Starting phenix.real_space_refine on Mon Mar 11 23:58:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xhj_22187/03_2024/6xhj_22187_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xhj_22187/03_2024/6xhj_22187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xhj_22187/03_2024/6xhj_22187.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xhj_22187/03_2024/6xhj_22187.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xhj_22187/03_2024/6xhj_22187_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xhj_22187/03_2024/6xhj_22187_neut_updated.pdb" } resolution = 3.62 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= 0.143 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 P 54 5.49 5 Mg 18 5.21 5 S 126 5.16 5 C 37746 2.51 5 N 10692 2.21 5 O 11988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B GLU 357": "OE1" <-> "OE2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B GLU 459": "OE1" <-> "OE2" Residue "B ARG 524": "NH1" <-> "NH2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C GLU 357": "OE1" <-> "OE2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C GLU 459": "OE1" <-> "OE2" Residue "C ARG 524": "NH1" <-> "NH2" Residue "D GLU 43": "OE1" <-> "OE2" Residue "D GLU 193": "OE1" <-> "OE2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D GLU 357": "OE1" <-> "OE2" Residue "D ARG 409": "NH1" <-> "NH2" Residue "D GLU 459": "OE1" <-> "OE2" Residue "D ARG 524": "NH1" <-> "NH2" Residue "E GLU 43": "OE1" <-> "OE2" Residue "E GLU 193": "OE1" <-> "OE2" Residue "E ARG 195": "NH1" <-> "NH2" Residue "E GLU 357": "OE1" <-> "OE2" Residue "E ARG 409": "NH1" <-> "NH2" Residue "E GLU 459": "OE1" <-> "OE2" Residue "E ARG 524": "NH1" <-> "NH2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 193": "OE1" <-> "OE2" Residue "F ARG 195": "NH1" <-> "NH2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "F ARG 409": "NH1" <-> "NH2" Residue "F GLU 459": "OE1" <-> "OE2" Residue "F ARG 524": "NH1" <-> "NH2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G GLU 193": "OE1" <-> "OE2" Residue "G ARG 195": "NH1" <-> "NH2" Residue "G GLU 357": "OE1" <-> "OE2" Residue "G ARG 409": "NH1" <-> "NH2" Residue "G GLU 459": "OE1" <-> "OE2" Residue "G ARG 524": "NH1" <-> "NH2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H GLU 193": "OE1" <-> "OE2" Residue "H ARG 195": "NH1" <-> "NH2" Residue "H GLU 357": "OE1" <-> "OE2" Residue "H ARG 409": "NH1" <-> "NH2" Residue "H GLU 459": "OE1" <-> "OE2" Residue "H ARG 524": "NH1" <-> "NH2" Residue "I GLU 43": "OE1" <-> "OE2" Residue "I GLU 193": "OE1" <-> "OE2" Residue "I ARG 195": "NH1" <-> "NH2" Residue "I GLU 357": "OE1" <-> "OE2" Residue "I ARG 409": "NH1" <-> "NH2" Residue "I GLU 459": "OE1" <-> "OE2" Residue "I ARG 524": "NH1" <-> "NH2" Residue "J GLU 43": "OE1" <-> "OE2" Residue "J GLU 193": "OE1" <-> "OE2" Residue "J ARG 195": "NH1" <-> "NH2" Residue "J GLU 357": "OE1" <-> "OE2" Residue "J ARG 409": "NH1" <-> "NH2" Residue "J GLU 459": "OE1" <-> "OE2" Residue "J ARG 524": "NH1" <-> "NH2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K GLU 193": "OE1" <-> "OE2" Residue "K ARG 195": "NH1" <-> "NH2" Residue "K GLU 357": "OE1" <-> "OE2" Residue "K ARG 409": "NH1" <-> "NH2" Residue "K GLU 459": "OE1" <-> "OE2" Residue "K ARG 524": "NH1" <-> "NH2" Residue "L GLU 43": "OE1" <-> "OE2" Residue "L GLU 193": "OE1" <-> "OE2" Residue "L ARG 195": "NH1" <-> "NH2" Residue "L GLU 357": "OE1" <-> "OE2" Residue "L ARG 409": "NH1" <-> "NH2" Residue "L GLU 459": "OE1" <-> "OE2" Residue "L ARG 524": "NH1" <-> "NH2" Residue "M GLU 43": "OE1" <-> "OE2" Residue "M GLU 193": "OE1" <-> "OE2" Residue "M ARG 195": "NH1" <-> "NH2" Residue "M GLU 357": "OE1" <-> "OE2" Residue "M ARG 409": "NH1" <-> "NH2" Residue "M GLU 459": "OE1" <-> "OE2" Residue "M ARG 524": "NH1" <-> "NH2" Residue "N GLU 43": "OE1" <-> "OE2" Residue "N GLU 193": "OE1" <-> "OE2" Residue "N ARG 195": "NH1" <-> "NH2" Residue "N GLU 357": "OE1" <-> "OE2" Residue "N ARG 409": "NH1" <-> "NH2" Residue "N GLU 459": "OE1" <-> "OE2" Residue "N ARG 524": "NH1" <-> "NH2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O GLU 193": "OE1" <-> "OE2" Residue "O ARG 195": "NH1" <-> "NH2" Residue "O GLU 357": "OE1" <-> "OE2" Residue "O ARG 409": "NH1" <-> "NH2" Residue "O GLU 459": "OE1" <-> "OE2" Residue "O ARG 524": "NH1" <-> "NH2" Residue "P GLU 43": "OE1" <-> "OE2" Residue "P GLU 193": "OE1" <-> "OE2" Residue "P ARG 195": "NH1" <-> "NH2" Residue "P GLU 357": "OE1" <-> "OE2" Residue "P ARG 409": "NH1" <-> "NH2" Residue "P GLU 459": "OE1" <-> "OE2" Residue "P ARG 524": "NH1" <-> "NH2" Residue "Q GLU 43": "OE1" <-> "OE2" Residue "Q GLU 193": "OE1" <-> "OE2" Residue "Q ARG 195": "NH1" <-> "NH2" Residue "Q GLU 357": "OE1" <-> "OE2" Residue "Q ARG 409": "NH1" <-> "NH2" Residue "Q GLU 459": "OE1" <-> "OE2" Residue "Q ARG 524": "NH1" <-> "NH2" Residue "R GLU 43": "OE1" <-> "OE2" Residue "R GLU 193": "OE1" <-> "OE2" Residue "R ARG 195": "NH1" <-> "NH2" Residue "R GLU 357": "OE1" <-> "OE2" Residue "R ARG 409": "NH1" <-> "NH2" Residue "R GLU 459": "OE1" <-> "OE2" Residue "R ARG 524": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 60624 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3368 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'peptide': 473, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 460, None: 2} Not linked: pdbres="ALA A 531 " pdbres=" MG A 601 " Not linked: pdbres=" MG A 601 " pdbres="ATP A 602 " Chain breaks: 7 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 133 Chain: "B" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3368 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'peptide': 473, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 460, None: 2} Not linked: pdbres="ALA B 531 " pdbres=" MG B 601 " Not linked: pdbres=" MG B 601 " pdbres="ATP B 602 " Chain breaks: 7 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 133 Chain: "C" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3368 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'peptide': 473, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 460, None: 2} Not linked: pdbres="ALA C 531 " pdbres=" MG C 601 " Not linked: pdbres=" MG C 601 " pdbres="ATP C 602 " Chain breaks: 7 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 133 Chain: "D" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3368 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'peptide': 473, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 460, None: 2} Not linked: pdbres="ALA D 531 " pdbres=" MG D 601 " Not linked: pdbres=" MG D 601 " pdbres="ATP D 602 " Chain breaks: 7 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 133 Chain: "E" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3368 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'peptide': 473, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 460, None: 2} Not linked: pdbres="ALA E 531 " pdbres=" MG E 601 " Not linked: pdbres=" MG E 601 " pdbres="ATP E 602 " Chain breaks: 7 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 133 Chain: "F" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3368 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'peptide': 473, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 460, None: 2} Not linked: pdbres="ALA F 531 " pdbres=" MG F 601 " Not linked: pdbres=" MG F 601 " pdbres="ATP F 602 " Chain breaks: 7 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 133 Chain: "G" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3368 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'peptide': 473, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 460, None: 2} Not linked: pdbres="ALA G 531 " pdbres=" MG G 601 " Not linked: pdbres=" MG G 601 " pdbres="ATP G 602 " Chain breaks: 7 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 133 Chain: "H" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3368 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'peptide': 473, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 460, None: 2} Not linked: pdbres="ALA H 531 " pdbres=" MG H 601 " Not linked: pdbres=" MG H 601 " pdbres="ATP H 602 " Chain breaks: 7 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 133 Chain: "I" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3368 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'peptide': 473, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 460, None: 2} Not linked: pdbres="ALA I 531 " pdbres=" MG I 601 " Not linked: pdbres=" MG I 601 " pdbres="ATP I 602 " Chain breaks: 7 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 133 Chain: "J" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3368 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'peptide': 473, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 460, None: 2} Not linked: pdbres="ALA J 531 " pdbres=" MG J 601 " Not linked: pdbres=" MG J 601 " pdbres="ATP J 602 " Chain breaks: 7 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 133 Chain: "K" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3368 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'peptide': 473, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 460, None: 2} Not linked: pdbres="ALA K 531 " pdbres=" MG K 601 " Not linked: pdbres=" MG K 601 " pdbres="ATP K 602 " Chain breaks: 7 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 133 Chain: "L" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3368 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'peptide': 473, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 460, None: 2} Not linked: pdbres="ALA L 531 " pdbres=" MG L 601 " Not linked: pdbres=" MG L 601 " pdbres="ATP L 602 " Chain breaks: 7 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 133 Chain: "M" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3368 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'peptide': 473, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 460, None: 2} Not linked: pdbres="ALA M 531 " pdbres=" MG M 601 " Not linked: pdbres=" MG M 601 " pdbres="ATP M 602 " Chain breaks: 7 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 133 Chain: "N" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3368 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'peptide': 473, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 460, None: 2} Not linked: pdbres="ALA N 531 " pdbres=" MG N 601 " Not linked: pdbres=" MG N 601 " pdbres="ATP N 602 " Chain breaks: 7 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 133 Chain: "O" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3368 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'peptide': 473, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 460, None: 2} Not linked: pdbres="ALA O 531 " pdbres=" MG O 601 " Not linked: pdbres=" MG O 601 " pdbres="ATP O 602 " Chain breaks: 7 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 133 Chain: "P" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3368 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'peptide': 473, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 460, None: 2} Not linked: pdbres="ALA P 531 " pdbres=" MG P 601 " Not linked: pdbres=" MG P 601 " pdbres="ATP P 602 " Chain breaks: 7 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 133 Chain: "Q" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3368 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'peptide': 473, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 460, None: 2} Not linked: pdbres="ALA Q 531 " pdbres=" MG Q 601 " Not linked: pdbres=" MG Q 601 " pdbres="ATP Q 602 " Chain breaks: 7 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 133 Chain: "R" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3368 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'peptide': 473, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 460, None: 2} Not linked: pdbres="ALA R 531 " pdbres=" MG R 601 " Not linked: pdbres=" MG R 601 " pdbres="ATP R 602 " Chain breaks: 7 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 133 Time building chain proxies: 22.97, per 1000 atoms: 0.38 Number of scatterers: 60624 At special positions: 0 Unit cell: (191.1, 188.16, 202.86, 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) S 126 16.00 P 54 15.00 Mg 18 11.99 O 11988 8.00 N 10692 7.00 C 37746 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.61 Conformation dependent library (CDL) restraints added in 8.4 seconds 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 288 helices and 144 sheets defined 51.0% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.65 Creating SS restraints... Processing helix chain 'A' and resid 27 through 48 removed outlier: 3.773A pdb=" N ARG A 32 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA A 36 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS A 39 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU A 42 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS A 46 " --> pdb=" O GLU A 43 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER A 47 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 76 removed outlier: 4.045A pdb=" N ASP A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 99 removed outlier: 3.556A pdb=" N GLN A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 123 removed outlier: 4.113A pdb=" N ALA A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 148 removed outlier: 3.734A pdb=" N SER A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 175 through 190 removed outlier: 5.942A pdb=" N TYR A 179 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 184 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 186 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 188 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN A 190 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 269 through 290 removed outlier: 3.779A pdb=" N LEU A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 326 through 334 Processing helix chain 'A' and resid 387 through 408 removed outlier: 3.637A pdb=" N GLU A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG A 395 " --> pdb=" O ASP A 391 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP A 406 " --> pdb=" O GLY A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 435 removed outlier: 3.827A pdb=" N GLU A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Proline residue: A 433 - end of helix Processing helix chain 'A' and resid 438 through 458 removed outlier: 3.752A pdb=" N GLU A 444 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 447 " --> pdb=" O GLU A 444 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN A 448 " --> pdb=" O ALA A 445 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU A 451 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY A 452 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET A 455 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 removed outlier: 4.352A pdb=" N LEU A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 519 Processing helix chain 'B' and resid 27 through 48 removed outlier: 3.773A pdb=" N ARG B 32 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA B 36 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS B 39 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU B 42 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS B 46 " --> pdb=" O GLU B 43 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER B 47 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 removed outlier: 4.045A pdb=" N ASP B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 99 removed outlier: 3.556A pdb=" N GLN B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU B 97 " --> pdb=" O LYS B 93 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU B 98 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 99 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 123 removed outlier: 4.113A pdb=" N ALA B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 148 removed outlier: 3.734A pdb=" N SER B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU B 139 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 175 through 190 removed outlier: 5.942A pdb=" N TYR B 179 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 184 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS B 186 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 188 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN B 190 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 269 through 290 removed outlier: 3.780A pdb=" N LEU B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS B 283 " --> pdb=" O GLU B 279 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS B 285 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 326 through 334 Processing helix chain 'B' and resid 387 through 408 removed outlier: 3.636A pdb=" N GLU B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG B 395 " --> pdb=" O ASP B 391 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP B 399 " --> pdb=" O ARG B 395 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP B 406 " --> pdb=" O GLY B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 435 removed outlier: 3.827A pdb=" N GLU B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 426 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) Proline residue: B 433 - end of helix Processing helix chain 'B' and resid 438 through 458 removed outlier: 3.751A pdb=" N GLU B 444 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 447 " --> pdb=" O GLU B 444 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN B 448 " --> pdb=" O ALA B 445 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU B 451 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY B 452 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET B 455 " --> pdb=" O GLY B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 477 removed outlier: 4.352A pdb=" N LEU B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 519 Processing helix chain 'C' and resid 27 through 48 removed outlier: 3.772A pdb=" N ARG C 32 " --> pdb=" O GLU C 29 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA C 36 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS C 39 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU C 42 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS C 46 " --> pdb=" O GLU C 43 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER C 47 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 removed outlier: 4.045A pdb=" N ASP C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 99 removed outlier: 3.557A pdb=" N GLN C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP C 96 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU C 97 " --> pdb=" O LYS C 93 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU C 98 " --> pdb=" O GLY C 94 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR C 99 " --> pdb=" O GLN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 123 removed outlier: 4.113A pdb=" N ALA C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP C 119 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 148 removed outlier: 3.734A pdb=" N SER C 132 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU C 139 " --> pdb=" O LYS C 135 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE C 140 " --> pdb=" O LYS C 136 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS C 143 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 168 Processing helix chain 'C' and resid 175 through 190 removed outlier: 5.941A pdb=" N TYR C 179 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 