final: 0.6670 (pmm) REVERT: C 1260 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7622 (pmm) REVERT: C 1981 MET cc_start: 0.8396 (mmm) cc_final: 0.8002 (mmp) REVERT: C 2178 MET cc_start: 0.8697 (ppp) cc_final: 0.8418 (ppp) REVERT: C 2186 MET cc_start: 0.8688 (mmt) cc_final: 0.8438 (mmt) REVERT: C 3250 MET cc_start: 0.7955 (mmm) cc_final: 0.7701 (ptp) REVERT: C 3573 MET cc_start: 0.8599 (mmt) cc_final: 0.8186 (mmp) REVERT: C 3673 MET cc_start: 0.9475 (tpp) cc_final: 0.8690 (tpp) REVERT: C 3999 MET cc_start: 0.9041 (mmm) cc_final: 0.8592 (mmm) REVERT: C 4047 MET cc_start: 0.8638 (tmm) cc_final: 0.8200 (tmm) REVERT: C 4048 LEU cc_start: 0.9521 (mt) cc_final: 0.9267 (mt) REVERT: C 4093 PHE cc_start: 0.4808 (m-10) cc_final: 0.4363 (m-10) REVERT: C 4157 ASP cc_start: 0.9180 (t0) cc_final: 0.8691 (t0) REVERT: C 4580 TYR cc_start: 0.7775 (OUTLIER) cc_final: 0.5945 (t80) REVERT: C 4806 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8306 (t0) REVERT: C 4818 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7451 (mmt) REVERT: C 5013 MET cc_start: 0.8748 (mmm) cc_final: 0.8467 (mmm) REVERT: C 5015 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8653 (mp10) REVERT: D 22 LEU cc_start: 0.9041 (mt) cc_final: 0.8776 (tp) REVERT: D 31 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7139 (pm20) REVERT: D 116 MET cc_start: 0.8552 (mpp) cc_final: 0.7928 (mpp) REVERT: D 202 MET cc_start: 0.8975 (tpt) cc_final: 0.8744 (tpt) REVERT: D 457 GLU cc_start: 0.9421 (tp30) cc_final: 0.9065 (tm-30) REVERT: D 891 TRP cc_start: 0.8471 (m-10) cc_final: 0.8113 (m-10) REVERT: D 903 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6391 (pp) REVERT: D 961 MET cc_start: 0.6993 (pmm) cc_final: 0.6671 (pmm) REVERT: D 1260 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7621 (pmm) REVERT: D 2178 MET cc_start: 0.8754 (ppp) cc_final: 0.8447 (ppp) REVERT: D 2186 MET cc_start: 0.8740 (mmt) cc_final: 0.8497 (mmt) REVERT: D 3250 MET cc_start: 0.7954 (mmm) cc_final: 0.7700 (ptp) REVERT: D 3573 MET cc_start: 0.8592 (mmt) cc_final: 0.8183 (mmp) REVERT: D 3673 MET cc_start: 0.9476 (tpp) cc_final: 0.8672 (tpp) REVERT: D 3999 MET cc_start: 0.9043 (mmm) cc_final: 0.8604 (mmm) REVERT: D 4047 MET cc_start: 0.8635 (tmm) cc_final: 0.8197 (tmm) REVERT: D 4048 LEU cc_start: 0.9520 (mt) cc_final: 0.9266 (mt) REVERT: D 4093 PHE cc_start: 0.4803 (m-10) cc_final: 0.4359 (m-10) REVERT: D 4157 ASP cc_start: 0.9181 (t0) cc_final: 0.8691 (t0) REVERT: D 4580 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.6014 (t80) REVERT: D 4806 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8286 (t0) REVERT: D 4818 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7454 (mmt) REVERT: D 4933 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8019 (mt0) REVERT: D 5013 MET cc_start: 0.8749 (mmm) cc_final: 0.8466 (mmm) REVERT: D 5015 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8651 (mp10) outliers start: 186 outliers final: 126 residues processed: 912 average time/residue: 1.1835 time to fit residues: 1938.6353 Evaluate side-chains 916 residues out of total 15540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 762 time to evaluate : 12.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1608 MET Chi-restraints excluded: chain A residue 1769 THR Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2307 LEU Chi-restraints excluded: chain A residue 2423 MET Chi-restraints excluded: chain A residue 2816 MET Chi-restraints excluded: chain A residue 3304 CYS Chi-restraints excluded: chain A residue 3468 SER Chi-restraints excluded: chain A residue 3511 VAL Chi-restraints excluded: chain A residue 3528 THR Chi-restraints excluded: chain A residue 3529 ASP Chi-restraints excluded: chain A residue 3546 ASP Chi-restraints excluded: chain A residue 4050 GLU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4088 ILE Chi-restraints excluded: chain A residue 4209 GLN Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4584 ASP Chi-restraints excluded: chain A residue 4628 VAL Chi-restraints excluded: chain A residue 4649 LEU Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4716 TRP Chi-restraints excluded: chain A residue 4800 LEU Chi-restraints excluded: chain A residue 4806 ASN Chi-restraints excluded: chain A residue 4852 THR Chi-restraints excluded: chain A residue 4876 CYS Chi-restraints excluded: chain A residue 4998 LYS Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 1260 MET Chi-restraints excluded: chain B residue 1608 MET Chi-restraints excluded: chain B residue 1769 THR Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2307 LEU Chi-restraints excluded: chain B residue 2423 MET Chi-restraints excluded: chain B residue 2816 MET Chi-restraints excluded: chain B residue 3304 CYS Chi-restraints excluded: chain B residue 3511 VAL Chi-restraints excluded: chain B residue 3529 ASP Chi-restraints excluded: chain B residue 3546 ASP Chi-restraints excluded: chain B residue 4050 GLU Chi-restraints excluded: chain B residue 4055 VAL Chi-restraints excluded: chain B residue 4057 MET Chi-restraints excluded: chain B residue 4088 ILE Chi-restraints excluded: chain B residue 4209 GLN Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4581 LYS Chi-restraints excluded: chain B residue 4584 ASP Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4649 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4716 TRP Chi-restraints excluded: chain B residue 4800 LEU Chi-restraints excluded: chain B residue 4806 ASN Chi-restraints excluded: chain B residue 4818 MET Chi-restraints excluded: chain B residue 4861 LYS Chi-restraints excluded: chain B residue 4932 ILE Chi-restraints excluded: chain B residue 4955 GLU Chi-restraints excluded: chain B residue 5015 GLN Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 1260 MET Chi-restraints excluded: chain C residue 1608 MET Chi-restraints excluded: chain C residue 1769 THR Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2307 LEU Chi-restraints excluded: chain C residue 2816 MET Chi-restraints excluded: chain C residue 3304 CYS Chi-restraints excluded: chain C residue 3511 VAL Chi-restraints excluded: chain C residue 3529 ASP Chi-restraints excluded: chain C residue 3546 ASP Chi-restraints excluded: chain C residue 4050 GLU Chi-restraints excluded: chain C residue 4055 VAL Chi-restraints excluded: chain C residue 4057 MET Chi-restraints excluded: chain C residue 4088 ILE Chi-restraints excluded: chain C residue 4209 GLN Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4581 LYS Chi-restraints excluded: chain C residue 4584 ASP Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4649 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4716 TRP Chi-restraints excluded: chain C residue 4800 LEU Chi-restraints excluded: chain C residue 4806 ASN Chi-restraints excluded: chain C residue 4818 MET Chi-restraints excluded: chain C residue 4852 THR Chi-restraints excluded: chain C residue 4861 LYS Chi-restraints excluded: chain C residue 4932 ILE Chi-restraints excluded: chain C residue 4955 GLU Chi-restraints excluded: chain C residue 5015 GLN Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1608 MET Chi-restraints excluded: chain D residue 1769 THR Chi-restraints excluded: chain D residue 2209 GLU Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2307 LEU Chi-restraints excluded: chain D residue 2816 MET Chi-restraints excluded: chain D residue 3304 CYS Chi-restraints excluded: chain D residue 3511 VAL Chi-restraints excluded: chain D residue 3529 ASP Chi-restraints excluded: chain D residue 3546 ASP Chi-restraints excluded: chain D residue 4050 GLU Chi-restraints excluded: chain D residue 4055 VAL Chi-restraints excluded: chain D residue 4088 ILE Chi-restraints excluded: chain D residue 4209 GLN Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4581 LYS Chi-restraints excluded: chain D residue 4584 ASP Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4649 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4716 TRP Chi-restraints excluded: chain D residue 4800 LEU Chi-restraints excluded: chain D residue 4806 ASN Chi-restraints excluded: chain D residue 4818 MET Chi-restraints excluded: chain D residue 4861 LYS Chi-restraints excluded: chain D residue 4932 ILE Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4955 GLU Chi-restraints excluded: chain D residue 5015 GLN Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 94 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1066 optimal weight: 2.9990 chunk 688 optimal weight: 30.0000 chunk 1029 optimal weight: 1.9990 chunk 519 optimal weight: 0.7980 chunk 338 optimal weight: 40.0000 chunk 333 optimal weight: 20.0000 chunk 1095 optimal weight: 10.0000 chunk 1174 optimal weight: 10.0000 chunk 852 optimal weight: 0.9980 chunk 160 optimal weight: 0.0060 chunk 1354 optimal weight: 6.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1133 HIS ** A2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4054 ASN ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A5015 GLN ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5015 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 146204 Z= 0.169 Angle : 0.607 14.192 198044 Z= 0.298 Chirality : 0.040 0.259 21776 Planarity : 0.004 0.057 25752 Dihedral : 5.054 149.885 19623 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.07 % Allowed : 12.94 % Favored : 85.99 % 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: 0.50 (0.07), residues: 17832 helix: 1.34 (0.06), residues: 8776 sheet: -1.07 (0.13), residues: 1560 loop : -0.49 (0.07), residues: 7496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2680 HIS 0.008 0.001 HIS A3771 PHE 0.031 0.001 PHE A3095 TYR 0.016 0.001 TYR A 565 ARG 0.005 0.000 ARG A 976 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 15540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 783 time to evaluate : 11.909 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: 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 31 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7221 (pm20) REVERT: A 116 MET cc_start: 0.8627 (mpp) cc_final: 0.8215 (mpp) REVERT: A 127 MET cc_start: 0.7830 (pmm) cc_final: 0.7625 (pmm) REVERT: A 457 GLU cc_start: 0.9417 (tp30) cc_final: 0.9070 (tm-30) REVERT: A 891 TRP cc_start: 0.8706 (m-10) cc_final: 0.8354 (m-10) REVERT: A 903 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6736 (pp) REVERT: A 961 MET cc_start: 0.6668 (pmm) cc_final: 0.6364 (pmm) REVERT: A 1260 MET cc_start: 0.8723 (pmm) cc_final: 0.8283 (pmm) REVERT: A 1573 MET cc_start: 0.8143 (tpp) cc_final: 0.7814 (tpp) REVERT: A 2153 MET cc_start: 0.9312 (mmp) cc_final: 0.8950 (mmp) REVERT: A 2178 MET cc_start: 0.8739 (ppp) cc_final: 0.8461 (ppp) REVERT: A 2530 MET cc_start: 0.6743 (ppp) cc_final: 0.5590 (ppp) REVERT: A 2639 MET cc_start: 0.8240 (ppp) cc_final: 0.7742 (ppp) REVERT: A 3201 MET cc_start: 0.6947 (ptm) cc_final: 0.6477 (ptm) REVERT: A 3250 MET cc_start: 0.7961 (mmm) cc_final: 0.7635 (ptp) REVERT: A 3335 MET cc_start: 0.7336 (mmm) cc_final: 0.7035 (mmm) REVERT: A 3467 MET cc_start: 0.5511 (tmm) cc_final: 0.5234 (tmm) REVERT: A 3573 MET cc_start: 0.8670 (mmt) cc_final: 0.8294 (mmp) REVERT: A 3673 MET cc_start: 0.9474 (tpp) cc_final: 0.8600 (tpp) REVERT: A 3757 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7258 (mt-10) REVERT: A 3999 MET cc_start: 0.8957 (mmm) cc_final: 0.8555 (mmm) REVERT: A 4093 PHE cc_start: 0.4779 (m-10) cc_final: 0.4444 (m-10) REVERT: A 4157 ASP cc_start: 0.9124 (t0) cc_final: 0.8632 (t0) REVERT: A 4580 TYR cc_start: 0.7616 (OUTLIER) cc_final: 0.5754 (t80) REVERT: A 4989 MET cc_start: 0.8898 (tmm) cc_final: 0.8648 (tpt) REVERT: A 4998 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7799 (tttm) REVERT: B 31 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7310 (pm20) REVERT: B 116 MET cc_start: 0.8543 (mpp) cc_final: 0.7908 (mpp) REVERT: B 413 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8578 (tm-30) REVERT: B 457 GLU cc_start: 0.9403 (tp30) cc_final: 0.9062 (tm-30) REVERT: B 891 TRP cc_start: 0.8449 (m-10) cc_final: 0.8212 (m100) REVERT: B 903 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6407 (pp) REVERT: B 961 MET cc_start: 0.6947 (pmm) cc_final: 0.6587 (pmm) REVERT: B 1260 MET cc_start: 0.8093 (pmm) cc_final: 0.7765 (pmm) REVERT: B 1981 MET cc_start: 0.8381 (mmm) cc_final: 0.7973 (mmp) REVERT: B 2178 MET cc_start: 0.8666 (ppp) cc_final: 0.8437 (ppp) REVERT: B 2203 MET cc_start: 0.9001 (pmm) cc_final: 0.8785 (pmm) REVERT: B 2639 MET cc_start: 0.8250 (ppp) cc_final: 0.7728 (ppp) REVERT: B 3201 MET cc_start: 0.7105 (ttm) cc_final: 0.6586 (ptm) REVERT: B 3250 MET cc_start: 0.7958 (mmm) cc_final: 0.7665 (ptp) REVERT: B 3437 