184 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS C 186 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 188 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN C 190 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 269 through 290 removed outlier: 3.778A pdb=" N LEU C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 326 through 334 Processing helix chain 'C' and resid 387 through 408 removed outlier: 3.636A pdb=" N GLU C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG C 395 " --> pdb=" O ASP C 391 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP C 399 " --> pdb=" O ARG C 395 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP C 406 " --> pdb=" O GLY C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 435 removed outlier: 3.827A pdb=" N GLU C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 426 " --> pdb=" O ILE C 422 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) Proline residue: C 433 - end of helix Processing helix chain 'C' and resid 438 through 458 removed outlier: 3.752A pdb=" N GLU C 444 " --> pdb=" O LEU C 441 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 447 " --> pdb=" O GLU C 444 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN C 448 " --> pdb=" O ALA C 445 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU C 451 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY C 452 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET C 455 " --> pdb=" O GLY C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 477 removed outlier: 4.351A pdb=" N LEU C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 519 Processing helix chain 'D' and resid 27 through 48 removed outlier: 3.773A pdb=" N ARG D 32 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA D 36 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS D 39 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU D 42 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS D 46 " --> pdb=" O GLU D 43 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N SER D 47 " --> pdb=" O ALA D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 76 removed outlier: 4.046A pdb=" N ASP D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 99 removed outlier: 3.556A pdb=" N GLN D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU D 97 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU D 98 " --> pdb=" O GLY D 94 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 123 removed outlier: 4.113A pdb=" N ALA D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 148 removed outlier: 3.734A pdb=" N SER D 132 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU D 139 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS D 143 " --> pdb=" O GLU D 139 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 168 Processing helix chain 'D' and resid 175 through 190 removed outlier: 5.942A pdb=" N TYR D 179 " --> pdb=" O ALA D 176 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 184 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS D 186 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL D 188 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN D 190 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 269 through 290 removed outlier: 3.779A pdb=" N LEU D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS D 285 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 326 through 334 Processing helix chain 'D' and resid 387 through 408 removed outlier: 3.637A pdb=" N GLU D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG D 395 " --> pdb=" O ASP D 391 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP D 399 " --> pdb=" O ARG D 395 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP D 406 " --> pdb=" O GLY D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 435 removed outlier: 3.827A pdb=" N GLU D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS D 426 " --> pdb=" O ILE D 422 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG D 429 " --> pdb=" O ALA D 425 " (cutoff:3.500A) Proline residue: D 433 - end of helix Processing helix chain 'D' and resid 438 through 458 removed outlier: 3.753A pdb=" N GLU D 444 " --> pdb=" O LEU D 441 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 447 " --> pdb=" O GLU D 444 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN D 448 " --> pdb=" O ALA D 445 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU D 451 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY D 452 " --> pdb=" O ALA D 449 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET D 455 " --> pdb=" O GLY D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 477 removed outlier: 4.352A pdb=" N LEU D 472 " --> pdb=" O LYS D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 519 Processing helix chain 'E' and resid 27 through 48 removed outlier: 3.772A pdb=" N ARG E 32 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA E 36 " --> pdb=" O ALA E 33 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS E 39 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU E 42 " --> pdb=" O LYS E 39 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS E 46 " --> pdb=" O GLU E 43 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER E 47 " --> pdb=" O ALA E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 76 removed outlier: 4.045A pdb=" N ASP E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 99 removed outlier: 3.556A pdb=" N GLN E 90 " --> pdb=" O LYS E 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU E 97 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU E 98 " --> pdb=" O GLY E 94 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR E 99 " --> pdb=" O GLN E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 123 removed outlier: 4.113A pdb=" N ALA E 110 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU E 120 " --> pdb=" O LYS E 116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS E 123 " --> pdb=" O ASP E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 148 removed outlier: 3.735A pdb=" N SER E 132 " --> pdb=" O THR E 128 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS E 143 " --> pdb=" O GLU E 139 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 175 through 190 removed outlier: 5.942A pdb=" N TYR E 179 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL E 184 " --> pdb=" O ALA E 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS E 186 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL E 188 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN E 190 " --> pdb=" O ALA E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 269 through 290 removed outlier: 3.779A pdb=" N LEU E 282 " --> pdb=" O GLU E 278 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS E 285 " --> pdb=" O ILE E 281 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 326 through 334 Processing helix chain 'E' and resid 387 through 408 removed outlier: 3.636A pdb=" N GLU E 392 " --> pdb=" O ARG E 388 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG E 395 " --> pdb=" O ASP E 391 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP E 399 " --> pdb=" O ARG E 395 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP E 406 " --> pdb=" O GLY E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 435 removed outlier: 3.828A pdb=" N GLU E 423 " --> pdb=" O ALA E 419 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS E 426 " --> pdb=" O ILE E 422 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG E 429 " --> pdb=" O ALA E 425 " (cutoff:3.500A) Proline residue: E 433 - end of helix Processing helix chain 'E' and resid 438 through 458 removed outlier: 3.752A pdb=" N GLU E 444 " --> pdb=" O LEU E 441 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA E 447 " --> pdb=" O GLU E 444 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASN E 448 " --> pdb=" O ALA E 445 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU E 451 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY E 452 " --> pdb=" O ALA E 449 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET E 455 " --> pdb=" O GLY E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 477 removed outlier: 4.352A pdb=" N LEU E 472 " --> pdb=" O LYS E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 519 Processing helix chain 'F' and resid 27 through 48 removed outlier: 3.773A pdb=" N ARG F 32 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA F 36 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS F 39 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU F 42 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS F 46 " --> pdb=" O GLU F 43 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER F 47 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 76 removed outlier: 4.045A pdb=" N ASP F 76 " --> pdb=" O ALA F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 99 removed outlier: 3.556A pdb=" N GLN F 90 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP F 96 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU F 97 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU F 98 " --> pdb=" O GLY F 94 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR F 99 " --> pdb=" O GLN F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 123 removed outlier: 4.113A pdb=" N ALA F 110 " --> pdb=" O ALA F 106 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU F 120 " --> pdb=" O LYS F 116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR F 122 " --> pdb=" O GLU F 118 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS F 123 " --> pdb=" O ASP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 148 removed outlier: 3.734A pdb=" N SER F 132 " --> pdb=" O THR F 128 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS F 136 " --> pdb=" O SER F 132 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU F 139 " --> pdb=" O LYS F 135 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE F 140 " --> pdb=" O LYS F 136 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS F 143 " --> pdb=" O GLU F 139 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN F 146 " --> pdb=" O LEU F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 168 Processing helix chain 'F' and resid 175 through 190 removed outlier: 5.942A pdb=" N TYR F 179 " --> pdb=" O ALA F 176 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL F 184 " --> pdb=" O ALA F 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS F 186 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL F 188 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN F 190 " --> pdb=" O ALA F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 269 through 290 removed outlier: 3.779A pdb=" N LEU F 282 " --> pdb=" O GLU F 278 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS F 283 " --> pdb=" O GLU F 279 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS F 285 " --> pdb=" O ILE F 281 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL F 286 " --> pdb=" O LEU F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 312 Processing helix chain 'F' and resid 326 through 334 Processing helix chain 'F' and resid 387 through 408 removed outlier: 3.637A pdb=" N GLU F 392 " --> pdb=" O ARG F 388 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG F 395 " --> pdb=" O ASP F 391 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP F 399 " --> pdb=" O ARG F 395 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP F 406 " --> pdb=" O GLY F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 435 removed outlier: 3.827A pdb=" N GLU F 423 " --> pdb=" O ALA F 419 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS F 426 " --> pdb=" O ILE F 422 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG F 429 " --> pdb=" O ALA F 425 " (cutoff:3.500A) Proline residue: F 433 - end of helix Processing helix chain 'F' and resid 438 through 458 removed outlier: 3.751A pdb=" N GLU F 444 " --> pdb=" O LEU F 441 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA F 447 " --> pdb=" O GLU F 444 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN F 448 " --> pdb=" O ALA F 445 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU F 451 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY F 452 " --> pdb=" O ALA F 449 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET F 455 " --> pdb=" O GLY F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 465 through 477 removed outlier: 4.352A pdb=" N LEU F 472 " --> pdb=" O LYS F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 505 through 519 Processing helix chain 'G' and resid 27 through 48 removed outlier: 3.774A pdb=" N ARG G 32 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA G 36 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS G 39 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU G 42 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS G 46 " --> pdb=" O GLU G 43 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER G 47 " --> pdb=" O ALA G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 76 removed outlier: 4.045A pdb=" N ASP G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 99 removed outlier: 3.555A pdb=" N GLN G 90 " --> pdb=" O LYS G 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP G 96 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU G 97 " --> pdb=" O LYS G 93 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU G 98 " --> pdb=" O GLY G 94 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR G 99 " --> pdb=" O GLN G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 123 removed outlier: 4.113A pdb=" N ALA G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP G 119 " --> pdb=" O LYS G 115 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU G 120 " --> pdb=" O LYS G 116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR G 122 " --> pdb=" O GLU G 118 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS G 123 " --> pdb=" O ASP G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 148 removed outlier: 3.733A pdb=" N SER G 132 " --> pdb=" O THR G 128 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS G 136 " --> pdb=" O SER G 132 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU G 139 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE G 140 " --> pdb=" O LYS G 136 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN G 146 " --> pdb=" O LEU G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 168 Processing helix chain 'G' and resid 175 through 190 removed outlier: 5.942A pdb=" N TYR G 179 " --> pdb=" O ALA G 176 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL G 184 " --> pdb=" O ALA G 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS G 186 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL G 188 " --> pdb=" O VAL G 185 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN G 190 " --> pdb=" O ALA G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'G' and resid 269 through 290 removed outlier: 3.779A pdb=" N LEU G 282 " --> pdb=" O GLU G 278 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS G 283 " --> pdb=" O GLU G 279 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS G 285 " --> pdb=" O ILE G 281 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL G 286 " --> pdb=" O LEU G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 312 Processing helix chain 'G' and resid 326 through 334 Processing helix chain 'G' and resid 387 through 408 removed outlier: 3.636A pdb=" N GLU G 392 " --> pdb=" O ARG G 388 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG G 395 " --> pdb=" O ASP G 391 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP G 399 " --> pdb=" O ARG G 395 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP G 406 " --> pdb=" O GLY G 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 419 through 435 removed outlier: 3.827A pdb=" N GLU G 423 " --> pdb=" O ALA G 419 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS G 426 " --> pdb=" O ILE G 422 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG G 429 " --> pdb=" O ALA G 425 " (cutoff:3.500A) Proline residue: G 433 - end of helix Processing helix chain 'G' and resid 438 through 458 removed outlier: 3.752A pdb=" N GLU G 444 " --> pdb=" O LEU G 441 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA G 447 " --> pdb=" O GLU G 444 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN G 448 " --> pdb=" O ALA G 445 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU G 451 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY G 452 " --> pdb=" O ALA G 449 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET G 455 " --> pdb=" O GLY G 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 465 through 477 removed outlier: 4.352A pdb=" N LEU G 472 " --> pdb=" O LYS G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 505 through 519 Processing helix chain 'H' and resid 27 through 48 removed outlier: 3.772A pdb=" N ARG H 32 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA H 36 " --> pdb=" O ALA H 33 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS H 39 " --> pdb=" O ALA H 36 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU H 42 " --> pdb=" O LYS H 39 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS H 46 " --> pdb=" O GLU H 43 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER H 47 " --> pdb=" O ALA H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 76 removed outlier: 4.044A pdb=" N ASP H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 99 removed outlier: 3.556A pdb=" N GLN H 90 " --> pdb=" O LYS H 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP H 96 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU H 97 " --> pdb=" O LYS H 93 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU H 98 " --> pdb=" O GLY H 94 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR H 99 " --> pdb=" O GLN H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 123 removed outlier: 4.113A pdb=" N ALA H 110 " --> pdb=" O ALA H 106 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP H 119 " --> pdb=" O LYS H 115 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR H 122 " --> pdb=" O GLU H 118 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS H 123 " --> pdb=" O ASP H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 148 removed outlier: 3.734A pdb=" N SER H 132 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS H 136 " --> pdb=" O SER H 132 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU H 139 " --> pdb=" O LYS H 135 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE H 140 " --> pdb=" O LYS H 136 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN H 146 " --> pdb=" O LEU H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 168 Processing helix chain 'H' and resid 175 through 190 removed outlier: 5.942A pdb=" N TYR H 179 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL H 184 " --> pdb=" O ALA H 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS H 186 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL H 188 " --> pdb=" O VAL H 185 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN H 190 " --> pdb=" O ALA H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 205 No H-bonds generated for 'chain 'H' and resid 203 through 205' Processing helix chain 'H' and resid 269 through 290 removed outlier: 3.779A pdb=" N LEU H 282 " --> pdb=" O GLU H 278 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS H 283 " --> pdb=" O GLU H 279 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS H 285 " --> pdb=" O ILE H 281 