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8265 (mpp) REVERT: B 3467 MET cc_start: 0.5466 (tmm) cc_final: 0.5165 (tmm) REVERT: B 3573 MET cc_start: 0.8594 (mmt) cc_final: 0.8188 (mmp) REVERT: B 3673 MET cc_start: 0.9462 (tpp) cc_final: 0.8614 (tpp) REVERT: B 3999 MET cc_start: 0.8961 (mmm) cc_final: 0.8553 (mmm) REVERT: B 4047 MET cc_start: 0.8569 (tmm) cc_final: 0.8171 (tmm) REVERT: B 4048 LEU cc_start: 0.9521 (mt) cc_final: 0.9280 (mt) REVERT: B 4093 PHE cc_start: 0.4902 (m-10) cc_final: 0.4530 (m-10) REVERT: B 4157 ASP cc_start: 0.9118 (t0) cc_final: 0.8624 (t0) REVERT: B 4231 MET cc_start: 0.9178 (mmm) cc_final: 0.8431 (mmm) REVERT: B 4580 TYR cc_start: 0.7688 (OUTLIER) cc_final: 0.5770 (t80) REVERT: B 4818 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7340 (mpp) REVERT: B 5013 MET cc_start: 0.8691 (mmm) cc_final: 0.8398 (mmm) REVERT: B 5015 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8616 (mp10) REVERT: B 5032 TYR cc_start: 0.8518 (m-80) cc_final: 0.7664 (m-80) REVERT: C 31 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7310 (pm20) REVERT: C 116 MET cc_start: 0.8546 (mpp) cc_final: 0.7907 (mpp) REVERT: C 457 GLU cc_start: 0.9402 (tp30) cc_final: 0.9063 (tm-30) REVERT: C 891 TRP cc_start: 0.8449 (m-10) cc_final: 0.8211 (m100) REVERT: C 903 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6408 (pp) REVERT: C 961 MET cc_start: 0.6947 (pmm) cc_final: 0.6586 (pmm) REVERT: C 1260 MET cc_start: 0.8096 (pmm) cc_final: 0.7768 (pmm) REVERT: C 1981 MET cc_start: 0.8381 (mmm) cc_final: 0.7972 (mmp) REVERT: C 2178 MET cc_start: 0.8614 (ppp) cc_final: 0.8399 (ppp) REVERT: C 2203 MET cc_start: 0.8994 (pmm) cc_final: 0.8777 (pmm) REVERT: C 2639 MET cc_start: 0.8250 (ppp) cc_final: 0.7727 (ppp) REVERT: C 3201 MET cc_start: 0.7112 (ttm) cc_final: 0.6589 (ptm) REVERT: C 3250 MET cc_start: 0.7958 (mmm) cc_final: 0.7664 (ptp) REVERT: C 3437 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8265 (mpp) REVERT: C 3467 MET cc_start: 0.5465 (tmm) cc_final: 0.5163 (tmm) REVERT: C 3573 MET cc_start: 0.8598 (mmt) cc_final: 0.8192 (mmp) REVERT: C 3673 MET cc_start: 0.9461 (tpp) cc_final: 0.8614 (tpp) REVERT: C 3999 MET cc_start: 0.8960 (mmm) cc_final: 0.8554 (mmm) REVERT: C 4047 MET cc_start: 0.8577 (tmm) cc_final: 0.8170 (tmm) REVERT: C 4048 LEU cc_start: 0.9522 (mt) cc_final: 0.9279 (mt) REVERT: C 4093 PHE cc_start: 0.4899 (m-10) cc_final: 0.4526 (m-10) REVERT: C 4157 ASP cc_start: 0.9114 (t0) cc_final: 0.8623 (t0) REVERT: C 4229 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8203 (pm20) REVERT: C 4231 MET cc_start: 0.9173 (mmm) cc_final: 0.8430 (mmm) REVERT: C 4580 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.5766 (t80) REVERT: C 4818 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7344 (mpp) REVERT: C 5013 MET cc_start: 0.8691 (mmm) cc_final: 0.8398 (mmm) REVERT: C 5015 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8613 (mp10) REVERT: C 5032 TYR cc_start: 0.8518 (m-80) cc_final: 0.7659 (m-80) REVERT: D 31 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7311 (pm20) REVERT: D 116 MET cc_start: 0.8544 (mpp) cc_final: 0.7907 (mpp) REVERT: D 413 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8580 (tm-30) REVERT: D 457 GLU cc_start: 0.9403 (tp30) cc_final: 0.9062 (tm-30) REVERT: D 891 TRP cc_start: 0.8467 (m-10) cc_final: 0.8240 (m100) REVERT: D 903 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6408 (pp) REVERT: D 961 MET cc_start: 0.6947 (pmm) cc_final: 0.6585 (pmm) REVERT: D 1260 MET cc_start: 0.8095 (pmm) cc_final: 0.7768 (pmm) REVERT: D 2178 MET cc_start: 0.8664 (ppp) cc_final: 0.8435 (ppp) REVERT: D 2203 MET cc_start: 0.8931 (pmm) cc_final: 0.8707 (pmm) REVERT: D 2639 MET cc_start: 0.8251 (ppp) cc_final: 0.7729 (ppp) REVERT: D 3201 MET cc_start: 0.7110 (ttm) cc_final: 0.6586 (ptm) REVERT: D 3250 MET cc_start: 0.7957 (mmm) cc_final: 0.7664 (ptp) REVERT: D 3437 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8265 (mpp) REVERT: D 3467 MET cc_start: 0.5466 (tmm) cc_final: 0.5165 (tmm) REVERT: D 3573 MET cc_start: 0.8564 (mmt) cc_final: 0.8134 (mmp) REVERT: D 3673 MET cc_start: 0.9462 (tpp) cc_final: 0.8613 (tpp) REVERT: D 3999 MET cc_start: 0.8961 (mmm) cc_final: 0.8557 (mmm) REVERT: D 4047 MET cc_start: 0.8576 (tmm) cc_final: 0.8168 (tmm) REVERT: D 4048 LEU cc_start: 0.9521 (mt) cc_final: 0.9278 (mt) REVERT: D 4093 PHE cc_start: 0.4896 (m-10) cc_final: 0.4525 (m-10) REVERT: D 4157 ASP cc_start: 0.9115 (t0) cc_final: 0.8622 (t0) REVERT: D 4229 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8214 (pm20) REVERT: D 4231 MET cc_start: 0.9177 (mmm) cc_final: 0.8435 (mmm) REVERT: D 4580 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.5875 (t80) REVERT: D 4818 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7323 (mpp) REVERT: D 5013 MET cc_start: 0.8695 (mmm) cc_final: 0.8402 (mmm) REVERT: D 5015 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8579 (mp10) REVERT: D 5032 TYR cc_start: 0.8515 (m-80) cc_final: 0.7659 (m-80) REVERT: E 66 MET cc_start: 0.6995 (pmm) cc_final: 0.6627 (pmm) REVERT: F 66 MET cc_start: 0.6997 (pmm) cc_final: 0.6627 (pmm) REVERT: G 66 MET cc_start: 0.6996 (pmm) cc_final: 0.6626 (pmm) REVERT: H 66 MET cc_start: 0.6994 (pmm) cc_final: 0.6626 (pmm) outliers start: 142 outliers final: 94 residues processed: 893 average time/residue: 1.2213 time to fit residues: 1969.6266 Evaluate side-chains 879 residues out of total 15540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 761 time to evaluate : 11.