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL H 286 " --> pdb=" O LEU H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 312 Processing helix chain 'H' and resid 326 through 334 Processing helix chain 'H' and resid 387 through 408 removed outlier: 3.637A pdb=" N GLU H 392 " --> pdb=" O ARG H 388 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG H 395 " --> pdb=" O ASP H 391 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP H 399 " --> pdb=" O ARG H 395 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP H 406 " --> pdb=" O GLY H 402 " (cutoff:3.500A) Processing helix chain 'H' and resid 419 through 435 removed outlier: 3.827A pdb=" N GLU H 423 " --> pdb=" O ALA H 419 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS H 426 " --> pdb=" O ILE H 422 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG H 429 " --> pdb=" O ALA H 425 " (cutoff:3.500A) Proline residue: H 433 - end of helix Processing helix chain 'H' and resid 438 through 458 removed outlier: 3.751A pdb=" N GLU H 444 " --> pdb=" O LEU H 441 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA H 447 " --> pdb=" O GLU H 444 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN H 448 " --> pdb=" O ALA H 445 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU H 451 " --> pdb=" O ASN H 448 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY H 452 " --> pdb=" O ALA H 449 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET H 455 " --> pdb=" O GLY H 452 " (cutoff:3.500A) Processing helix chain 'H' and resid 465 through 477 removed outlier: 4.352A pdb=" N LEU H 472 " --> pdb=" O LYS H 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 505 through 519 Processing helix chain 'I' and resid 27 through 48 removed outlier: 3.773A pdb=" N ARG I 32 " --> pdb=" O GLU I 29 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA I 36 " --> pdb=" O ALA I 33 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS I 39 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU I 42 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS I 46 " --> pdb=" O GLU I 43 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER I 47 " --> pdb=" O ALA I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 76 removed outlier: 4.044A pdb=" N ASP I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 99 removed outlier: 3.555A pdb=" N GLN I 90 " --> pdb=" O LYS I 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP I 96 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU I 97 " --> pdb=" O LYS I 93 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU I 98 " --> pdb=" O GLY I 94 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR I 99 " --> pdb=" O GLN I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 123 removed outlier: 4.113A pdb=" N ALA I 110 " --> pdb=" O ALA I 106 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP I 119 " --> pdb=" O LYS I 115 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU I 120 " --> pdb=" O LYS I 116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR I 122 " --> pdb=" O GLU I 118 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS I 123 " --> pdb=" O ASP I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 148 removed outlier: 3.734A pdb=" N SER I 132 " --> pdb=" O THR I 128 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS I 136 " --> pdb=" O SER I 132 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU I 139 " --> pdb=" O LYS I 135 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE I 140 " --> pdb=" O LYS I 136 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS I 143 " --> pdb=" O GLU I 139 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN I 146 " --> pdb=" O LEU I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 168 Processing helix chain 'I' and resid 175 through 190 removed outlier: 5.942A pdb=" N TYR I 179 " --> pdb=" O ALA I 176 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL I 184 " --> pdb=" O ALA I 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS I 186 " --> pdb=" O LEU I 183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL I 188 " --> pdb=" O VAL I 185 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN I 190 " --> pdb=" O ALA I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 269 through 290 removed outlier: 3.778A pdb=" N LEU I 282 " --> pdb=" O GLU I 278 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS I 283 " --> pdb=" O GLU I 279 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS I 285 " --> pdb=" O ILE I 281 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL I 286 " --> pdb=" O LEU I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 312 Processing helix chain 'I' and resid 326 through 334 Processing helix chain 'I' and resid 387 through 408 removed outlier: 3.637A pdb=" N GLU I 392 " --> pdb=" O ARG I 388 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG I 395 " --> pdb=" O ASP I 391 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP I 399 " --> pdb=" O ARG I 395 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP I 406 " --> pdb=" O GLY I 402 " (cutoff:3.500A) Processing helix chain 'I' and resid 419 through 435 removed outlier: 3.827A pdb=" N GLU I 423 " --> pdb=" O ALA I 419 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS I 426 " --> pdb=" O ILE I 422 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG I 429 " --> pdb=" O ALA I 425 " (cutoff:3.500A) Proline residue: I 433 - end of helix Processing helix chain 'I' and resid 438 through 458 removed outlier: 3.751A pdb=" N GLU I 444 " --> pdb=" O LEU I 441 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA I 447 " --> pdb=" O GLU I 444 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASN I 448 " --> pdb=" O ALA I 445 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU I 451 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY I 452 " --> pdb=" O ALA I 449 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET I 455 " --> pdb=" O GLY I 452 " (cutoff:3.500A) Processing helix chain 'I' and resid 465 through 477 removed outlier: 4.352A pdb=" N LEU I 472 " --> pdb=" O LYS I 468 " (cutoff:3.500A) Processing helix chain 'I' and resid 505 through 519 Processing helix chain 'J' and resid 27 through 48 removed outlier: 3.773A pdb=" N ARG J 32 " --> pdb=" O GLU J 29 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA J 36 " --> pdb=" O ALA J 33 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS J 39 " --> pdb=" O ALA J 36 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU J 42 " --> pdb=" O LYS J 39 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS J 46 " --> pdb=" O GLU J 43 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER J 47 " --> pdb=" O ALA J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 76 removed outlier: 4.045A pdb=" N ASP J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 99 removed outlier: 3.556A pdb=" N GLN J 90 " --> pdb=" O LYS J 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP J 96 " --> pdb=" O ALA J 92 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU J 97 " --> pdb=" O LYS J 93 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU J 98 " --> pdb=" O GLY J 94 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR J 99 " --> pdb=" O GLN J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 123 removed outlier: 4.113A pdb=" N ALA J 110 " --> pdb=" O ALA J 106 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA J 114 " --> pdb=" O ALA J 110 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP J 119 " --> pdb=" O LYS J 115 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU J 120 " --> pdb=" O LYS J 116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR J 122 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS J 123 " --> pdb=" O ASP J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 148 removed outlier: 3.734A pdb=" N SER J 132 " --> pdb=" O THR J 128 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS J 136 " --> pdb=" O SER J 132 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU J 139 " --> pdb=" O LYS J 135 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE J 140 " --> pdb=" O LYS J 136 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS J 143 " --> pdb=" O GLU J 139 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN J 146 " --> pdb=" O LEU J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 168 Processing helix chain 'J' and resid 175 through 190 removed outlier: 5.942A pdb=" N TYR J 179 " --> pdb=" O ALA J 176 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL J 184 " --> pdb=" O ALA J 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS J 186 " --> pdb=" O LEU J 183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL J 188 " --> pdb=" O VAL J 185 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN J 190 " --> pdb=" O ALA J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 205 No H-bonds generated for 'chain 'J' and resid 203 through 205' Processing helix chain 'J' and resid 269 through 290 removed outlier: 3.779A pdb=" N LEU J 282 " --> pdb=" O GLU J 278 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS J 283 " --> pdb=" O GLU J 279 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS J 285 " --> pdb=" O ILE J 281 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL J 286 " --> pdb=" O LEU J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 312 Processing helix chain 'J' and resid 326 through 334 Processing helix chain 'J' and resid 387 through 408 removed outlier: 3.637A pdb=" N GLU J 392 " --> pdb=" O ARG J 388 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG J 395 " --> pdb=" O ASP J 391 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP J 399 " --> pdb=" O ARG J 395 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP J 406 " --> pdb=" O GLY J 402 " (cutoff:3.500A) Processing helix chain 'J' and resid 419 through 435 removed outlier: 3.827A pdb=" N GLU J 423 " --> pdb=" O ALA J 419 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS J 426 " --> pdb=" O ILE J 422 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG J 429 " --> pdb=" O ALA J 425 " (cutoff:3.500A) Proline residue: J 433 - end of helix Processing helix chain 'J' and resid 438 through 458 removed outlier: 3.752A pdb=" N GLU J 444 " --> pdb=" O LEU J 441 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA J 447 " --> pdb=" O GLU J 444 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN J 448 " --> pdb=" O ALA J 445 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU J 451 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY J 452 " --> pdb=" O ALA J 449 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET J 455 " --> pdb=" O GLY J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 465 through 477 removed outlier: 4.352A pdb=" N LEU J 472 " --> pdb=" O LYS J 468 " (cutoff:3.500A) Processing helix chain 'J' and resid 505 through 519 Processing helix chain 'K' and resid 27 through 48 removed outlier: 3.773A pdb=" N ARG K 32 " --> pdb=" O GLU K 29 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA K 36 " --> pdb=" O ALA K 33 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS K 39 " --> pdb=" O ALA K 36 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU K 42 " --> pdb=" O LYS K 39 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS K 46 " --> pdb=" O GLU K 43 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER K 47 " --> pdb=" O ALA K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 76 removed outlier: 4.045A pdb=" N ASP K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 99 removed outlier: 3.557A pdb=" N GLN K 90 " --> pdb=" O LYS K 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP K 96 " --> pdb=" O ALA K 92 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU K 97 " --> pdb=" O LYS K 93 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU K 98 " --> pdb=" O GLY K 94 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR K 99 " --> pdb=" O GLN K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 123 removed outlier: 4.113A pdb=" N ALA K 110 " --> pdb=" O ALA K 106 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA K 114 " --> pdb=" O ALA K 110 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP K 119 " --> pdb=" O LYS K 115 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU K 120 " --> pdb=" O LYS K 116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR K 122 " --> pdb=" O GLU K 118 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS K 123 " --> pdb=" O ASP K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 148 removed outlier: 3.734A pdb=" N SER K 132 " --> pdb=" O THR K 128 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS K 136 " --> pdb=" O SER K 132 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU K 139 " --> pdb=" O LYS K 135 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE K 140 " --> pdb=" O LYS K 136 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS K 143 " --> pdb=" O GLU K 139 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN K 146 " --> pdb=" O LEU K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 168 Processing helix chain 'K' and resid 175 through 190 removed outlier: 5.942A pdb=" N TYR K 179 " --> pdb=" O ALA K 176 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL K 184 " --> pdb=" O ALA K 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS K 186 " --> pdb=" O LEU K 183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL K 188 " --> pdb=" O VAL K 185 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN K 190 " --> pdb=" O ALA K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'K' and resid 269 through 290 removed outlier: 3.779A pdb=" N LEU K 282 " --> pdb=" O GLU K 278 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS K 283 " --> pdb=" O GLU K 279 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS K 285 " --> pdb=" O ILE K 281 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL K 286 " --> pdb=" O LEU K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 312 Processing helix chain 'K' and resid 326 through 334 Processing helix chain 'K' and resid 387 through 408 removed outlier: 3.637A pdb=" N GLU K 392 " --> pdb=" O ARG K 388 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG K 395 " --> pdb=" O ASP K 391 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP K 399 " --> pdb=" O ARG K 395 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP K 406 " --> pdb=" O GLY K 402 " (cutoff:3.500A) Processing helix chain 'K' and resid 419 through 435 removed outlier: 3.828A pdb=" N GLU K 423 " --> pdb=" O ALA K 419 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS K 426 " --> pdb=" O ILE K 422 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG K 429 " --> pdb=" O ALA K 425 " (cutoff:3.500A) Proline residue: K 433 - end of helix Processing helix chain 'K' and resid 438 through 458 removed outlier: 3.752A pdb=" N GLU K 444 " --> pdb=" O LEU K 441 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA K 447 " --> pdb=" O GLU K 444 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN K 448 " --> pdb=" O ALA K 445 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU K 451 " --> pdb=" O ASN K 448 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY K 452 " --> pdb=" O ALA K 449 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET K 455 " --> pdb=" O GLY K 452 " (cutoff:3.500A) Processing helix chain 'K' and resid 465 through 477 removed outlier: 4.352A pdb=" N LEU K 472 " --> pdb=" O LYS K 468 " (cutoff:3.500A) Processing helix chain 'K' and resid 505 through 519 Processing helix chain 'L' and resid 27 through 48 removed outlier: 3.773A pdb=" N ARG L 32 " --> pdb=" O GLU L 29 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA L 36 " --> pdb=" O ALA L 33 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS L 39 " --> pdb=" O ALA L 36 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU L 42 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS L 46 " --> pdb=" O GLU L 43 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER L 47 " --> pdb=" O ALA L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 76 removed outlier: 4.044A pdb=" N ASP L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 99 removed outlier: 3.556A pdb=" N GLN L 90 " --> pdb=" O LYS L 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP L 96 " --> pdb=" O ALA L 92 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU L 97 " --> pdb=" O LYS L 93 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU L 98 " --> pdb=" O GLY L 94 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR L 99 " --> pdb=" O GLN L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 123 removed outlier: 4.113A pdb=" N ALA L 110 " --> pdb=" O ALA L 106 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA L 114 " --> pdb=" O ALA L 110 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP L 119 " --> pdb=" O LYS L 115 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU L 120 " --> pdb=" O LYS L 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR L 122 " --> pdb=" O GLU L 118 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS L 123 " --> pdb=" O ASP L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 148 removed outlier: 3.734A pdb=" N SER L 132 " --> pdb=" O THR L 128 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS L 136 " --> pdb=" O SER L 132 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU L 139 " --> pdb=" O LYS L 135 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE L 140 " --> pdb=" O LYS L 136 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS L 143 " --> pdb=" O GLU L 139 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN L 146 " --> pdb=" O LEU L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 168 Processing helix chain 'L' and resid 175 through 190 removed outlier: 5.941A pdb=" N TYR L 179 " --> pdb=" O ALA L 176 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL L 184 " --> pdb=" O ALA L 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS L 186 " --> pdb=" O LEU L 183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL L 188 " --> pdb=" O VAL L 185 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN L 190 " --> pdb=" O ALA L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'L' and resid 269 through 290 removed outlier: 3.779A pdb=" N LEU L 282 " --> pdb=" O GLU L 278 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS L 283 " --> pdb=" O GLU L 279 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS L 285 " --> pdb=" O ILE L 281 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL L 286 " --> pdb=" O LEU L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 312 Processing helix chain 'L' and resid 326 through 334 Processing helix chain 'L' and resid 387 through 408 removed outlier: 3.636A pdb=" N GLU L 392 " --> pdb=" O ARG L 388 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG L 395 " --> pdb=" O ASP L 391 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP L 399 " --> pdb=" O ARG L 395 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP L 406 " --> pdb=" O GLY L 402 " (cutoff:3.500A) Processing helix chain 'L' and resid 419 through 435 removed outlier: 3.828A pdb=" N GLU L 423 " --> pdb=" O ALA L 419 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS L 426 " --> pdb=" O ILE L 422 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG L 429 " --> pdb=" O ALA L 425 " (cutoff:3.500A) Proline residue: L 433 - end of helix Processing helix chain 'L' and resid 438 through 458 removed outlier: 3.751A pdb=" N GLU L 444 " --> pdb=" O LEU L 441 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA L 447 " --> pdb=" O GLU L 444 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN L 448 " --> pdb=" O ALA L 445 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU L 451 " --> pdb=" O ASN L 448 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY L 452 " --> pdb=" O ALA L 449 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET L 455 " --> pdb=" O GLY L 452 " (cutoff:3.500A) Processing helix chain 'L' and resid 465 through 477 removed outlier: 4.352A pdb=" N LEU L 472 " --> pdb=" O LYS L 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 505 through 519 Processing helix chain 'M' and resid 27 through 48 removed outlier: 3.773A pdb=" N ARG M 32 " --> pdb=" O GLU M 29 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA M 36 " --> pdb=" O ALA M 33 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS M 39 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU M 42 " --> pdb=" O LYS M 39 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS M 46 " --> pdb=" O GLU M 43 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER M 47 " --> pdb=" O ALA M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 76 removed outlier: 4.044A pdb=" N ASP M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 99 removed outlier: 3.557A pdb=" N GLN M 90 " --> pdb=" O LYS M 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP M 96 " --> pdb=" O ALA M 92 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU M 97 " --> pdb=" O LYS M 93 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU M 98 " --> pdb=" O GLY M 94 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR M 99 " --> pdb=" O GLN M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 123 removed outlier: 4.113A pdb=" N ALA M 110 " --> pdb=" O ALA M 106 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA M 114 " --> pdb=" O ALA M 110 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP M 119 " --> pdb=" O LYS M 115 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU M 120 " --> pdb=" O LYS M 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR M 122 " --> pdb=" O GLU M 118 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS M 123 " --> pdb=" O ASP M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 148 removed outlier: 3.735A pdb=" N SER M 132 " --> pdb=" O THR M 128 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS M 136 " --> pdb=" O SER M 132 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU M 139 " --> pdb=" O LYS M 135 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE M 140 " --> pdb=" O LYS M 136 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS M 143 " --> pdb=" O GLU M 139 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN M 146 " --> pdb=" O LEU M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 168 Processing helix chain 'M' and resid 175 through 190 removed outlier: 5.941A pdb=" N TYR M 179 " --> pdb=" O ALA M 176 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL M 184 " --> pdb=" O ALA M 181 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS M 186 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL M 188 " --> pdb=" O VAL M 185 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN M 190 " --> pdb=" O ALA M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 205 No H-bonds generated for 'chain 'M' and resid 203 through 205' Processing helix chain 'M' and resid 269 through 290 removed outlier: 3.778A pdb=" N LEU M 282 " --> pdb=" O GLU M 278 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS M 283 " --> pdb=" O GLU M 279 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS M 285 " --> pdb=" O ILE M 281 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL M 286 " --> pdb=" O LEU M 282 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 312 Processing helix chain 'M' and resid 326 through 334 Processing helix chain 'M' and resid 387 through 408 removed outlier: 3.637A pdb=" N GLU M 392 " --> pdb=" O ARG M 388 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG M 395 " --> pdb=" O ASP M 391 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP M 399 " --> pdb=" O ARG M 395 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP M 406 " --> pdb=" O GLY M 402 " (cutoff:3.500A) Processing helix chain 'M' and resid 419 through 435 removed outlier: 3.827A pdb=" N GLU M 423 " --> pdb=" O ALA M 419 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS M 426 " --> pdb=" O ILE M 422 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG M 429 " --> pdb=" O ALA M 425 " (cutoff:3.500A) Proline residue: M 433 - end of helix Processing helix chain 'M' and resid 438 through 461 removed outlier: 3.751A pdb=" N GLU M 444 " --> pdb=" O LEU M 441 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA M 447 " --> pdb=" O GLU M 444 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN M 448 " --> pdb=" O ALA M 445 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU M 451 " --> pdb=" O ASN M 448 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY M 452 " --> pdb=" O ALA M 449 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET M 455 " --> pdb=" O GLY M 452 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU M 459 " --> pdb=" O ILE M 456 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN M 460 " --> pdb=" O LEU M 457 " (cutoff:3.500A) Processing helix chain 'M' and resid 465 through 477 removed outlier: 4.352A pdb=" N LEU M 472 " --> pdb=" O LYS M 468 " (cutoff:3.500A) Processing helix chain 'M' and resid 505 through 519 Processing helix chain 'N' and resid 27 through 48 removed outlier: 3.773A pdb=" N ARG N 32 " --> pdb=" O GLU N 29 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA N 36 " --> pdb=" O ALA N 33 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS N 39 " --> pdb=" O ALA N 36 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU N 42 " --> pdb=" O LYS N 39 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS N 46 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER N 47 " --> pdb=" O ALA N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 76 removed outlier: 4.044A pdb=" N ASP N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 99 removed outlier: 3.556A pdb=" N GLN N 90 " --> pdb=" O LYS N 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP N 96 " --> pdb=" O ALA N 92 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU N 97 " --> pdb=" O LYS N 93 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU N 98 " --> pdb=" O GLY N 94 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR N 99 " --> pdb=" O GLN N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 123 removed outlier: 4.113A pdb=" N ALA N 110 " --> pdb=" O ALA N 106 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA N 114 " --> pdb=" O ALA N 110 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP N 119 " --> pdb=" O LYS N 115 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU N 120 " --> pdb=" O LYS N 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR N 122 " --> pdb=" O GLU N 118 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS N 123 " --> pdb=" O ASP N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 127 through 148 removed outlier: 3.734A pdb=" N SER N 132 " --> pdb=" O THR N 128 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS N 136 " --> pdb=" O SER N 132 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU N 139 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE N 140 " --> pdb=" O LYS N 136 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS N 143 " --> pdb=" O GLU N 139 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN N 146 " --> pdb=" O LEU N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 157 through 168 Processing helix chain 'N' and resid 175 through 190 removed outlier: 5.942A pdb=" N TYR N 179 " --> pdb=" O ALA N 176 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL N 184 " --> pdb=" O ALA N 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS N 186 " --> pdb=" O LEU N 183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL N 188 " --> pdb=" O VAL N 185 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN N 190 " --> pdb=" O ALA N 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 203 through 205 No H-bonds generated for 'chain 'N' and resid 203 through 205' Processing helix chain 'N' and resid 269 through 290 removed outlier: 3.779A pdb=" N LEU N 282 " --> pdb=" O GLU N 278 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS N 283 " --> pdb=" O GLU N 279 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL N 286 " --> pdb=" O LEU N 282 " (cutoff:3.500A) Processing helix chain 'N' and resid 308 through 312 Processing helix chain 'N' and resid 326 through 334 Processing helix chain 'N' and resid 387 through 408 removed outlier: 3.637A pdb=" N GLU N 392 " --> pdb=" O ARG N 388 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG N 395 " --> pdb=" O ASP N 391 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP N 399 " --> pdb=" O ARG N 395 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP N 406 " --> pdb=" O GLY N 402 " (cutoff:3.500A) Processing helix chain 'N' and resid 419 through 435 removed outlier: 3.828A pdb=" N GLU N 423 " --> pdb=" O ALA N 419 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS N 426 " --> pdb=" O ILE N 422 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG N 429 " --> pdb=" O ALA N 425 " (cutoff:3.500A) Proline residue: N 433 - end of helix Processing helix chain 'N' and resid 438 through 458 removed outlier: 3.753A pdb=" N GLU N 444 " --> pdb=" O LEU N 441 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA N 447 " --> pdb=" O GLU N 444 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN N 448 " --> pdb=" O ALA N 445 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU N 451 " --> pdb=" O ASN N 448 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY N 452 " --> pdb=" O ALA N 449 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET N 455 " --> pdb=" O GLY N 452 " (cutoff:3.500A) Processing helix chain 'N' and resid 465 through 477 removed outlier: 4.352A pdb=" N LEU N 472 " --> pdb=" O LYS N 468 " (cutoff:3.500A) Processing helix chain 'N' and resid 505 through 519 Processing helix chain 'O' and resid 27 through 48 removed outlier: 3.773A pdb=" N ARG O 32 " --> pdb=" O GLU O 29 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA O 36 " --> pdb=" O ALA O 33 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS O 39 " --> pdb=" O ALA O 36 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU O 42 " --> pdb=" O LYS O 39 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS O 46 " --> pdb=" O GLU O 43 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER O 47 " --> pdb=" O ALA O 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 76 removed outlier: 4.044A pdb=" N ASP O 76 " --> pdb=" O ALA O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 99 removed outlier: 3.556A pdb=" N GLN O 90 " --> pdb=" O LYS O 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP O 96 " --> pdb=" O ALA O 92 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU O 97 " --> pdb=" O LYS O 93 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU O 98 " --> pdb=" O GLY O 94 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR O 99 " --> pdb=" O GLN O 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 123 removed outlier: 4.113A pdb=" N ALA O 110 " --> pdb=" O ALA O 106 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP O 119 " --> pdb=" O LYS O 115 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU O 120 " --> pdb=" O LYS O 116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR O 122 " --> pdb=" O GLU O 118 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS O 123 " --> pdb=" O ASP O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 148 removed outlier: 3.735A pdb=" N SER O 132 " --> pdb=" O THR O 128 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS O 136 " --> pdb=" O SER O 132 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU O 139 " --> pdb=" O LYS O 135 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE O 140 " --> pdb=" O LYS O 136 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS O 143 " --> pdb=" O GLU O 139 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN O 146 " --> pdb=" O LEU O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 157 through 168 Processing helix chain 'O' and resid 175 through 190 removed outlier: 5.941A pdb=" N TYR O 179 " --> pdb=" O ALA O 176 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL O 184 " --> pdb=" O ALA O 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS O 186 " --> pdb=" O LEU O 183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL O 188 " --> pdb=" O VAL O 185 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN O 190 " --> pdb=" O ALA O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 203 through 205 No H-bonds generated for 'chain 'O' and resid 203 through 205' Processing helix chain 'O' and resid 269 through 290 removed outlier: 3.779A pdb=" N LEU O 282 " --> pdb=" O GLU O 278 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS O 283 " --> pdb=" O GLU O 279 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS O 285 " --> pdb=" O ILE O 281 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL O 286 " --> pdb=" O LEU O 282 " (cutoff:3.500A) Processing helix chain 'O' and resid 308 through 312 Processing helix chain 'O' and resid 326 through 334 Processing helix chain 'O' and resid 387 through 408 removed outlier: 3.637A pdb=" N GLU O 392 " --> pdb=" O ARG O 388 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG O 395 " --> pdb=" O ASP O 391 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP O 399 " --> pdb=" O ARG O 395 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP O 406 " --> pdb=" O GLY O 402 " (cutoff:3.500A) Processing helix chain 'O' and resid 419 through 435 removed outlier: 3.827A pdb=" N GLU O 423 " --> pdb=" O ALA O 419 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS O 426 " --> pdb=" O ILE O 422 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG O 429 " --> pdb=" O ALA O 425 " (cutoff:3.500A) Proline residue: O 433 - end of helix Processing helix chain 'O' and resid 438 through 461 removed outlier: 3.751A pdb=" N GLU O 444 " --> pdb=" O LEU O 441 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA O 447 " --> pdb=" O GLU O 444 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN O 448 " --> pdb=" O ALA O 445 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU O 451 " --> pdb=" O ASN O 448 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY O 452 " --> pdb=" O ALA O 449 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET O 455 " --> pdb=" O GLY O 452 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU O 459 " --> pdb=" O ILE O 456 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN O 460 " --> pdb=" O LEU O 457 " (cutoff:3.500A) Processing helix chain 'O' and resid 465 through 477 removed outlier: 4.352A pdb=" N LEU O 472 " --> pdb=" O LYS O 468 " (cutoff:3.500A) Processing helix chain 'O' and resid 505 through 519 Processing helix chain 'P' and resid 27 through 48 removed outlier: 3.773A pdb=" N ARG P 32 " --> pdb=" O GLU P 29 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA P 36 " --> pdb=" O ALA P 33 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS P 39 " --> pdb=" O ALA P 36 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU P 42 " --> pdb=" O LYS P 39 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS P 46 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER P 47 " --> pdb=" O ALA P 44 " (cutoff:3.500A) Processing helix chain 'P' and resid 71 through 76 removed outlier: 4.044A pdb=" N ASP P 76 " --> pdb=" O ALA P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 99 removed outlier: 3.557A pdb=" N GLN P 90 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP P 96 " --> pdb=" O ALA P 92 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU P 97 " --> pdb=" O LYS P 93 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU P 98 " --> pdb=" O GLY P 94 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR P 99 " --> pdb=" O GLN P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 123 removed outlier: 4.113A pdb=" N ALA P 110 " --> pdb=" O ALA P 106 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA P 114 " --> pdb=" O ALA P 110 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP P 119 " --> pdb=" O LYS P 115 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU P 120 " --> pdb=" O LYS P 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR P 122 " --> pdb=" O GLU P 118 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS P 123 " --> pdb=" O ASP P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 148 removed outlier: 3.735A pdb=" N SER P 132 " --> pdb=" O THR P 128 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS P 136 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU P 139 " --> pdb=" O LYS P 135 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE P 140 " --> pdb=" O LYS P 136 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS P 143 " --> pdb=" O GLU P 139 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN P 146 " --> pdb=" O LEU P 142 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 168 Processing helix chain 'P' and resid 175 through 190 removed outlier: 5.941A pdb=" N TYR P 179 " --> pdb=" O ALA P 176 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL P 184 " --> pdb=" O ALA P 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS P 186 " --> pdb=" O LEU P 183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL P 188 " --> pdb=" O VAL P 185 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN P 190 " --> pdb=" O ALA P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 203 through 205 No H-bonds generated for 'chain 'P' and resid 203 through 205' Processing helix chain 'P' and resid 269 through 290 removed outlier: 3.779A pdb=" N LEU P 282 " --> pdb=" O GLU P 278 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS P 283 " --> pdb=" O GLU P 279 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS P 285 " --> pdb=" O ILE P 281 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL P 286 " --> pdb=" O LEU P 282 " (cutoff:3.500A) Processing helix chain 'P' and resid 308 through 312 Processing helix chain 'P' and resid 326 through 334 Processing helix chain 'P' and resid 387 through 408 removed outlier: 3.637A pdb=" N GLU P 392 " --> pdb=" O ARG P 388 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG P 395 " --> pdb=" O ASP P 391 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP P 399 " --> pdb=" O ARG P 395 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP P 406 " --> pdb=" O GLY P 402 " (cutoff:3.500A) Processing helix chain 'P' and resid 419 through 435 removed outlier: 3.827A pdb=" N GLU P 423 " --> pdb=" O ALA P 419 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS P 426 " --> pdb=" O ILE P 422 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG P 429 " --> pdb=" O ALA P 425 " (cutoff:3.500A) Proline residue: P 433 - end of helix Processing helix chain 'P' and resid 438 through 458 removed outlier: 3.751A pdb=" N GLU P 444 " --> pdb=" O LEU P 441 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA P 447 " --> pdb=" O GLU P 444 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN P 448 " --> pdb=" O