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1769 THR Chi-restraints excluded: chain A residue 2307 LEU Chi-restraints excluded: chain A residue 2423 MET Chi-restraints excluded: chain A residue 2816 MET Chi-restraints excluded: chain A residue 3304 CYS Chi-restraints excluded: chain A residue 3468 SER Chi-restraints excluded: chain A residue 3511 VAL Chi-restraints excluded: chain A residue 3529 ASP Chi-restraints excluded: chain A residue 4050 GLU Chi-restraints excluded: chain A residue 4057 MET Chi-restraints excluded: chain A residue 4555 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4584 ASP Chi-restraints excluded: chain A residue 4628 VAL Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4716 TRP Chi-restraints excluded: chain A residue 4800 LEU Chi-restraints excluded: chain A residue 4876 CYS Chi-restraints excluded: chain A residue 4998 LYS Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 1769 THR Chi-restraints excluded: chain B residue 2307 LEU Chi-restraints excluded: chain B residue 2423 MET Chi-restraints excluded: chain B residue 2585 THR Chi-restraints excluded: chain B residue 2816 MET Chi-restraints excluded: chain B residue 3304 CYS Chi-restraints excluded: chain B residue 3437 MET Chi-restraints excluded: chain B residue 3511 VAL Chi-restraints excluded: chain B residue 3546 ASP Chi-restraints excluded: chain B residue 4050 GLU Chi-restraints excluded: chain B residue 4057 MET Chi-restraints excluded: chain B residue 4209 GLN Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4581 LYS Chi-restraints excluded: chain B residue 4584 ASP Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4649 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4716 TRP Chi-restraints excluded: chain B residue 4800 LEU Chi-restraints excluded: chain B residue 4818 MET Chi-restraints excluded: chain B residue 4861 LYS Chi-restraints excluded: chain B residue 4932 ILE Chi-restraints excluded: chain B residue 4955 GLU Chi-restraints excluded: chain B residue 5015 GLN Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 1769 THR Chi-restraints excluded: chain C residue 2307 LEU Chi-restraints excluded: chain C residue 2585 THR Chi-restraints excluded: chain C residue 2816 MET Chi-restraints excluded: chain C residue 3304 CYS Chi-restraints excluded: chain C residue 3437 MET Chi-restraints excluded: chain C residue 3511 VAL Chi-restraints excluded: chain C residue 3546 ASP Chi-restraints excluded: chain C residue 4050 GLU Chi-restraints excluded: chain C residue 4057 MET Chi-restraints excluded: chain C residue 4209 GLN Chi-restraints excluded: chain C residue 4229 GLU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4581 LYS Chi-restraints excluded: chain C residue 4584 ASP Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4649 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4716 TRP Chi-restraints excluded: chain C residue 4800 LEU Chi-restraints excluded: chain C residue 4818 MET Chi-restraints excluded: chain C residue 4861 LYS Chi-restraints excluded: chain C residue 4932 ILE Chi-restraints excluded: chain C residue 4955 GLU Chi-restraints excluded: chain C residue 5015 GLN Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1769 THR Chi-restraints excluded: chain D residue 2209 GLU Chi-restraints excluded: chain D residue 2307 LEU Chi-restraints excluded: chain D residue 2585 THR Chi-restraints excluded: chain D residue 2816 MET Chi-restraints excluded: chain D residue 3304 CYS Chi-restraints excluded: chain D residue 3437 MET Chi-restraints excluded: chain D residue 3511 VAL Chi-restraints excluded: chain D residue 3546 ASP Chi-restraints excluded: chain D residue 4050 GLU Chi-restraints excluded: chain D residue 4209 GLN Chi-restraints excluded: chain D residue 4229 GLU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4581 LYS Chi-restraints excluded: chain D residue 4584 ASP Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4649 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4716 TRP Chi-restraints excluded: chain D residue 4800 LEU Chi-restraints excluded: chain D residue 4818 MET Chi-restraints excluded: chain D residue 4861 LYS Chi-restraints excluded: chain D residue 4955 GLU Chi-restraints excluded: chain D residue 5015 GLN Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain H residue 79 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1567 optimal weight: 5.9990 chunk 1651 optimal weight: 5.9990 chunk 1506 optimal weight: 3.9990 chunk 1605 optimal weight: 20.0000 chunk 1650 optimal weight: 6.9990 chunk 966 optimal weight: 30.0000 chunk 699 optimal weight: 5.9990 chunk 1261 optimal weight: 3.9990 chunk 492 optimal weight: 3.9990 chunk 1451 optimal weight: 0.9990 chunk 1518 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4094 GLN ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4094 GLN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4094 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 146204 Z= 0.257 Angle : 0.639 13.803 198044 Z= 0.314 Chirality : 0.041 0.265 21776 Planarity : 0.004 0.056 25752 Dihedral : 5.064 150.271 19623 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.08 % Allowed : 12.97 % Favored : 85.95 % 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: 0.40 (0.06), residues: 17832 helix: 1.25 (0.06), residues: 8828 sheet: -1.13 (0.13), residues: 1548 loop : -0.53 (0.07), residues: 7456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A5011 HIS 0.008 0.001 HIS D2498 PHE 0.031 0.002 PHE C3096 TYR 0.038 0.001 TYR D5014 ARG 0.005 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 15540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 765 time to evaluate : 12.473 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7298 (pm20) REVERT: A 116 MET cc_start: 0.8627 (mpp) cc_final: 0.7940 (mpp) REVERT: A 457 GLU cc_start: 0.9418 (tp30) cc_final: 0.9075 (tm-30) REVERT: A 891 TRP cc_start: 0.8649 (m-10) cc_final: 0.8286 (m-10) REVERT: A 903 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6584 (pp) REVERT: A 961 MET cc_start: 0.6820 (pmm) cc_final: 0.6519 (pmm) REVERT: A 1152 MET cc_start: 0.8712 (mmm) cc_final: 0.7842 (mmm) REVERT: A 1260 MET cc_start: 0.8742 (pmm) cc_final: 0.8296 (pmm) REVERT: A 1573 MET cc_start: 0.8198 (tpp) cc_final: 0.7951 (tpp) REVERT: A 2153 MET cc_start: 0.9318 (mmp) cc_final: 0.8948 (mmp) REVERT: A 2170 MET cc_start: 0.8255 (tpp) cc_final: 0.7966 (tpt) REVERT: A 2178 MET cc_start: 0.8725 (ppp) cc_final: 0.8465 (ppp) REVERT: A 2198 MET cc_start: 0.8788 (mmp) cc_final: 0.8527 (mmp) REVERT: A 2530 MET cc_start: 0.6843 (ppp) cc_final: 0.5726 (ppp) REVERT: A 3201 MET cc_start: 0.6963 (ptm) cc_final: 0.6498 (ptm) REVERT: A 3250 MET cc_start: 0.7983 (mmm) cc_final: 0.7707 (ptp) REVERT: A 3467 MET cc_start: 0.5512 (tmm) cc_final: 0.5228 (tmm) REVERT: A 3573 MET cc_start: 0.8610 (mmt) cc_final: 0.8265 (mmp) REVERT: A 3757 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7316 (mt-10) REVERT: A 3999 MET cc_start: 0.8972 (mmm) cc_final: 0.8674 (mmm) REVERT: A 4047 MET cc_start: 0.8457 (tmm) cc_final: 0.8182 (tmm) REVERT: A 4093 PHE cc_start: 0.4982 (m-10) cc_final: 0.4623 (m-10) REVERT: A 4157 ASP cc_start: 0.9153 (t0) cc_final: 0.8662 (t0) REVERT: A 4580 