ALA P 445 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU P 451 " --> pdb=" O ASN P 448 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY P 452 " --> pdb=" O ALA P 449 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET P 455 " --> pdb=" O GLY P 452 " (cutoff:3.500A) Processing helix chain 'P' and resid 465 through 477 removed outlier: 4.352A pdb=" N LEU P 472 " --> pdb=" O LYS P 468 " (cutoff:3.500A) Processing helix chain 'P' and resid 505 through 519 Processing helix chain 'Q' and resid 27 through 48 removed outlier: 3.773A pdb=" N ARG Q 32 " --> pdb=" O GLU Q 29 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA Q 36 " --> pdb=" O ALA Q 33 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS Q 39 " --> pdb=" O ALA Q 36 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU Q 42 " --> pdb=" O LYS Q 39 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS Q 46 " --> pdb=" O GLU Q 43 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N SER Q 47 " --> pdb=" O ALA Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 76 removed outlier: 4.044A pdb=" N ASP Q 76 " --> pdb=" O ALA Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 99 removed outlier: 3.556A pdb=" N GLN Q 90 " --> pdb=" O LYS Q 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP Q 96 " --> pdb=" O ALA Q 92 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU Q 97 " --> pdb=" O LYS Q 93 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU Q 98 " --> pdb=" O GLY Q 94 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR Q 99 " --> pdb=" O GLN Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 123 removed outlier: 4.113A pdb=" N ALA Q 110 " --> pdb=" O ALA Q 106 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA Q 114 " --> pdb=" O ALA Q 110 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP Q 119 " --> pdb=" O LYS Q 115 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU Q 120 " --> pdb=" O LYS Q 116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR Q 122 " --> pdb=" O GLU Q 118 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS Q 123 " --> pdb=" O ASP Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 148 removed outlier: 3.734A pdb=" N SER Q 132 " --> pdb=" O THR Q 128 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS Q 136 " --> pdb=" O SER Q 132 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU Q 139 " --> pdb=" O LYS Q 135 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE Q 140 " --> pdb=" O LYS Q 136 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS Q 143 " --> pdb=" O GLU Q 139 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN Q 146 " --> pdb=" O LEU Q 142 " (cutoff:3.500A) Processing helix chain 'Q' and resid 157 through 168 Processing helix chain 'Q' and resid 175 through 190 removed outlier: 5.941A pdb=" N TYR Q 179 " --> pdb=" O ALA Q 176 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL Q 184 " --> pdb=" O ALA Q 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS Q 186 " --> pdb=" O LEU Q 183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL Q 188 " --> pdb=" O VAL Q 185 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN Q 190 " --> pdb=" O ALA Q 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 203 through 205 No H-bonds generated for 'chain 'Q' and resid 203 through 205' Processing helix chain 'Q' and resid 269 through 290 removed outlier: 3.778A pdb=" N LEU Q 282 " --> pdb=" O GLU Q 278 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS Q 283 " --> pdb=" O GLU Q 279 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS Q 285 " --> pdb=" O ILE Q 281 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL Q 286 " --> pdb=" O LEU Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 308 through 312 Processing helix chain 'Q' and resid 326 through 334 Processing helix chain 'Q' and resid 387 through 408 removed outlier: 3.637A pdb=" N GLU Q 392 " --> pdb=" O ARG Q 388 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG Q 395 " --> pdb=" O ASP Q 391 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP Q 399 " --> pdb=" O ARG Q 395 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP Q 406 " --> pdb=" O GLY Q 402 " (cutoff:3.500A) Processing helix chain 'Q' and resid 419 through 435 removed outlier: 3.827A pdb=" N GLU Q 423 " --> pdb=" O ALA Q 419 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS Q 426 " --> pdb=" O ILE Q 422 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG Q 429 " --> pdb=" O ALA Q 425 " (cutoff:3.500A) Proline residue: Q 433 - end of helix Processing helix chain 'Q' and resid 438 through 458 removed outlier: 3.752A pdb=" N GLU Q 444 " --> pdb=" O LEU Q 441 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA Q 447 " --> pdb=" O GLU Q 444 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN Q 448 " --> pdb=" O ALA Q 445 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU Q 451 " --> pdb=" O ASN Q 448 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY Q 452 " --> pdb=" O ALA Q 449 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET Q 455 " --> pdb=" O GLY Q 452 " (cutoff:3.500A) Processing helix chain 'Q' and resid 465 through 477 removed outlier: 4.352A pdb=" N LEU Q 472 " --> pdb=" O LYS Q 468 " (cutoff:3.500A) Processing helix chain 'Q' and resid 505 through 519 Processing helix chain 'R' and resid 27 through 48 removed outlier: 3.773A pdb=" N ARG R 32 " --> pdb=" O GLU R 29 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA R 36 " --> pdb=" O ALA R 33 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS R 39 " --> pdb=" O ALA R 36 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU R 42 " --> pdb=" O LYS R 39 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS R 46 " --> pdb=" O GLU R 43 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER R 47 " --> pdb=" O ALA R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 76 removed outlier: 4.045A pdb=" N ASP R 76 " --> pdb=" O ALA R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 99 removed outlier: 3.556A pdb=" N GLN R 90 " --> pdb=" O LYS R 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP R 96 " --> pdb=" O ALA R 92 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU R 97 " --> pdb=" O LYS R 93 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU R 98 " --> pdb=" O GLY R 94 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR R 99 " --> pdb=" O GLN R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 123 removed outlier: 4.113A pdb=" N ALA R 110 " --> pdb=" O ALA R 106 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP R 119 " --> pdb=" O LYS R 115 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU R 120 " --> pdb=" O LYS R 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR R 122 " --> pdb=" O GLU R 118 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS R 123 " --> pdb=" O ASP R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 148 removed outlier: 3.734A pdb=" N SER R 132 " --> pdb=" O THR R 128 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS R 136 " --> pdb=" O SER R 132 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU R 139 " --> pdb=" O LYS R 135 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE R 140 " --> pdb=" O LYS R 136 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS R 143 " --> pdb=" O GLU R 139 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN R 146 " --> pdb=" O LEU R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 168 Processing helix chain 'R' and resid 175 through 190 removed outlier: 5.942A pdb=" N TYR R 179 " --> pdb=" O ALA R 176 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL R 184 " --> pdb=" O ALA R 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS R 186 " --> pdb=" O LEU R 183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL R 188 " --> pdb=" O VAL R 185 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN R 190 " --> pdb=" O ALA R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 205 No H-bonds generated for 'chain 'R' and resid 203 through 205' Processing helix chain 'R' and resid 269 through 290 removed outlier: 3.780A pdb=" N LEU R 282 " --> pdb=" O GLU R 278 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS R 283 " --> pdb=" O GLU R 279 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS R 285 " --> pdb=" O ILE R 281 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL R 286 " --> pdb=" O LEU R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 312 Processing helix chain 'R' and resid 326 through 334 Processing helix chain 'R' and resid 387 through 408 removed outlier: 3.636A pdb=" N GLU R 392 " --> pdb=" O ARG R 388 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG R 395 " --> pdb=" O ASP R 391 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP R 399 " --> pdb=" O ARG R 395 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP R 406 " --> pdb=" O GLY R 402 " (cutoff:3.500A) Processing helix chain 'R' and resid 419 through 435 removed outlier: 3.827A pdb=" N GLU R 423 " --> pdb=" O ALA R 419 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS R 426 " --> pdb=" O ILE R 422 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG R 429 " --> pdb=" O ALA R 425 " (cutoff:3.500A) Proline residue: R 433 - end of helix Processing helix chain 'R' and resid 438 through 458 removed outlier: 3.752A pdb=" N GLU R 444 " --> pdb=" O LEU R 441 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA R 447 " --> pdb=" O GLU R 444 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN R 448 " --> pdb=" O ALA R 445 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU R 451 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY R 452 " --> pdb=" O ALA R 449 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET R 455 " --> pdb=" O GLY R 452 " (cutoff:3.500A) Processing helix chain 'R' and resid 465 through 477 removed outlier: 4.352A pdb=" N LEU R 472 " --> pdb=" O LYS R 468 " (cutoff:3.500A) Processing helix chain 'R' and resid 505 through 519 Processing sheet with id= A, first strand: chain 'A' and resid 24 through 26 Processing sheet with id= B, first strand: chain 'A' and resid 56 through 59 Processing sheet with id= C, first strand: chain 'A' and resid 193 through 195 Processing sheet with id= D, first strand: chain 'A' and resid 206 through 212 removed outlier: 6.722A pdb=" N VAL A 378 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL A 209 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 380 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LYS A 211 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE A 382 " --> pdb=" O LYS A 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 224 through 227 Processing sheet with id= F, first strand: chain 'A' and resid 351 through 353 removed outlier: 6.606A pdb=" N VAL A 296 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU A 248 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE A 298 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 413 through 415 Processing sheet with id= H, first strand: chain 'A' and resid 484 through 486 Processing sheet with id= I, first strand: chain 'B' and resid 24 through 26 Processing sheet with id= J, first strand: chain 'B' and resid 56 through 59 Processing sheet with id= K, first strand: chain 'B' and resid 193 through 195 Processing sheet with id= L, first strand: chain 'B' and resid 206 through 212 removed outlier: 6.722A pdb=" N VAL B 378 " --> pdb=" O GLN B 207 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL B 209 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE B 380 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LYS B 211 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE B 382 " --> pdb=" O LYS B 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 224 through 227 Processing sheet with id= N, first strand: chain 'B' and resid 351 through 353 removed outlier: 6.606A pdb=" N VAL B 296 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU B 248 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE B 298 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 413 through 415 Processing sheet with id= P, first strand: chain 'B' and resid 484 through 486 Processing sheet with id= Q, first strand: chain 'C' and resid 24 through 26 Processing sheet with id= R, first strand: chain 'C' and resid 56 through 59 Processing sheet with id= S, first strand: chain 'C' and resid 193 through 195 Processing sheet with id= T, first strand: chain 'C' and resid 206 through 212 removed outlier: 6.723A pdb=" N VAL C 378 " --> pdb=" O GLN C 207 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL C 209 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE C 380 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LYS C 211 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE C 382 " --> pdb=" O LYS C 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'C' and resid 224 through 227 Processing sheet with id= V, first strand: chain 'C' and resid 351 through 353 removed outlier: 6.607A pdb=" N VAL C 296 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU C 248 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE C 298 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 413 through 415 Processing sheet with id= X, first strand: chain 'C' and resid 484 through 486 Processing sheet with id= Y, first strand: chain 'D' and resid 24 through 26 Processing sheet with id= Z, first strand: chain 'D' and resid 56 through 59 Processing sheet with id= AA, first strand: chain 'D' and resid 193 through 195 Processing sheet with id= AB, first strand: chain 'D' and resid 206 through 212 removed outlier: 6.723A pdb=" N VAL D 378 " --> pdb=" O GLN D 207 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL D 209 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE D 380 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LYS D 211 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE D 382 " --> pdb=" O LYS D 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'D' and resid 224 through 227 Processing sheet with id= AD, first strand: chain 'D' and resid 351 through 353 removed outlier: 6.606A pdb=" N VAL D 296 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU D 248 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE D 298 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 413 through 415 Processing sheet with id= AF, first strand: chain 'D' and resid 484 through 486 Processing sheet with id= AG, first strand: chain 'E' and resid 24 through 26 Processing sheet with id= AH, first strand: chain 'E' and resid 56 through 59 Processing sheet with id= AI, first strand: chain 'E' and resid 193 through 195 Processing sheet with id= AJ, first strand: chain 'E' and resid 206 through 212 removed outlier: 6.722A pdb=" N VAL E 378 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL E 209 " --> pdb=" O VAL E 378 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE E 380 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LYS E 211 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE E 382 " --> pdb=" O LYS E 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'E' and resid 224 through 227 Processing sheet with id= AL, first strand: chain 'E' and resid 351 through 353 removed outlier: 6.606A pdb=" N VAL E 296 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU E 248 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE E 298 " --> pdb=" O LEU E 248 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'E' and resid 413 through 415 Processing sheet with id= AN, first strand: chain 'E' and resid 484 through 486 Processing sheet with id= AO, first strand: chain 'F' and resid 24 through 26 Processing sheet with id= AP, first strand: chain 'F' and resid 56 through 59 Processing sheet with id= AQ, first strand: chain 'F' and resid 193 through 195 Processing sheet with id= AR, first strand: chain 'F' and resid 206 through 212 removed outlier: 6.723A pdb=" N VAL F 378 " --> pdb=" O GLN F 207 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL F 209 " --> pdb=" O VAL F 378 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE F 380 " --> pdb=" O VAL F 209 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N LYS F 211 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE F 382 " --> pdb=" O LYS F 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'F' and resid 224 through 227 Processing sheet with id= AT, first strand: chain 'F' and resid 351 through 353 removed outlier: 6.607A pdb=" N VAL F 296 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU F 248 " --> pdb=" O VAL F 296 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE F 298 " --> pdb=" O LEU F 248 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'F' and resid 413 through 415 Processing sheet with id= AV, first strand: chain 'F' and resid 484 through 486 Processing sheet with id= AW, first strand: chain 'G' and resid 24 through 26 Processing sheet with id= AX, first strand: chain 'G' and resid 56 through 59 Processing sheet with id= AY, first strand: chain 'G' and resid 193 through 195 Processing sheet with id= AZ, first strand: chain 'G' and resid 206 through 212 removed outlier: 6.723A pdb=" N VAL G 378 " --> pdb=" O GLN G 207 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL G 209 " --> pdb=" O VAL G 378 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE G 380 " --> pdb=" O VAL G 209 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LYS G 211 " --> pdb=" O ILE G 380 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE G 382 " --> pdb=" O LYS G 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= AZ Processing sheet with id= BA, first strand: chain 'G' and resid 224 through 227 Processing sheet with id= BB, first strand: chain 'G' and resid 351 through 353 removed outlier: 6.606A pdb=" N VAL G 296 " --> pdb=" O ALA G 246 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LEU G 248 " --> pdb=" O VAL G 296 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE G 298 " --> pdb=" O LEU G 248 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'G' and resid 413 through 415 Processing sheet with id= BD, first strand: chain 'G' and resid 484 through 486 Processing sheet with id= BE, first strand: chain 'H' and resid 24 through 26 Processing sheet with id= BF, first strand: chain 'H' and resid 56 through 59 Processing sheet with id= BG, first strand: chain 'H' and resid 193 through 195 Processing sheet with id= BH, first strand: chain 'H' and resid 206 through 212 removed outlier: 6.722A pdb=" N VAL H 378 " --> pdb=" O GLN H 207 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL H 209 " --> pdb=" O VAL H 378 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE H 380 " --> pdb=" O VAL H 209 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LYS H 211 " --> pdb=" O ILE H 380 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE H 382 " --> pdb=" O LYS H 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= BH Processing sheet with id= BI, first strand: chain 'H' and resid 224 through 227 Processing sheet with id= BJ, first strand: chain 'H' and resid 351 through 353 removed outlier: 6.606A pdb=" N VAL H 296 " --> pdb=" O ALA H 246 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU H 248 " --> pdb=" O VAL H 296 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE H 298 " --> pdb=" O LEU H 248 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'H' and resid 413 through 415 Processing sheet with id= BL, first strand: chain 'H' and resid 484 through 486 Processing sheet with id= BM, first strand: chain 'I' and resid 24 through 26 Processing sheet with id= BN, first strand: chain 'I' and resid 56 through 59 Processing sheet with id= BO, first strand: chain 'I' and resid 193 through 195 Processing sheet with id= BP, first strand: chain 'I' and resid 206 through 212 removed outlier: 6.722A pdb=" N VAL I 378 " --> pdb=" O GLN I 207 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL I 209 " --> pdb=" O VAL I 378 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE I 380 " --> pdb=" O VAL I 209 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N LYS I 211 " --> pdb=" O ILE I 380 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE I 382 " --> pdb=" O LYS I 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= BP Processing sheet with id= BQ, first strand: chain 'I' and resid 224 through 227 Processing sheet with id= BR, first strand: chain 'I' and resid 351 through 353 removed outlier: 6.606A pdb=" N VAL I 296 " --> pdb=" O ALA I 246 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU I 248 " --> pdb=" O VAL I 296 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE I 298 " --> pdb=" O LEU I 248 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'I' and resid 413 through 415 Processing sheet with id= BT, first strand: chain 'I' and resid 484 through 486 Processing sheet with id= BU, first strand: chain 'J' and resid 24 through 26 Processing sheet with id= BV, first strand: chain 'J' and resid 56 through 59 Processing sheet with id= BW, first strand: chain 'J' and resid 193 through 195 Processing sheet with id= BX, first strand: chain 'J' and resid 206 through 212 removed outlier: 6.722A pdb=" N VAL J 378 " --> pdb=" O GLN J 207 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL J 209 " --> pdb=" O VAL J 378 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE J 380 " --> pdb=" O VAL J 209 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LYS J 211 " --> pdb=" O ILE J 380 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE J 382 " --> pdb=" O LYS J 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= BX Processing sheet with id= BY, first strand: chain 'J' and resid 224 through 227 Processing sheet with id= BZ, first strand: chain 'J' and resid 351 through 353 removed outlier: 6.606A pdb=" N VAL J 296 " --> pdb=" O ALA J 246 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU J 248 " --> pdb=" O VAL J 296 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE J 298 " --> pdb=" O LEU J 248 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'J' and resid 413 through 415 Processing sheet with id= CB, first strand: chain 'J' and resid 484 through 486 Processing sheet with id= CC, first strand: chain 'K' and resid 24 through 26 Processing sheet with id= CD, first strand: chain 'K' and resid 56 through 59 Processing sheet with id= CE, first strand: chain 'K' and resid 193 through 195 Processing sheet with id= CF, first strand: chain 'K' and resid 206 through 212 removed outlier: 6.722A pdb=" N VAL K 378 " --> pdb=" O GLN K 207 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL K 209 " --> pdb=" O VAL K 378 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE K 380 " --> pdb=" O VAL K 209 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N LYS K 211 " --> pdb=" O ILE K 380 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE K 382 " --> pdb=" O LYS K 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= CF Processing sheet with id= CG, first strand: chain 'K' and resid 224 through 227 Processing sheet with id= CH, first strand: chain 'K' and resid 351 through 353 removed outlier: 6.606A pdb=" N VAL K 296 " --> pdb=" O ALA K 246 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU K 248 " --> pdb=" O VAL K 296 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE K 298 " --> pdb=" O LEU K 248 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'K' and resid 413 through 415 Processing sheet with id= CJ, first strand: chain 'K' and resid 484 through 486 Processing sheet with id= CK, first strand: chain 'L' and resid 24 through 26 Processing sheet with id= CL, first strand: chain 'L' and resid 56 through 59 Processing sheet with id= CM, first strand: chain 'L' and resid 193 through 195 Processing sheet with id= CN, first strand: chain 'L' and resid 206 through 212 removed outlier: 6.721A pdb=" N VAL L 378 " --> pdb=" O GLN L 207 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL L 209 " --> pdb=" O VAL L 378 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE L 380 " --> pdb=" O VAL L 209 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LYS L 211 " --> pdb=" O ILE L 380 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE L 382 " --> pdb=" O LYS L 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= CN Processing sheet with id= CO, first strand: chain 'L' and resid 224 through 227 Processing sheet with id= CP, first strand: chain 'L' and resid 351 through 353 removed outlier: 6.607A pdb=" N VAL L 296 " --> pdb=" O ALA L 246 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU L 248 " --> pdb=" O VAL L 296 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE L 298 " --> pdb=" O LEU L 248 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain 'L' and resid 413 through 415 Processing sheet with id= CR, first strand: chain 'L' and resid 484 through 486 Processing sheet with id= CS, first strand: chain 'M' and resid 24 through 26 Processing sheet with id= CT, first strand: chain 'M' and resid 56 through 59 Processing sheet with id= CU, first strand: chain 'M' and resid 193 through 195 Processing sheet with id= CV, first strand: chain 'M' and resid 206 through 212 removed outlier: 6.722A pdb=" N VAL M 378 " --> pdb=" O GLN M 207 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL M 209 " --> pdb=" O VAL M 378 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE M 380 " --> pdb=" O VAL M 209 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N LYS M 211 " --> pdb=" O ILE M 380 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE M 382 " --> pdb=" O LYS M 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= CV Processing sheet with id= CW, first strand: chain 'M' and resid 224 through 227 Processing sheet with id= CX, first strand: chain 'M' and resid 351 through 353 removed outlier: 6.606A pdb=" N VAL M 296 " --> pdb=" O ALA M 246 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU M 248 " --> pdb=" O VAL M 296 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE M 298 " --> pdb=" O LEU M 248 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'M' and resid 413 through 415 Processing sheet with id= CZ, first strand: chain 'M' and resid 484 through 486 Processing sheet with id= DA, first strand: chain 'N' and resid 24 through 26 Processing sheet with id= DB, first strand: chain 'N' and resid 56 through 59 Processing sheet with id= DC, first strand: chain 'N' and resid 193 through 195 Processing sheet with id= DD, first strand: chain 'N' and resid 206 through 212 removed outlier: 6.722A pdb=" N VAL N 378 " --> pdb=" O GLN N 207 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL N 209 " --> pdb=" O VAL N 378 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE N 380 " --> pdb=" O VAL N 209 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N LYS N 211 " --> pdb=" O ILE N 380 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE N 382 " --> pdb=" O LYS N 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= DD Processing sheet with id= DE, first strand: chain 'N' and resid 224 through 227 Processing sheet with id= DF, first strand: chain 'N' and resid 351 through 353 removed outlier: 6.606A pdb=" N VAL N 296 " --> pdb=" O ALA N 246 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU N 248 " --> pdb=" O VAL N 296 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE N 298 " --> pdb=" O LEU N 248 " (cutoff:3.500A) Processing sheet with id= DG, first strand: chain 'N' and resid 413 through 415 Processing sheet with id= DH, first strand: chain 'N' and resid 484 through 486 Processing sheet with id= DI, first strand: chain 'O' and resid 24 through 26 Processing sheet with id= DJ, first strand: chain 'O' and resid 56 through 59 Processing sheet with id= DK, first strand: chain 'O' and resid 193 through 195 Processing sheet with id= DL, first strand: chain 'O' and resid 206 through 212 removed outlier: 6.723A pdb=" N VAL O 378 " --> pdb=" O GLN O 207 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL O 209 " --> pdb=" O VAL O 378 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE O 380 " --> pdb=" O VAL O 209 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LYS O 211 " --> pdb=" O ILE O 380 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE O 382 " --> pdb=" O LYS O 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= DL Processing sheet with id= DM, first strand: chain 'O' and resid 224 through 227 Processing sheet with id= DN, first strand: chain 'O' and resid 351 through 353 removed outlier: 6.606A pdb=" N VAL O 296 " --> pdb=" O ALA O 246 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU O 248 " --> pdb=" O VAL O 296 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE O 298 " --> pdb=" O LEU O 248 " (cutoff:3.500A) Processing sheet with id= DO, first strand: chain 'O' and resid 413 through 415 Processing sheet with id= DP, first strand: chain 'O' and resid 484 through 486 Processing sheet with id= DQ, first strand: chain 'P' and resid 24 through 26 Processing sheet with id= DR, first strand: chain 'P' and resid 56 through 59 Processing sheet with id= DS, first strand: chain 'P' and resid 193 through 195 Processing sheet with id= DT, first strand: chain 'P' and resid 206 through 212 removed outlier: 6.722A pdb=" N VAL P 378 " --> pdb=" O GLN P 207 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL P 209 " --> pdb=" O VAL P 378 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE P 380 " --> pdb=" O VAL P 209 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N LYS P 211 " --> pdb=" O ILE P 380 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE P 382 " --> pdb=" O LYS P 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= DT Processing sheet with id= DU, first strand: chain 'P' and resid 224 through 227 Processing sheet with id= DV, first strand: chain 'P' and resid 351 through 353 removed outlier: 6.605A pdb=" N VAL P 296 " --> pdb=" O ALA P 246 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU P 248 " --> pdb=" O VAL P 296 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE P 298 " --> pdb=" O LEU P 248 " (cutoff:3.500A) Processing sheet with id= DW, first strand: chain 'P' and resid 413 through 415 Processing sheet with id= DX, first strand: chain 'P' and resid 484 through 486 Processing sheet with id= ), first strand: chain 'Q' and resid 24 through 26 Processing sheet with id= *, first strand: chain 'Q' and resid 56 through 59 Processing sheet with id= +, first strand: chain 'Q' and resid 193 through 195 Processing sheet with id= ,, first strand: chain 'Q' and resid 206 through 212 removed outlier: 6.723A pdb=" N VAL Q 378 " --> pdb=" O GLN Q 207 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL Q 209 " --> pdb=" O VAL Q 378 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE Q 380 " --> pdb=" O VAL Q 209 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LYS Q 211 " --> pdb=" O ILE Q 380 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE Q 382 " --> pdb=" O LYS Q 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= , Processing sheet with id= -, first strand: chain 'Q' and resid 224 through 227 Processing sheet with id= ., first strand: chain 'Q' and resid 351 through 353 removed outlier: 6.606A pdb=" N VAL Q 296 " --> pdb=" O ALA Q 246 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU Q 248 " --> pdb=" O VAL Q 296 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE Q 298 " --> pdb=" O LEU Q 248 " (cutoff:3.500A) Processing sheet with id= /, first strand: chain 'Q' and resid 413 through 415 Processing sheet with id= 0, first strand: chain 'Q' and resid 484 through 486 Processing sheet with id= 1, first strand: chain 'R' and resid 24 through 26 Processing sheet with id= 2, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= 3, first strand: chain 'R' and resid 193 through 195 Processing sheet with id= 4, first strand: chain 'R' and resid 206 through 212 removed outlier: 6.722A pdb=" N VAL R 378 " --> pdb=" O GLN R 207 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL R 209 " --> pdb=" O VAL R 378 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE R 380 " --> pdb=" O VAL R 209 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LYS R 211 " --> pdb=" O ILE R 380 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE R 382 " --> pdb=" O LYS R 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= 4 Processing sheet with id= 5, first strand: chain 'R' and resid 224 through 227 Processing sheet with id= 6, first strand: chain 'R' and resid 351 through 353 removed outlier: 6.606A pdb=" N VAL R 296 " --> pdb=" O ALA R 246 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU R 248 " --> pdb=" O VAL R 296 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE R 298 " --> pdb=" O LEU R 248 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'R' and resid 413 through 415 Processing sheet with id= 8, first strand: chain 'R' and resid 484 through 486 2900 hydrogen bonds defined for protein. 6534 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: 21.99 Time building geometry restraints manager: 19.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 17397 1.33 - 1.45: 7003 1.45 - 1.57: 36350 1.57 - 1.68: 90 1.68 - 1.80: 252 Bond restraints: 61092 Sorted by residual: bond pdb=" N THR C 99 " pdb=" CA THR C 99 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.36e-02 5.41e+03 9.59e+00 bond pdb=" N ALA P 100 " pdb=" CA ALA P 100 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.58e+00 bond pdb=" N ALA M 100 " pdb=" CA ALA M 100 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.57e+00 bond pdb=" N THR G 99 " pdb=" CA THR G 99 " ideal model delta sigma weight residual 1.456 1.497 -0.042 1.36e-02 5.41e+03 9.53e+00 bond pdb=" N ALA H 100 " pdb=" CA ALA H 100 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.51e+00 ... (remaining 61087 not shown) Histogram of bond angle deviations from ideal: 97.51 - 104.84: 1098 104.84 - 112.16: 29430 112.16 - 119.49: 23275 119.49 - 126.81: 28529 126.81 - 134.13: 630 Bond angle restraints: 82962 Sorted by residual: angle pdb=" PA ATP N 602 " pdb=" O3A ATP N 602 " pdb=" PB ATP N 602 " ideal model delta sigma weight residual 136.83 127.87 8.96 1.00e+00 1.00e+00 8.02e+01 angle pdb=" PA ATP H 602 " pdb=" O3A ATP H 602 " pdb=" PB ATP H 602 " ideal model delta sigma weight residual 136.83 127.88 8.95 1.00e+00 1.00e+00 8.01e+01 angle pdb=" PA ATP R 602 " pdb=" O3A ATP R 602 " pdb=" PB ATP R 602 " ideal model delta sigma weight residual 136.83 127.90 8.93 1.00e+00 1.00e+00 7.98e+01 angle pdb=" PA ATP O 602 " pdb=" O3A ATP O 602 " pdb=" PB ATP O 602 " ideal model delta sigma weight residual 136.83 127.90 8.93 1.00e+00 1.00e+00 7.97e+01 angle pdb=" PA ATP I 602 " pdb=" O3A ATP I 602 " pdb=" PB ATP I 602 " ideal model delta sigma weight residual 136.83 127.90 8.93 1.00e+00 1.00e+00 7.97e+01 ... (remaining 82957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 34360 17.62 - 35.24: 2492 35.24 - 52.86: 498 52.86 - 70.49: 144 70.49 - 88.11: 108 Dihedral angle restraints: 37602 sinusoidal: 13356 harmonic: 24246 Sorted by residual: dihedral pdb=" CA LYS M 77 " pdb=" C LYS M 77 " pdb=" N MET M 78 " pdb=" CA MET M 78 " ideal model delta harmonic sigma weight residual 180.00 150.88 29.12 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LYS H 77 " pdb=" C LYS H 77 " pdb=" N MET H 78 " pdb=" CA MET H 78 " ideal model delta harmonic sigma weight residual 180.00 150.88 29.12 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LYS O 77 " pdb=" C LYS O 77 " pdb=" N MET O 78 " pdb=" CA MET O 78 " ideal model delta harmonic sigma weight residual 180.00 150.88 29.12 0 5.00e+00 4.00e-02 3.39e+01 ... (remaining 37599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 7739 0.088 - 0.176: 2251 0.176 - 0.264: 180 0.264 - 0.352: 18 0.352 - 0.441: 18 Chirality restraints: 10206 Sorted by residual: chirality pdb=" CA SER K 170 " pdb=" N SER K 170 " pdb=" C SER K 170 " pdb=" CB SER K 170 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CA SER G 170 " pdb=" N SER G 170 " pdb=" C SER G 170 " pdb=" CB SER G 170 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" CA SER Q 170 " pdb=" N SER Q 170 " pdb=" C SER Q 170 " pdb=" CB SER Q 170 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.81e+00 ... (remaining 10203 not shown) Planarity restraints: 10674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP Q 483 " -0.046 2.00e-02 2.50e+03 2.89e-02 2.09e+01 pdb=" CG TRP Q 483 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP Q 483 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP Q 483 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP Q 483 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP Q 483 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP Q 483 " 0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP Q 483 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP Q 483 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP Q 483 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 483 " 0.045 2.00e-02 2.50e+03 2.89e-02 2.09e+01 pdb=" CG TRP L 483 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP L 483 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP L 483 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP L 483 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP L 483 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP L 483 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 483 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 483 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP L 483 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 483 " 0.045 2.00e-02 2.50e+03 2.89e-02 2.09e+01 pdb=" CG TRP B 483 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP B 483 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP B 483 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP B 483 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP B 483 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 483 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 483 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 483 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 483 " 0.012 2.00e-02 2.50e+03 ... (remaining 10671 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 7516 2.76 - 3.30: 60899 3.30 - 3.83: 88567 3.83 - 4.37: 104983 4.37 - 4.90: 177609 Nonbonded interactions: 439574 Sorted by model distance: nonbonded pdb="MG MG D 601 " pdb=" O1B ATP D 602 " model vdw 2.225 2.170 nonbonded pdb="MG MG R 601 " pdb=" O1B ATP R 602 " model vdw 2.226 2.170 nonbonded pdb="MG MG H 601 " pdb=" O1B ATP H 602 " model vdw 2.226 2.170 nonbonded pdb="MG MG M 601 " pdb=" O1B ATP M 602 " model vdw 2.226 2.170 nonbonded pdb="MG MG G 601 " pdb=" O1B ATP G 602 " model vdw 2.226 2.170 ... (remaining 439569 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 18.830 Check model and map are aligned: 0.650 Set scattering table: 0.420 Process input model: 121.870 Find NCS groups from input model: 3.200 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5188 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 : 0.014 0.098 61092 Z= 0.920 Angle : 1.375 9.863 82962 Z= 0.818 Chirality : 0.076 0.441 10206 Planarity : 0.009 0.038 10674 Dihedral : 14.538 88.107 21906 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.08), residues: 8226 helix: -2.37 (0.07), residues: 4428 sheet: 1.89 (0.15), residues: 990 loop : -1.65 (0.10), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.009 TRP L 483 HIS 0.009 0.003 HIS E 476 PHE 0.017 0.004 PHE H 489 TYR 0.054 0.010 TYR G 446 ARG 0.051 0.008 ARG O 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1337 residues out of total 6786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1337 time to evaluate : 4.940 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: D 65 ILE cc_start: 0.8550 (mm) cc_final: 0.7974 (mt) REVERT: F 526 ASP cc_start: 0.6575 (t0) cc_final: 0.6352 (t0) outliers start: 0 outliers final: 0 residues processed: 1337 average time/residue: 0.6246 time to fit residues: 1335.8154 Evaluate side-chains 743 residues out of total 6786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 743 time to evaluate : 4.