TYR cc_start: 0.7706 (OUTLIER) cc_final: 0.5794 (t80) REVERT: A 4989 MET cc_start: 0.8870 (tmm) cc_final: 0.8201 (tmm) REVERT: B 31 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7161 (pm20) REVERT: B 116 MET cc_start: 0.8545 (mpp) cc_final: 0.7681 (mpp) REVERT: B 413 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8564 (tm-30) REVERT: B 457 GLU cc_start: 0.9412 (tp30) cc_final: 0.9056 (tm-30) REVERT: B 891 TRP cc_start: 0.8489 (m-10) cc_final: 0.8269 (m100) REVERT: B 903 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6468 (pp) REVERT: B 961 MET cc_start: 0.7048 (pmm) cc_final: 0.6751 (pmm) REVERT: B 1152 MET cc_start: 0.8635 (mmm) cc_final: 0.7802 (mmm) REVERT: B 1260 MET cc_start: 0.8291 (pmm) cc_final: 0.7710 (pmm) REVERT: B 1981 MET cc_start: 0.8389 (mmm) cc_final: 0.7980 (mmp) REVERT: B 2178 MET cc_start: 0.8727 (ppp) cc_final: 0.8426 (ppp) REVERT: B 2203 MET cc_start: 0.8950 (pmm) cc_final: 0.8737 (pmm) REVERT: B 3201 MET cc_start: 0.7138 (ttm) cc_final: 0.6605 (ptm) REVERT: B 3250 MET cc_start: 0.7957 (mmm) cc_final: 0.7702 (ptp) REVERT: B 3437 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8278 (mpp) REVERT: B 3573 MET cc_start: 0.8607 (mmt) cc_final: 0.8223 (mmp) REVERT: B 3673 MET cc_start: 0.9453 (tpp) cc_final: 0.8626 (tpp) REVERT: B 3999 MET cc_start: 0.8972 (mmm) cc_final: 0.8665 (mmm) REVERT: B 4093 PHE cc_start: 0.5010 (m-10) cc_final: 0.4621 (m-10) REVERT: B 4157 ASP cc_start: 0.9152 (t0) cc_final: 0.8655 (t0) REVERT: B 4229 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8223 (pm20) REVERT: B 4580 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.5867 (t80) REVERT: B 4818 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7199 (mmt) REVERT: B 5013 MET cc_start: 0.8768 (mmm) cc_final: 0.8326 (mmm) REVERT: B 5015 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8647 (mp10) REVERT: C 31 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7161 (pm20) REVERT: C 116 MET cc_start: 0.8543 (mpp) cc_final: 0.7679 (mpp) REVERT: C 457 GLU cc_start: 0.9412 (tp30) cc_final: 0.9057 (tm-30) REVERT: C 891 TRP cc_start: 0.8487 (m-10) cc_final: 0.8267 (m100) REVERT: C 903 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6469 (pp) REVERT: C 961 MET cc_start: 0.7049 (pmm) cc_final: 0.6749 (pmm) REVERT: C 1152 MET cc_start: 0.8635 (mmm) cc_final: 0.7805 (mmm) REVERT: C 1260 MET cc_start: 0.8291 (pmm) cc_final: 0.7709 (pmm) REVERT: C 1981 MET cc_start: 0.8389 (mmm) cc_final: 0.7980 (mmp) REVERT: C 2178 MET cc_start: 0.8716 (ppp) cc_final: 0.8419 (ppp) REVERT: C 2203 MET cc_start: 0.8972 (pmm) cc_final: 0.8768 (pmm) REVERT: C 3201 MET cc_start: 0.7146 (ttm) cc_final: 0.6609 (ptm) REVERT: C 3250 MET cc_start: 0.7956 (mmm) cc_final: 0.7701 (ptp) REVERT: C 3437 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8276 (mpp) REVERT: C 3573 MET cc_start: 0.8610 (mmt) cc_final: 0.8226 (mmp) REVERT: C 3673 MET cc_start: 0.9449 (tpp) cc_final: 0.8626 (tpp) REVERT: C 3999 MET cc_start: 0.8972 (mmm) cc_final: 0.8665 (mmm) REVERT: C 4093 PHE cc_start: 0.5010 (m-10) cc_final: 0.4621 (m-10) REVERT: C 4157 ASP cc_start: 0.9152 (t0) cc_final: 0.8657 (t0) REVERT: C 4229 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8222 (pm20) REVERT: C 4231 MET cc_start: 0.9208 (mmm) cc_final: 0.8410 (mmm) REVERT: C 4580 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.5844 (t80) REVERT: C 4818 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7205 (mmt) REVERT: C 5013 MET cc_start: 0.8766 (mmm) cc_final: 0.8328 (mmm) REVERT: C 5015 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8645 (mp10) REVERT: D 31 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7162 (pm20) REVERT: D 116 MET cc_start: 0.8542 (mpp) cc_final: 0.7680 (mpp) REVERT: D 413 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8566 (tm-30) REVERT: D 457 GLU cc_start: 0.9412 (tp30) cc_final: 0.9056 (tm-30) REVERT: D 891 TRP cc_start: 0.8486 (m-10) cc_final: 0.8267 (m100) REVERT: D 903 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6468 (pp) REVERT: D 961 MET cc_start: 0.7049 (pmm) cc_final: 0.6746 (pmm) REVERT: D 1152 MET cc_start: 0.8637 (mmm) cc_final: 0.7807 (mmm) REVERT: D 1260 MET cc_start: 0.8293 (pmm) cc_final: 0.7711 (pmm) REVERT: D 2178 MET cc_start: 0.8727 (ppp) cc_final: 0.8424 (ppp) REVERT: D 2203 MET cc_start: 0.8956 (pmm) cc_final: 0.8727 (pmm) REVERT: D 3201 MET cc_start: 0.7144 (ttm) cc_final: 0.6609 (ptm) REVERT: D 3250 MET cc_start: 0.7976 (mmm) cc_final: 0.7680 (ptp) REVERT: D 3437 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8278 (mpp) REVERT: D 3517 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8370 (tmm) REVERT: D 3573 MET cc_start: 0.8572 (mmt) cc_final: 0.8166 (mmp) REVERT: D 3673 MET cc_start: 0.9450 (tpp) cc_final: 0.8626 (tpp) REVERT: D 3999 MET cc_start: 0.8975 (mmm) cc_final: 0.8671 (mmm) REVERT: D 4093 PHE cc_start: 0.5002 (m-10) cc_final: 0.4616 (m-10) REVERT: D 4157 ASP cc_start: 0.9152 (t0) cc_final: 0.8657 (t0) REVERT: D 4229 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8226 (pm20) REVERT: D 4580 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.5896 (t80) REVERT: D 4818 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7249 (mmt) REVERT: D 5013 MET cc_start: 0.8842 (mmm) cc_final: 0.8437 (mmm) outliers start: 143 outliers final: 113 residues processed: 879 average time/residue: 1.1860 time to fit residues: 1888.3124 Evaluate side-chains 895 residues out of total 15540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 758 time to evaluate : 12.