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 714 optimal weight: 2.9990 chunk 641 optimal weight: 0.6980 chunk 355 optimal weight: 0.2980 chunk 219 optimal weight: 4.9990 chunk 432 optimal weight: 2.9990 chunk 342 optimal weight: 0.0170 chunk 663 optimal weight: 0.7980 chunk 256 optimal weight: 2.9990 chunk 403 optimal weight: 20.0000 chunk 493 optimal weight: 4.9990 chunk 768 optimal weight: 7.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 HIS B 95 GLN C 476 HIS E 95 GLN F 95 GLN F 476 HIS ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 476 HIS I 95 GLN J 207 GLN ** J 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 GLN ** K 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN ** L 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 GLN M 207 GLN ** M 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 95 GLN P 207 GLN ** P 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 61092 Z= 0.244 Angle : 0.659 10.732 82962 Z= 0.348 Chirality : 0.045 0.209 10206 Planarity : 0.004 0.037 10674 Dihedral : 7.970 81.216 9486 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.08 % Allowed : 9.77 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.19 (0.09), residues: 8226 helix: -1.13 (0.08), residues: 4356 sheet: 1.82 (0.14), residues: 1152 loop : -1.12 (0.11), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 497 HIS 0.011 0.001 HIS I 212 PHE 0.007 0.001 PHE M 489 TYR 0.029 0.002 TYR N 122 ARG 0.014 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 6786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1024 time to evaluate : 4.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 526 ASP cc_start: 0.6818 (t0) cc_final: 0.6546 (t0) REVERT: F 147 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7773 (tm-30) REVERT: F 526 ASP cc_start: 0.6365 (t0) cc_final: 0.6100 (t0) REVERT: H 194 LEU cc_start: 0.7702 (tt) cc_final: 0.7468 (mp) REVERT: H 526 ASP cc_start: 0.6608 (t0) cc_final: 0.6358 (t0) REVERT: I 95 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.6996 (tp-100) REVERT: K 54 MET cc_start: 0.6904 (mpp) cc_final: 0.6524 (mpp) REVERT: K 113 LEU cc_start: 0.4683 (mt) cc_final: 0.4438 (mt) REVERT: K 529 VAL cc_start: 0.4280 (t) cc_final: 0.4075 (t) REVERT: L 54 MET cc_start: 0.7071 (mpp) cc_final: 0.6849 (mpp) REVERT: L 75 LEU cc_start: 0.3614 (OUTLIER) cc_final: 0.3142 (mt) REVERT: L 81 GLN cc_start: 0.5716 (OUTLIER) cc_final: 0.5228 (pm20) REVERT: M 54 MET cc_start: 0.6773 (mpp) cc_final: 0.6500 (mpp) REVERT: M 75 LEU cc_start: 0.4107 (OUTLIER) cc_final: 0.3517 (mt) REVERT: N 81 GLN cc_start: 0.6348 (pp30) cc_final: 0.6083 (pp30) REVERT: O 75 LEU cc_start: 0.3826 (OUTLIER) cc_final: 0.3441 (mt) REVERT: P 54 MET cc_start: 0.7032 (mpp) cc_final: 0.6815 (mpp) REVERT: Q 54 MET cc_start: 0.6952 (mpp) cc_final: 0.6697 (mpp) REVERT: R 455 MET cc_start: 0.6229 (tpp) cc_final: 0.5754 (tpp) outliers start: 113 outliers final: 67 residues processed: 1085 average time/residue: 0.5416 time to fit residues: 998.1022 Evaluate side-chains 843 residues out of total 6786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 771 time to evaluate : 4.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 403 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 95 GLN Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain J residue 170 SER Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 207 GLN Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 170 SER Chi-restraints excluded: chain L residue 414 VAL Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 78 MET Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 207 GLN Chi-restraints excluded: chain M residue 414 VAL Chi-restraints excluded: chain M residue 435 VAL Chi-restraints excluded: chain N residue 78 MET Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 170 SER Chi-restraints excluded: chain N residue 414 VAL Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain O residue 414 VAL Chi-restraints excluded: chain O residue 435 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 170 SER Chi-restraints excluded: chain P residue 207 GLN Chi-restraints excluded: chain P residue 414 VAL Chi-restraints excluded: chain P residue 435 VAL Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain Q residue 414 VAL Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 170 SER Chi-restraints excluded: chain R residue 414 VAL Chi-restraints excluded: chain R residue 528 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 426 optimal weight: 0.8980 chunk 238 optimal weight: 5.9990 chunk 639 optimal weight: 40.0000 chunk 523 optimal weight: 0.8980 chunk 211 optimal weight: 4.9990 chunk 769 optimal weight: 7.9990 chunk 831 optimal weight: 10.0000 chunk 685 optimal weight: 40.0000 chunk 763 optimal weight: 0.8980 chunk 262 optimal weight: 6.9990 chunk 617 optimal weight: 0.0870 overall best weight: 1.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 434 GLN B 476 HIS C 95 GLN D 95 GLN D 476 HIS ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 476 HIS F 95 GLN G 476 HIS H 126 HIS I 126 HIS I 476 HIS J 476 HIS J 510 ASN K 476 HIS K 510 ASN L 81 GLN L 476 HIS L 510 ASN M 476 HIS M 510 ASN N 510 ASN O 95 GLN O 510 ASN P 95 GLN P 476 HIS P 510 ASN Q 207 GLN Q 476 HIS Q 510 ASN R 476 HIS R 510 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.7669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 61092 Z= 0.282 Angle : 0.678 11.186 82962 Z= 0.348 Chirality : 0.047 0.429 10206 Planarity : 0.004 0.054 10674 Dihedral : 7.127 72.959 9486 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.69 % Favored : 97.29 % Rotamer: Outliers : 3.72 % Allowed : 14.74 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.12 (0.09), residues: 8226 helix: -1.00 (0.08), residues: 4212 sheet: 1.38 (0.20), residues: 666 loop : -0.61 (0.10), residues: 3348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 497 HIS 0.008 0.001 HIS N 476 PHE 0.011 0.002 PHE F 489 TYR 0.021 0.002 TYR G 446 ARG 0.015 0.001 ARG H 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 6786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 894 time to evaluate : 4.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLN cc_start: 0.7374 (tp-100) cc_final: 0.7042 (tp-100) REVERT: A 147 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7836 (tm-30) REVERT: B 194 LEU cc_start: 0.8139 (tt) cc_final: 0.7939 (mp) REVERT: C 95 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7132 (tp-100) REVERT: C 496 MET cc_start: 0.8254 (mmm) cc_final: 0.8030 (tpp) REVERT: D 95 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.6509 (tp-100) REVERT: D 496 MET cc_start: 0.8293 (mmm) cc_final: 0.8076 (mpp) REVERT: E 496 MET cc_start: 0.8348 (mmm) cc_final: 0.8134 (tpp) REVERT: F 496 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8282 (mmp) REVERT: G 57 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.6195 (ttp) REVERT: G 496 MET cc_start: 0.8295 (mmm) cc_final: 0.8077 (mpp) REVERT: H 194 LEU cc_start: 0.8168 (tt) cc_final: 0.7872 (mp) REVERT: H 526 ASP cc_start: 0.6733 (t0) cc_final: 0.6478 (t0) REVERT: I 496 MET cc_start: 0.8324 (mmm) cc_final: 0.8114 (mpp) REVERT: K 64 ASP cc_start: 0.7832 (t70) cc_final: 0.7579 (t0) REVERT: K 75 LEU cc_start: 0.6002 (OUTLIER) cc_final: 0.5641 (mt) REVERT: K 81 GLN cc_start: 0.6005 (pp30) cc_final: 0.5581 (pm20) REVERT: L 64 ASP cc_start: 0.7757 (t70) cc_final: 0.7517 (t0) REVERT: M 64 ASP cc_start: 0.7752 (t70) cc_final: 0.7473 (t0) REVERT: M 81 GLN cc_start: 0.6301 (pp30) cc_final: 0.5920 (pm20) REVERT: M 529 VAL cc_start: 0.5399 (t) cc_final: 0.5197 (t) REVERT: N 64 ASP cc_start: 0.7802 (t70) cc_final: 0.7540 (t0) REVERT: O 64 ASP cc_start: 0.7958 (t70) cc_final: 0.7747 (t0) REVERT: O 81 GLN cc_start: 0.6424 (pm20) cc_final: 0.5866 (pp30) REVERT: P 81 GLN cc_start: 0.6119 (pp30) cc_final: 0.5782 (pm20) REVERT: R 68 THR cc_start: 0.7139 (t) cc_final: 0.6878 (t) REVERT: R 81 GLN cc_start: 0.6042 (pp30) cc_final: 0.5660 (pm20) REVERT: R 521 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8250 (mt) outliers start: 202 outliers final: 89 residues processed: 1035 average time/residue: 0.5272 time to fit residues: 938.6988 Evaluate side-chains 807 residues out of total 6786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 712 time to evaluate : 4.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 450 ILE Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 496 MET Chi-restraints excluded: chain G residue 57 MET Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 450 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 450 ILE Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 450 ILE Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 145 ILE Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 525 ILE Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 525 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 78 MET Chi-restraints excluded: chain M residue 145 ILE Chi-restraints excluded: chain M residue 165 LEU Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 525 ILE Chi-restraints excluded: chain N residue 35 ILE Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 78 MET Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 165 LEU Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain O residue 484 TYR Chi-restraints excluded: chain O residue 525 ILE Chi-restraints excluded: chain P residue 35 ILE Chi-restraints excluded: chain P residue 78 MET Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 170 SER Chi-restraints excluded: chain Q residue 35 ILE Chi-restraints excluded: chain Q residue 165 LEU Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain Q residue 207 GLN Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 484 TYR Chi-restraints excluded: chain R residue 521 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 760 optimal weight: 0.9980 chunk 578 optimal weight: 1.9990 chunk 399 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 367 optimal weight: 0.5980 chunk 516 optimal weight: 1.9990 chunk 772 optimal weight: 9.9990 chunk 817 optimal weight: 0.0050 chunk 403 optimal weight: 50.0000 chunk 732 optimal weight: 50.0000 chunk 220 optimal weight: 30.0000 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN B 126 HIS C 95 GLN ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN D 126 HIS E 95 GLN E 126 HIS G 95 GLN ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 434 GLN K 146 GLN L 69 ASN L 95 GLN M 69 ASN N 69 ASN P 69 ASN Q 69 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.8346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 61092 Z= 0.159 Angle : 0.515 10.512 82962 Z= 0.261 Chirality : 0.042 0.200 10206 Planarity : 0.003 0.036 10674 Dihedral : 5.985 56.048 9486 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.13 % Allowed : 19.52 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.45 (0.09), residues: 8226 helix: -0.24 (0.08), residues: 4176 sheet: 1.57 (0.20), residues: 684 loop : -0.60 (0.10), residues: 3366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 199 HIS 0.004 0.001 HIS N 476 PHE 0.004 0.001 PHE R 489 TYR 0.016 0.001 TYR B 179 ARG 0.007 0.000 ARG N 195 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 6786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 805 time to evaluate : 4.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7003 (tp-100) REVERT: A 147 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7636 (tm-30) REVERT: B 95 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6636 (tp-100) REVERT: C 26 TYR cc_start: 0.6958 (p90) cc_final: 0.6552 (p90) REVERT: C 95 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6957 (tp-100) REVERT: C 147 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7772 (tm-30) REVERT: D 57 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6580 (ttp) REVERT: D 95 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.6631 (tp-100) REVERT: D 496 MET cc_start: 0.8285 (mmm) cc_final: 0.7833 (mmm) REVERT: E 90 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8406 (tm-30) REVERT: E 496 MET cc_start: 0.8364 (mmm) cc_final: 0.7896 (mmp) REVERT: G 95 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.6915 (tp-100) REVERT: H 194 LEU cc_start: 0.8082 (tt) cc_final: 0.7836 (mp) REVERT: I 496 MET cc_start: 0.8272 (mmm) cc_final: 0.7733 (mmm) REVERT: J 49 TYR cc_start: 0.8849 (t80) cc_final: 0.8644 (t80) REVERT: K 64 ASP cc_start: 0.7992 (t70) cc_final: 0.7744 (t0) REVERT: K 75 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5919 (mt) REVERT: K 81 GLN cc_start: 0.6473 (pp30) cc_final: 0.6197 (pm20) REVERT: K 103 THR cc_start: 0.8510 (m) cc_final: 0.8249 (m) REVERT: K 496 MET cc_start: 0.8669 (mmm) cc_final: 0.8258 (mmp) REVERT: K 528 ILE cc_start: 0.6941 (mt) cc_final: 0.6446 (mt) REVERT: L 64 ASP cc_start: 0.7906 (t70) cc_final: 0.7626 (t0) REVERT: L 112 GLU cc_start: 0.6828 (tp30) cc_final: 0.6561 (tp30) REVERT: L 389 VAL cc_start: 0.8133 (t) cc_final: 0.7908 (p) REVERT: M 54 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8274 (mmm) REVERT: M 64 ASP cc_start: 0.7878 (t70) cc_final: 0.7600 (t0) REVERT: M 528 ILE cc_start: 0.7095 (mt) cc_final: 0.6871 (mt) REVERT: N 64 ASP cc_start: 0.7802 (t70) cc_final: 0.7597 (t0) REVERT: N 528 ILE cc_start: 0.6839 (mt) cc_final: 0.6623 (mt) REVERT: O 64 ASP cc_start: 0.7985 (t70) cc_final: 0.7781 (t0) REVERT: O 146 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7299 (mt0) REVERT: O 528 ILE cc_start: 0.6898 (mt) cc_final: 0.6594 (mt) REVERT: P 64 ASP cc_start: 0.7773 (t70) cc_final: 0.7570 (t0) REVERT: P 517 GLU cc_start: 0.7069 (tt0) cc_final: 0.6808 (tt0) REVERT: R 81 GLN cc_start: 0.6296 (pp30) cc_final: 0.5898 (pm20) REVERT: R 521 LEU cc_start: 0.8812 (mm) cc_final: 0.8300 (mt) outliers start: 116 outliers final: 71 residues processed: 881 average time/residue: 0.5307 time to fit residues: 808.8105 Evaluate side-chains 792 residues out of total 6786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 712 time to evaluate : 4.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 95 GLN Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 490 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain I residue 490 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 484 TYR Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain M residue 54 MET Chi-restraints excluded: chain M residue 78 MET Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 104 LYS Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain O residue 146 GLN Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain O residue 484 TYR Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain P residue 78 MET Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 170 SER Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain Q residue 159 VAL Chi-restraints excluded: chain Q residue 526 ASP Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 484 TYR Chi-restraints excluded: chain R residue 525 ILE Chi-restraints excluded: chain R residue 528 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 681 optimal weight: 0.4980 chunk 464 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 608 optimal weight: 0.4980 chunk 337 optimal weight: 0.9990 chunk 697 optimal weight: 0.6980 chunk 565 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 417 optimal weight: 0.6980 chunk 733 optimal weight: 20.0000 chunk 206 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 95 GLN C 95 GLN D 95 GLN E 95 GLN ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 GLN ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 GLN H 434 GLN I 95 GLN I 146 GLN J 90 GLN K 90 GLN L 90 GLN L 126 HIS L 146 GLN M 126 HIS ** M 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 146 GLN Q 90 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.8801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 61092 Z= 0.138 Angle : 0.494 9.790 82962 Z= 0.248 Chirality : 0.041 0.161 10206 Planarity : 0.003 0.037 10674 Dihedral : 5.596 53.338 9486 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.71 % Allowed : 20.88 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.10 (0.09), residues: 8226 helix: 0.16 (0.08), residues: 4320 sheet: 1.89 (0.17), residues: 864 loop : -0.86 (0.10), residues: 3042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 199 HIS 0.003 0.000 HIS E 126 PHE 0.005 0.001 PHE A 489 TYR 0.029 0.001 TYR L 122 ARG 0.006 0.000 ARG F 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 6786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 832 time to evaluate : 4.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 496 MET cc_start: 0.8221 (mmm) cc_final: 0.7463 (mmm) REVERT: C 147 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7746 (tm-30) REVERT: D 95 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.6983 (tp-100) REVERT: D 496 MET cc_start: 0.8358 (mmm) cc_final: 0.7942 (mmm) REVERT: E 496 MET cc_start: 0.8263 (mmm) cc_final: 0.7975 (mmp) REVERT: I 90 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8267 (tm-30) REVERT: J 160 LEU cc_start: 0.7306 (mm) cc_final: 0.7073 (mm) REVERT: K 64 ASP cc_start: 0.7909 (t70) cc_final: 0.7667 (t0) REVERT: K 496 MET cc_start: 0.8623 (mmm) cc_final: 0.8333 (mmp) REVERT: L 64 ASP cc_start: 0.7878 (t70) cc_final: 0.7666 (t0) REVERT: L 389 VAL cc_start: 0.8199 (t) cc_final: 0.7997 (p) REVERT: L 496 MET cc_start: 0.8513 (mmm) cc_final: 0.8251 (mmp) REVERT: M 64 ASP cc_start: 0.7851 (t70) cc_final: 0.7576 (t0) REVERT: M 521 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8605 (tt) REVERT: M 528 ILE cc_start: 0.7506 (mt) cc_final: 0.7198 (mt) REVERT: N 64 ASP cc_start: 0.7867 (t70) cc_final: 0.7643 (t0) REVERT: N 496 MET cc_start: 0.8514 (mmm) cc_final: 0.8120 (mmp) REVERT: N 528 ILE cc_start: 0.7277 (mt) cc_final: 0.7044 (mt) REVERT: O 64 ASP cc_start: 0.8079 (t70) cc_final: 0.7872 (t0) REVERT: O 496 MET cc_start: 0.8381 (mmm) cc_final: 0.7973 (mmp) REVERT: O 528 ILE cc_start: 0.7087 (mt) cc_final: 0.6805 (mt) REVERT: P 64 ASP cc_start: 0.7748 (t70) cc_final: 0.7512 (t0) REVERT: P 517 GLU cc_start: 0.7076 (tt0) cc_final: 0.6848 (tt0) REVERT: R 527 ASP cc_start: 0.5780 (OUTLIER) cc_final: 0.5341 (m-30) outliers start: 93 outliers final: 64 residues processed: 884 average time/residue: 0.5354 time to fit residues: 811.9721 Evaluate side-chains 779 residues out of total 6786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 712 time to evaluate : 5.