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1769 THR Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2307 LEU Chi-restraints excluded: chain A residue 2423 MET Chi-restraints excluded: chain A residue 2816 MET Chi-restraints excluded: chain A residue 3304 CYS Chi-restraints excluded: chain A residue 3468 SER Chi-restraints excluded: chain A residue 3511 VAL Chi-restraints excluded: chain A residue 3529 ASP Chi-restraints excluded: chain A residue 4050 GLU Chi-restraints excluded: chain A residue 4057 MET Chi-restraints excluded: chain A residue 4088 ILE Chi-restraints excluded: chain A residue 4209 GLN Chi-restraints excluded: chain A residue 4555 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4584 ASP Chi-restraints excluded: chain A residue 4628 VAL Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4716 TRP Chi-restraints excluded: chain A residue 4800 LEU Chi-restraints excluded: chain A residue 4876 CYS Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 1769 THR Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2307 LEU Chi-restraints excluded: chain B residue 2423 MET Chi-restraints excluded: chain B residue 2585 THR Chi-restraints excluded: chain B residue 2816 MET Chi-restraints excluded: chain B residue 3304 CYS Chi-restraints excluded: chain B residue 3437 MET Chi-restraints excluded: chain B residue 3511 VAL Chi-restraints excluded: chain B residue 3517 MET Chi-restraints excluded: chain B residue 3546 ASP Chi-restraints excluded: chain B residue 4050 GLU Chi-restraints excluded: chain B residue 4057 MET Chi-restraints excluded: chain B residue 4088 ILE Chi-restraints excluded: chain B residue 4209 GLN Chi-restraints excluded: chain B residue 4229 GLU Chi-restraints excluded: chain B residue 4555 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4581 LYS Chi-restraints excluded: chain B residue 4584 ASP Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4649 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4716 TRP Chi-restraints excluded: chain B residue 4800 LEU Chi-restraints excluded: chain B residue 4818 MET Chi-restraints excluded: chain B residue 4852 THR Chi-restraints excluded: chain B residue 4861 LYS Chi-restraints excluded: chain B residue 4932 ILE Chi-restraints excluded: chain B residue 4955 GLU Chi-restraints excluded: chain B residue 5015 GLN Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 1769 THR Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2307 LEU Chi-restraints excluded: chain C residue 2585 THR Chi-restraints excluded: chain C residue 2816 MET Chi-restraints excluded: chain C residue 3304 CYS Chi-restraints excluded: chain C residue 3437 MET Chi-restraints excluded: chain C residue 3511 VAL Chi-restraints excluded: chain C residue 3517 MET Chi-restraints excluded: chain C residue 3546 ASP Chi-restraints excluded: chain C residue 4050 GLU Chi-restraints excluded: chain C residue 4057 MET Chi-restraints excluded: chain C residue 4088 ILE Chi-restraints excluded: chain C residue 4209 GLN Chi-restraints excluded: chain C residue 4229 GLU Chi-restraints excluded: chain C residue 4555 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4581 LYS Chi-restraints excluded: chain C residue 4584 ASP Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4649 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4716 TRP Chi-restraints excluded: chain C residue 4800 LEU Chi-restraints excluded: chain C residue 4818 MET Chi-restraints excluded: chain C residue 4861 LYS Chi-restraints excluded: chain C residue 4932 ILE Chi-restraints excluded: chain C residue 4955 GLU Chi-restraints excluded: chain C residue 5015 GLN Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1769 THR Chi-restraints excluded: chain D residue 2209 GLU Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2307 LEU Chi-restraints excluded: chain D residue 2585 THR Chi-restraints excluded: chain D residue 2816 MET Chi-restraints excluded: chain D residue 3304 CYS Chi-restraints excluded: chain D residue 3437 MET Chi-restraints excluded: chain D residue 3511 VAL Chi-restraints excluded: chain D residue 3517 MET Chi-restraints excluded: chain D residue 3546 ASP Chi-restraints excluded: chain D residue 4050 GLU Chi-restraints excluded: chain D residue 4088 ILE Chi-restraints excluded: chain D residue 4209 GLN Chi-restraints excluded: chain D residue 4229 GLU Chi-restraints excluded: chain D residue 4555 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4581 LYS Chi-restraints excluded: chain D residue 4584 ASP Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4649 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4716 TRP Chi-restraints excluded: chain D residue 4800 LEU Chi-restraints excluded: chain D residue 4818 MET Chi-restraints excluded: chain D residue 4852 THR Chi-restraints excluded: chain D residue 4861 LYS Chi-restraints excluded: chain D residue 4932 ILE Chi-restraints excluded: chain D residue 4955 GLU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain H residue 79 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1600 optimal weight: 9.9990 chunk 1054 optimal weight: 0.2980 chunk 1698 optimal weight: 0.6980 chunk 1036 optimal weight: 0.0000 chunk 805 optimal weight: 3.9990 chunk 1180 optimal weight: 0.8980 chunk 1781 optimal weight: 9.9990 chunk 1639 optimal weight: 0.9990 chunk 1418 optimal weight: 0.6980 chunk 147 optimal weight: 8.9990 chunk 1095 optimal weight: 3.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 GLN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2498 HIS A2514 ASN ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2498 HIS B2962 GLN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 GLN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C5015 GLN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 GLN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2962 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 146204 Z= 0.154 Angle : 0.612 14.585 198044 Z= 0.298 Chirality : 0.040 0.248 21776 Planarity : 0.004 0.056 25752 Dihedral : 4.945 147.548 19623 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.84 % Allowed : 13.31 % Favored : 85.85 % 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: 0.60 (0.07), residues: 17832 helix: 1.42 (0.06), residues: 8800 sheet: -1.07 (0.13), residues: 1580 loop : -0.42 (0.08), residues: 7452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C2680 HIS 0.008 0.001 HIS A3771 PHE 0.033 0.001 PHE A3095 TYR 0.016 0.001 TYR D5032 ARG 0.005 0.000 ARG A1982 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 15540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 800 time to evaluate : 12.313 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 31 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7214 (pm20) REVERT: A 116 MET cc_start: 0.8598 (mpp) cc_final: 0.8189 (mpp) REVERT: A 127 MET cc_start: 0.7813 (pmm) cc_final: 0.7595 (pmm) REVERT: A 457 GLU cc_start: 0.9403 (tp30) cc_final: 0.9025 (tm-30) REVERT: A 891 TRP cc_start: 0.8714 (m-10) cc_final: 0.8356 (m-10) REVERT: A 903 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6740 (pp) REVERT: A 1152 MET cc_start: 0.8548 (mmm) cc_final: 0.7703 (mmm) REVERT: A 1260 MET cc_start: 0.8723 (pmm) cc_final: 0.8256 (pmm) REVERT: A 1573 MET cc_start: 0.8157 (tpp) cc_final: 0.7911 (tpp) REVERT: A 2153 MET cc_start: 0.9293 (mmp) cc_final: 0.8969 (mmp) REVERT: A 2170 MET cc_start: 0.8131 (tpp) cc_final: 0.7820 (tpt) REVERT: A 2178 MET cc_start: 0.8680 (ppp) cc_final: 0.8390 (ppp) REVERT: A 2198 MET cc_start: 0.8716 (mmp) cc_final: 0.8505 (mmp) REVERT: A 2530 MET cc_start: 0.6915 (ppp) cc_final: 0.5763 (ppp) REVERT: A 2639 MET cc_start: 0.8206 (ppp) cc_final: 0.7656 (ppp) REVERT: A 3201 MET cc_start: 0.6984 (ptm) cc_final: 0.6528 (ptm) REVERT: A 3250 MET cc_start: 0.8007 (mmm) cc_final: 0.7711 (ptp) REVERT: A 3335 MET cc_start: 0.7113 (mmm) cc_final: 0.6834 (mmm) REVERT: A 3573 MET cc_start: 0.8608 (mmt) cc_final: 0.8223 (mmp) REVERT: A 3673 MET cc_start: 0.9448 (tpp) cc_final: 0.8793 (ttm) REVERT: A 3757 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7271 (mt-10) REVERT: A 3999 MET cc_start: 0.8952 (mmm) cc_final: 0.8610 (mmm) REVERT: A 4047 MET cc_start: 0.8444 (tmm) cc_final: 0.8177 (tmm) REVERT: A 4093 PHE cc_start: 0.4986 (m-10) cc_final: 0.4587 (m-10) REVERT: A 4157 ASP cc_start: 0.9092 (t0) cc_final: 0.8600 (t0) REVERT: A 4231 MET cc_start: 0.8967 (mmm) cc_final: 0.8409 (mmm) REVERT: A 4580 TYR cc_start: 0.7554 (OUTLIER) cc_final: 0.5745 (t80) REVERT: A 4989 MET cc_start: 0.8870 (tmm) cc_final: 0.8624 (tpt) REVERT: B 31 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7312 (pm20) REVERT: B 116 MET cc_start: 0.8526 (mpp) cc_final: 0.8047 (mpp) REVERT: B 413 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8530 (tm-30) REVERT: B 457 GLU cc_start: 0.9406 (tp30) cc_final: 0.9056 (tm-30) REVERT: B 891 TRP cc_start: 0.8461 (m-10) cc_final: 0.8240 (m100) REVERT: B 903 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6381 (pp) REVERT: B 961 MET cc_start: 0.6761 (pmm) cc_final: 0.6395 (pmm) REVERT: B 1152 MET cc_start: 0.8610 (mmm) cc_final: 0.7767 (mmm) REVERT: B 1260 MET cc_start: 0.8092 (pmm) cc_final: 0.7724 (pmm) REVERT: B 1494 MET cc_start: 0.7730 (mmt) cc_final: 0.7356 (mmp) REVERT: B 1981 MET cc_start: 0.8371 (mmm) cc_final: 0.7972 (mmp) REVERT: B 2178 MET cc_start: 0.8664 (ppp) cc_final: 0.8440 (ppp) REVERT: B 2546 MET cc_start: 0.6899 (tpp) cc_final: 0.6424 (tpp) REVERT: B 2639 MET cc_start: 0.8266 (ppp) cc_final: 0.7708 (ppp) REVERT: B 3201 MET cc_start: 0.7364 (ttm) cc_final: 0.6772 (ptm) REVERT: B 3250 MET cc_start: 0.7976 (mmm) cc_final: 0.7638 (ptp) REVERT: B 3437 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8365 (mpp) REVERT: B 3467 MET cc_start: 0.5458 (tmm) cc_final: 0.5169 (tmm) REVERT: B 3573 MET cc_start: 0.8512 (mmt) cc_final: 0.8068 (mmp) REVERT: B 3673 MET cc_start: 0.9434 (tpp) cc_final: 0.8581 (tpp) REVERT: B 3999 MET cc_start: 0.8932 (mmm) cc_final: 0.8570 (mmm) REVERT: B 4047 MET cc_start: 0.8449 (tmm) cc_final: 0.8192 (tmm) REVERT: B 4093 PHE cc_start: 0.5132 (m-10) cc_final: 0.4777 (m-10) REVERT: B 4157 ASP cc_start: 0.9085 (t0) cc_final: 0.8591 (t0) REVERT: B 4229 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8288 (pm20) REVERT: B 4231 MET cc_start: 0.8952 (mmm) cc_final: 0.8356 (mmm) REVERT: B 4580 TYR cc_start: 0.7616 (OUTLIER) cc_final: 0.5770 (t80) REVERT: B 4581 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7293 (tptp) REVERT: B 4818 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.6990 (mmt) REVERT: B 5013 MET cc_start: 0.8754 (mmm) cc_final: 0.8437 (mmm) REVERT: B 5015 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8581 (mp10) REVERT: C 31 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7310 (pm20) REVERT: C 116 MET cc_start: 0.8523 (mpp) cc_final: 0.8047 (mpp) REVERT: C 457 GLU cc_start: 0.9405 (tp30) cc_final: 0.9057 (tm-30) REVERT: C 891 TRP cc_start: 0.8461 (m-10) cc_final: 0.8240 (m100) REVERT: C 903 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6385 (pp) REVERT: C 961 MET cc_start: 0.6826 (pmm) cc_final: 0.6465 (pmm) REVERT: C 1152 MET cc_start: 0.8617 (mmm) cc_final: 0.7774 (mmm) REVERT: C 1260 MET cc_start: 0.8093 (pmm) cc_final: 0.7724 (pmm) REVERT: C 1494 MET cc_start: 0.7728 (mmt) cc_final: 0.7355 (mmp) REVERT: C 1981 MET cc_start: 0.8371 (mmm) cc_final: 0.7975 (mmp) REVERT: C 2178 MET cc_start: 0.8644 (ppp) cc_final: 0.8430 (ppp) REVERT: C 2639 MET cc_start: 0.8267 (ppp) cc_final: 0.7706 (ppp) REVERT: C 3201 MET cc_start: 0.7374 (ttm) cc_final: 0.6777 (ptm) REVERT: C 3250 MET cc_start: 0.7976 (mmm) cc_final: 0.7637 (ptp) REVERT: C 3437 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8364 (mpp) REVERT: C 3467 MET cc_start: 0.5454 (tmm) cc_final: 0.5167 (tmm) REVERT: C 3517 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8302 (tmm) REVERT: C 3573 MET cc_start: 0.8516 (mmt) cc_final: 0.8071 (mmp) REVERT: C 3673 MET cc_start: 0.9432 (tpp) cc_final: 0.8579 (tpp) REVERT: C 3999 MET cc_start: 0.8931 (mmm) cc_final: 0.8570 (mmm) REVERT: C 4047 MET cc_start: 0.8447 (tmm) cc_final: 0.8193 (tmm) REVERT: C 4093 PHE cc_start: 0.5040 (m-10) cc_final: 0.4670 (m-10) REVERT: C 4157 ASP cc_start: 0.9084 (t0) cc_final: 0.8590 (t0) REVERT: C 4231 MET cc_start: 0.9096 (mmm) cc_final: 0.8349 (mmm) REVERT: C 4580 TYR cc_start: 0.7613 (OUTLIER) cc_final: 0.5771 (t80) REVERT: C 4581 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7294 (tptp) REVERT: C 4989 MET cc_start: 0.8870 (tmm) cc_final: 0.8633 (tmm) REVERT: C 5013 MET cc_start: 0.8752 (mmm) cc_final: 0.8437 (mmm) REVERT: C 5015 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8546 (mp10) REVERT: D 31 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7310 (pm20) REVERT: D 116 MET cc_start: 0.8524 (mpp) cc_final: 0.8048 (mpp) REVERT: D 413 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8530 (tm-30) REVERT: D 457 GLU cc_start: 0.9406 (tp30) cc_final: 0.9057 (tm-30) REVERT: D 891 TRP cc_start: 0.8461 (m-10) cc_final: 0.8239 (m100) REVERT: D 903 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6386 (pp) REVERT: D 961 MET cc_start: 0.6824 (pmm) cc_final: 0.6463 (pmm) REVERT: D 1152 MET cc_start: 0.8621 (mmm) cc_final: 0.7779 (mmm) REVERT: D 1260 MET cc_start: 0.8093 (pmm) cc_final: 0.7725 (pmm) REVERT: D 1494 MET cc_start: 0.7728 (mmt) cc_final: 0.7355 (mmp) REVERT: D 2178 MET cc_start: 0.8663 (ppp) cc_final: 0.8436 (ppp) REVERT: D 2639 MET cc_start: 0.8269 (ppp) cc_final: 0.7709 (ppp) REVERT: D 3201 MET cc_start: 0.7368 (ttm) cc_final: 0.6774 (ptm) REVERT: D 3250 MET cc_start: 0.7976 (mmm) cc_final: 0.7638 (ptp) REVERT: D 3437 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8365 (mpp) REVERT: D 3467 MET cc_start: 0.5453 (tmm) cc_final: 0.5164 (tmm) REVERT: D 3517 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8384 (tmm) REVERT: D 3573 MET cc_start: 0.8508 (mmt) cc_final: 0.8055 (mmp) REVERT: D 3673 MET cc_start: 0.9416 (tpp) cc_final: 0.8600 (tpp) REVERT: D 3999 MET cc_start: 0.8933 (mmm) cc_final: 0.8526 (mmm) REVERT: D 4047 MET cc_start: 0.8447 (tmm) cc_final: 0.8193 (tmm) REVERT: D 4093 PHE cc_start: 0.5124 (m-10) cc_final: 0.4769 (m-10) REVERT: D 4157 ASP cc_start: 0.9085 (t0) cc_final: 0.8590 (t0) REVERT: D 4229 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8291 (pm20) REVERT: D 4231 MET cc_start: 0.8952 (mmm) cc_final: 0.8359 (mmm) REVERT: D 4580 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.5813 (t80) REVERT: D 5013 MET cc_start: 0.8768 (mmm) cc_final: 0.8402 (mmm) REVERT: E 66 MET cc_start: 0.7153 (pmm) cc_final: 0.6764 (pmm) REVERT: F 66 MET cc_start: 0.7153 (pmm) cc_final: 0.6764 (pmm) REVERT: G 66 MET cc_start: 0.7151 (pmm) cc_final: 0.6767 (pmm) REVERT: H 66 MET cc_start: 0.7153 (pmm) cc_final: 0.6766 (pmm) outliers start: 106 outliers final: 65 residues processed: 880 average time/residue: 1.2223 time to fit residues: 1946.6973 Evaluate side-chains 862 residues out of total 15540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 773 time to evaluate : 12.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1769 THR Chi-restraints excluded: chain A residue 2307 LEU Chi-restraints excluded: chain A residue 2423 MET Chi-restraints excluded: chain A residue 2816 MET Chi-restraints excluded: chain A residue 3304 CYS Chi-restraints excluded: chain A residue 3468 SER Chi-restraints excluded: chain A residue 3511 VAL Chi-restraints excluded: chain A residue 3529 ASP Chi-restraints excluded: chain A residue 4050 GLU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4584 ASP Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4716 TRP Chi-restraints excluded: chain A residue 4800 LEU Chi-restraints excluded: chain A residue 4876 CYS Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 1769 THR Chi-restraints excluded: chain B residue 2307 LEU Chi-restraints excluded: chain B residue 2423 MET Chi-restraints excluded: chain B residue 2585 THR Chi-restraints excluded: chain B residue 2816 MET Chi-restraints excluded: chain B residue 3304 CYS Chi-restraints excluded: chain B residue 3437 MET Chi-restraints excluded: chain B residue 3511 VAL Chi-restraints excluded: chain B residue 4050 GLU Chi-restraints excluded: chain B residue 4229 GLU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4581 LYS Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4716 TRP Chi-restraints excluded: chain B residue 4800 LEU Chi-restraints excluded: chain B residue 4818 MET Chi-restraints excluded: chain B residue 4861 LYS Chi-restraints excluded: chain B residue 4932 ILE Chi-restraints excluded: chain B residue 5015 GLN Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 1769 THR Chi-restraints excluded: chain C residue 2307 LEU Chi-restraints excluded: chain C residue 2585 THR Chi-restraints excluded: chain C residue 2816 MET Chi-restraints excluded: chain C residue 3304 CYS Chi-restraints excluded: chain C residue 3437 MET Chi-restraints excluded: chain C residue 3511 VAL Chi-restraints excluded: chain C residue 3517 MET Chi-restraints excluded: chain C residue 4050 GLU Chi-restraints excluded: chain C residue 4088 ILE Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4581 LYS Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4716 TRP Chi-restraints excluded: chain C residue 4800 LEU Chi-restraints excluded: chain C residue 4861 LYS Chi-restraints excluded: chain C residue 4932 ILE Chi-restraints excluded: chain C residue 5015 GLN Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1769 THR Chi-restraints excluded: chain D residue 2307 LEU Chi-restraints excluded: chain D residue 2585 THR Chi-restraints excluded: chain D residue 2816 MET Chi-restraints excluded: chain D residue 3304 CYS Chi-restraints excluded: chain D residue 3437 MET Chi-restraints excluded: chain D residue 3511 VAL Chi-restraints excluded: chain D residue 3517 MET Chi-restraints excluded: chain D residue 4050 GLU Chi-restraints excluded: chain D residue 4229 GLU Chi-restraints excluded: chain D residue 4555 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4581 LYS Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4716 TRP Chi-restraints excluded: chain D residue 4800 LEU Chi-restraints excluded: chain D residue 4861 LYS Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain H residue 79 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 869 optimal weight: 6.9990 chunk 1126 optimal weight: 1.9990 chunk 1510 optimal weight: 0.8980 chunk 434 optimal weight: 5.9990 chunk 1307 optimal weight: 2.9990 chunk 209 optimal weight: 0.2980 chunk 394 optimal weight: 0.9990 chunk 1420 optimal weight: 20.0000 chunk 594 optimal weight: 8.9990 chunk 1458 optimal weight: 0.9980 chunk 179 optimal weight: 20.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2003 GLN ** B2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.087233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.061090 restraints weight = 1912622.078| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 11.23 r_work: 0.3213 rms_B_bonded: 8.01 restraints_weight: 2.0000 r_work: 0.3325 rms_B_bonded: 5.35 restraints_weight: 4.0000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 146204 Z= 0.158 Angle : 0.604 14.169 198044 Z= 0.294 Chirality : 0.040 0.244 21776 Planarity : 0.004 0.065 25752 Dihedral : 4.857 146.498 19615 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.80 % Allowed : 13.42 % Favored : 85.79 % 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: 0.62 (0.07), residues: 17832 helix: 1.44 (0.06), residues: 8836 sheet: -1.00 (0.13), residues: 1556 loop : -0.45 (0.07), residues: 7440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C2680 HIS 0.008 0.001 HIS D3771 PHE 0.032 0.001 PHE A3095 TYR 0.041 0.001 TYR C5014 ARG 0.007 0.000 ARG C5017 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44755.29 seconds wall clock time: 778 minutes 5.55 seconds (46685.55 seconds total)