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 222 VAL Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 502 ILE Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 525 ILE Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 165 LEU Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 467 ASP Chi-restraints excluded: chain M residue 521 LEU Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 476 HIS Chi-restraints excluded: chain N residue 521 LEU Chi-restraints excluded: chain N residue 525 ILE Chi-restraints excluded: chain N residue 529 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain O residue 165 LEU Chi-restraints excluded: chain O residue 484 TYR Chi-restraints excluded: chain O residue 521 LEU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 459 GLU Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain Q residue 165 LEU Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 484 TYR Chi-restraints excluded: chain R residue 521 LEU Chi-restraints excluded: chain R residue 527 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 275 optimal weight: 0.7980 chunk 736 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 480 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 chunk 818 optimal weight: 0.4980 chunk 679 optimal weight: 1.9990 chunk 378 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 270 optimal weight: 5.9990 chunk 429 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 146 GLN ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 GLN G 212 HIS H 434 GLN J 126 HIS J 146 GLN K 126 HIS L 146 GLN N 146 GLN O 476 HIS P 126 HIS R 126 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.9394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 61092 Z= 0.185 Angle : 0.530 10.795 82962 Z= 0.266 Chirality : 0.042 0.152 10206 Planarity : 0.003 0.056 10674 Dihedral : 5.669 51.805 9486 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.89 % Allowed : 21.41 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.08 (0.09), residues: 8226 helix: 0.24 (0.08), residues: 4284 sheet: 1.83 (0.17), residues: 864 loop : -0.92 (0.10), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 483 HIS 0.004 0.001 HIS I 126 PHE 0.007 0.001 PHE E 489 TYR 0.025 0.001 TYR Q 122 ARG 0.012 0.001 ARG P 388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 6786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 761 time to evaluate : 4.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 496 MET cc_start: 0.8285 (mmm) cc_final: 0.7859 (mmp) REVERT: C 95 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7097 (tp-100) REVERT: C 147 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7858 (tm-30) REVERT: D 190 GLN cc_start: 0.7732 (pm20) cc_final: 0.7510 (pm20) REVERT: G 95 GLN cc_start: 0.7125 (tp40) cc_final: 0.6703 (tp-100) REVERT: H 496 MET cc_start: 0.8374 (mmm) cc_final: 0.7790 (mmm) REVERT: I 90 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8300 (tm-30) REVERT: I 95 GLN cc_start: 0.7253 (tp40) cc_final: 0.6911 (tp-100) REVERT: K 80 LEU cc_start: 0.6943 (mt) cc_final: 0.6700 (mt) REVERT: L 167 SER cc_start: 0.6362 (t) cc_final: 0.6156 (t) REVERT: N 496 MET cc_start: 0.8541 (mmm) cc_final: 0.8211 (mmp) REVERT: O 122 TYR cc_start: 0.7318 (m-80) cc_final: 0.7094 (m-10) REVERT: O 167 SER cc_start: 0.6624 (t) cc_final: 0.6340 (t) REVERT: O 528 ILE cc_start: 0.7655 (mt) cc_final: 0.7386 (mt) REVERT: P 64 ASP cc_start: 0.7701 (t70) cc_final: 0.7492 (t0) REVERT: P 496 MET cc_start: 0.8463 (mmm) cc_final: 0.8253 (mmp) REVERT: P 517 GLU cc_start: 0.7119 (tt0) cc_final: 0.6868 (tt0) REVERT: Q 78 MET cc_start: 0.6882 (tpt) cc_final: 0.6219 (ttt) REVERT: R 95 GLN cc_start: 0.5921 (tt0) cc_final: 0.5709 (tt0) outliers start: 157 outliers final: 105 residues processed: 866 average time/residue: 0.5167 time to fit residues: 778.9179 Evaluate side-chains 796 residues out of total 6786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 690 time to evaluate : 4.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 450 ILE Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 450 ILE Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 204 ASP Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 170 SER Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 502 ILE Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 170 SER Chi-restraints excluded: chain L residue 525 ILE Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 430 LYS Chi-restraints excluded: chain M residue 459 GLU Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 104 LYS Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 519 VAL Chi-restraints excluded: chain N residue 521 LEU Chi-restraints excluded: chain N residue 525 ILE Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain O residue 191 VAL Chi-restraints excluded: chain O residue 476 HIS Chi-restraints excluded: chain O residue 484 TYR Chi-restraints excluded: chain O residue 521 LEU Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain P residue 170 SER Chi-restraints excluded: chain P residue 459 GLU Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain Q residue 459 GLU Chi-restraints excluded: chain R residue 78 MET Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 484 TYR Chi-restraints excluded: chain R residue 521 LEU Chi-restraints excluded: chain R residue 525 ILE Chi-restraints excluded: chain R residue 527 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 789 optimal weight: 0.1980 chunk 92 optimal weight: 0.6980 chunk 466 optimal weight: 3.9990 chunk 597 optimal weight: 6.9990 chunk 463 optimal weight: 0.0570 chunk 689 optimal weight: 6.9990 chunk 457 optimal weight: 6.9990 chunk 815 optimal weight: 0.0970 chunk 510 optimal weight: 0.7980 chunk 497 optimal weight: 50.0000 chunk 376 optimal weight: 7.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN C 190 GLN D 95 GLN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN H 434 GLN J 90 GLN J 95 GLN K 146 GLN K 492 ASN M 95 GLN M 146 GLN N 95 GLN O 476 HIS O 492 ASN P 95 GLN P 492 ASN Q 95 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.9593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 61092 Z= 0.125 Angle : 0.484 10.498 82962 Z= 0.244 Chirality : 0.040 0.149 10206 Planarity : 0.003 0.035 10674 Dihedral : 5.452 58.782 9486 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.88 % Allowed : 22.77 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.25 (0.09), residues: 8226 helix: 0.56 (0.08), residues: 4284 sheet: 1.90 (0.18), residues: 864 loop : -0.82 (0.10), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 199 HIS 0.013 0.000 HIS O 476 PHE 0.002 0.000 PHE A 489 TYR 0.025 0.001 TYR G 179 ARG 0.007 0.000 ARG F 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 6786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 760 time to evaluate : 4.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 GLN cc_start: 0.6862 (tp40) cc_final: 0.6355 (tp-100) REVERT: C 147 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7713 (tm-30) REVERT: D 95 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7053 (tp-100) REVERT: E 496 MET cc_start: 0.8169 (mmm) cc_final: 0.7450 (mmm) REVERT: G 95 GLN cc_start: 0.7106 (tp40) cc_final: 0.6854 (tp-100) REVERT: H 190 GLN cc_start: 0.7999 (pm20) cc_final: 0.7687 (pm20) REVERT: I 90 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8305 (tm-30) REVERT: I 95 GLN cc_start: 0.7252 (tp40) cc_final: 0.6911 (tp-100) REVERT: J 496 MET cc_start: 0.8423 (mmm) cc_final: 0.8082 (mmp) REVERT: K 95 GLN cc_start: 0.6368 (tt0) cc_final: 0.6136 (tt0) REVERT: L 167 SER cc_start: 0.6476 (t) cc_final: 0.6269 (t) REVERT: N 496 MET cc_start: 0.8446 (mmm) cc_final: 0.8132 (mmp) REVERT: O 122 TYR cc_start: 0.7252 (m-80) cc_final: 0.7013 (m-10) REVERT: O 167 SER cc_start: 0.6484 (t) cc_final: 0.6254 (t) REVERT: O 527 ASP cc_start: 0.5358 (m-30) cc_final: 0.4976 (m-30) REVERT: O 528 ILE cc_start: 0.7701 (mt) cc_final: 0.7472 (mt) REVERT: P 517 GLU cc_start: 0.7090 (tt0) cc_final: 0.6826 (tt0) REVERT: Q 78 MET cc_start: 0.6626 (tpt) cc_final: 0.6234 (ttt) outliers start: 102 outliers final: 77 residues processed: 828 average time/residue: 0.5542 time to fit residues: 796.9404 Evaluate side-chains 770 residues out of total 6786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 692 time to evaluate : 4.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain G residue 57 MET Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 490 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 450 ILE Chi-restraints excluded: chain I residue 490 THR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 126 HIS Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 126 HIS Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 484 TYR Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 521 LEU Chi-restraints excluded: chain N residue 525 ILE Chi-restraints excluded: chain O residue 191 VAL Chi-restraints excluded: chain O residue 476 HIS Chi-restraints excluded: chain O residue 484 TYR Chi-restraints excluded: chain P residue 95 GLN Chi-restraints excluded: chain P residue 126 HIS Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 191 VAL Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 112 GLU Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain Q residue 450 ILE Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 484 TYR Chi-restraints excluded: chain R residue 521 LEU Chi-restraints excluded: chain R residue 527 ASP Chi-restraints excluded: chain R residue 528 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 504 optimal weight: 8.9990 chunk 325 optimal weight: 2.9990 chunk 487 optimal weight: 9.9990 chunk 245 optimal weight: 0.6980 chunk 160 optimal weight: 20.0000 chunk 157 optimal weight: 10.0000 chunk 518 optimal weight: 0.6980 chunk 555 optimal weight: 0.9980 chunk 403 optimal weight: 50.0000 chunk 75 optimal weight: 5.9990 chunk 640 optimal weight: 50.0000 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS B 190 GLN C 146 GLN C 190 GLN C 212 HIS ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 HIS H 90 GLN H 212 HIS H 434 GLN I 212 HIS K 95 GLN M 90 GLN M 146 GLN N 69 ASN P 69 ASN ** R 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 1.0170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 61092 Z= 0.336 Angle : 0.644 11.449 82962 Z= 0.322 Chirality : 0.045 0.159 10206 Planarity : 0.004 0.048 10674 Dihedral : 6.526 60.789 9486 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.02 % Allowed : 22.63 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.23 (0.09), residues: 8226 helix: 0.03 (0.08), residues: 4266 sheet: 1.38 (0.18), residues: 900 loop : -0.73 (0.10), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 483 HIS 0.035 0.002 HIS O 476 PHE 0.010 0.001 PHE E 489 TYR 0.025 0.002 TYR G 179 ARG 0.009 0.001 ARG D 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 6786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 736 time to evaluate : 4.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8463 (tm-30) REVERT: A 496 MET cc_start: 0.8504 (mmm) cc_final: 0.8185 (mmp) REVERT: B 95 GLN cc_start: 0.7327 (tp40) cc_final: 0.6746 (tp-100) REVERT: B 496 MET cc_start: 0.8313 (mmm) cc_final: 0.7676 (mmm) REVERT: C 95 GLN cc_start: 0.7714 (tp40) cc_final: 0.7339 (tp-100) REVERT: C 496 MET cc_start: 0.8314 (mmm) cc_final: 0.7607 (mmm) REVERT: D 95 GLN cc_start: 0.7568 (tp40) cc_final: 0.6712 (tp-100) REVERT: E 496 MET cc_start: 0.8407 (mmm) cc_final: 0.8176 (mmp) REVERT: F 421 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6810 (mm-30) REVERT: H 142 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8157 (mp) REVERT: I 90 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8406 (tm-30) REVERT: I 496 MET cc_start: 0.8370 (mmm) cc_final: 0.7943 (mmp) REVERT: J 496 MET cc_start: 0.8481 (mmm) cc_final: 0.8243 (mmp) REVERT: K 95 GLN cc_start: 0.6541 (OUTLIER) cc_final: 0.5585 (tt0) REVERT: L 496 MET cc_start: 0.8450 (mmm) cc_final: 0.7999 (mmm) REVERT: M 496 MET cc_start: 0.8600 (mmm) cc_final: 0.8244 (mmp) REVERT: N 496 MET cc_start: 0.8502 (mmm) cc_final: 0.8288 (mmp) REVERT: N 517 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7116 (tt0) REVERT: P 484 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.7131 (t80) REVERT: P 517 GLU cc_start: 0.7104 (tt0) cc_final: 0.6886 (tt0) REVERT: Q 78 MET cc_start: 0.6479 (tpt) cc_final: 0.6184 (ttp) REVERT: Q 496 MET cc_start: 0.8415 (mmm) cc_final: 0.8186 (mmp) REVERT: R 496 MET cc_start: 0.8570 (mmm) cc_final: 0.7967 (mmp) REVERT: R 521 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8509 (mp) outliers start: 164 outliers final: 105 residues processed: 856 average time/residue: 0.5302 time to fit residues: 780.0635 Evaluate side-chains 782 residues out of total 6786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 672 time to evaluate : 4.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 450 ILE Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 421 GLU Chi-restraints excluded: chain F residue 496 MET Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 450 ILE Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 204 ASP Chi-restraints excluded: chain I residue 450 ILE Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 420 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 450 ILE Chi-restraints excluded: chain M residue 459 GLU Chi-restraints excluded: chain N residue 69 ASN Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 104 LYS Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 450 ILE Chi-restraints excluded: chain N residue 484 TYR Chi-restraints excluded: chain N residue 519 VAL Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 165 LEU Chi-restraints excluded: chain O residue 191 VAL Chi-restraints excluded: chain O residue 484 TYR Chi-restraints excluded: chain O residue 521 LEU Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 420 VAL Chi-restraints excluded: chain P residue 459 GLU Chi-restraints excluded: chain P residue 484 TYR Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 112 GLU Chi-restraints excluded: chain Q residue 145 ILE Chi-restraints excluded: chain Q residue 450 ILE Chi-restraints excluded: chain Q residue 459 GLU Chi-restraints excluded: chain Q residue 484 TYR Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 420 VAL Chi-restraints excluded: chain R residue 484 TYR Chi-restraints excluded: chain R residue 521 LEU Chi-restraints excluded: chain R residue 527 ASP Chi-restraints excluded: chain R residue 528 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 741 optimal weight: 0.6980 chunk 781 optimal weight: 50.0000 chunk 712 optimal weight: 3.9990 chunk 759 optimal weight: 4.9990 chunk 780 optimal weight: 50.0000 chunk 457 optimal weight: 0.9980 chunk 331 optimal weight: 0.9980 chunk 596 optimal weight: 10.0000 chunk 233 optimal weight: 0.9990 chunk 686 optimal weight: 50.0000 chunk 718 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 GLN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 GLN M 146 GLN R 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 1.0377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 61092 Z= 0.174 Angle : 0.522 10.303 82962 Z= 0.265 Chirality : 0.041 0.168 10206 Planarity : 0.003 0.056 10674 Dihedral : 5.733 54.735 9486 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.80 % Allowed : 24.03 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.04 (0.09), residues: 8226 helix: 0.32 (0.08), residues: 4302 sheet: 1.76 (0.18), residues: 864 loop : -0.96 (0.10), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 199 HIS 0.003 0.001 HIS E 126 PHE 0.004 0.001 PHE R 489 TYR 0.029 0.001 TYR G 179 ARG 0.013 0.000 ARG M 388 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 6786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 698 time to evaluate : 4.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 GLN cc_start: 0.7172 (tp40) cc_final: 0.6671 (tp-100) REVERT: B 239 ARG cc_start: 0.7099 (ttm110) cc_final: 0.6195 (mmt-90) REVERT: B 496 MET cc_start: 0.8167 (mmm) cc_final: 0.7494 (mmm) REVERT: C 95 GLN cc_start: 0.7515 (tp40) cc_final: 0.7091 (tp-100) REVERT: E 496 MET cc_start: 0.8290 (mmm) cc_final: 0.7909 (mmp) REVERT: F 421 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6475 (mm-30) REVERT: G 95 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.7064 (tp40) REVERT: H 496 MET cc_start: 0.8314 (mmm) cc_final: 0.7917 (mmm) REVERT: I 90 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8366 (tm-30) REVERT: I 496 MET cc_start: 0.8279 (mmm) cc_final: 0.7515 (mmm) REVERT: J 95 GLN cc_start: 0.6876 (tp40) cc_final: 0.6404 (tp-100) REVERT: J 484 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.7810 (m-10) REVERT: J 496 MET cc_start: 0.8398 (mmm) cc_final: 0.8162 (mmp) REVERT: K 80 LEU cc_start: 0.7770 (mt) cc_final: 0.7568 (mt) REVERT: K 496 MET cc_start: 0.8165 (mmp) cc_final: 0.7823 (mmm) REVERT: L 496 MET cc_start: 0.8370 (mmm) cc_final: 0.7908 (mmm) REVERT: M 496 MET cc_start: 0.8396 (mmm) cc_final: 0.8002 (mmp) REVERT: M 502 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8119 (mm) REVERT: N 517 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6915 (tt0) REVERT: P 95 GLN cc_start: 0.7367 (tp40) cc_final: 0.7085 (tp40) REVERT: P 484 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.6976 (t80) REVERT: P 496 MET cc_start: 0.8436 (mmm) cc_final: 0.7962 (mmp) REVERT: P 517 GLU cc_start: 0.7035 (tt0) cc_final: 0.6819 (tt0) REVERT: Q 496 MET cc_start: 0.8308 (mmm) cc_final: 0.7911 (mmp) REVERT: R 496 MET cc_start: 0.8465 (mmm) cc_final: 0.8081 (mmp) REVERT: R 521 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8419 (mp) outliers start: 98 outliers final: 74 residues processed: 774 average time/residue: 0.5319 time to fit residues: 713.4832 Evaluate side-chains 750 residues out of total 6786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 670 time to evaluate : 4.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 450 ILE Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 421 GLU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 95 GLN Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 450 ILE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 490 THR Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 450 ILE Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 484 TYR Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 450 ILE Chi-restraints excluded: chain M residue 502 ILE Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 484 TYR Chi-restraints excluded: chain O residue 95 GLN Chi-restraints excluded: chain O residue 191 VAL Chi-restraints excluded: chain O residue 201 VAL Chi-restraints excluded: chain O residue 450 ILE Chi-restraints excluded: chain O residue 484 TYR Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 191 VAL Chi-restraints excluded: chain P residue 420 VAL Chi-restraints excluded: chain P residue 484 TYR Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 450 ILE Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 521 LEU Chi-restraints excluded: chain R residue 527 ASP Chi-restraints excluded: chain R residue 528 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 757 optimal weight: 5.9990 chunk 498 optimal weight: 7.9990 chunk 803 optimal weight: 2.9990 chunk 490 optimal weight: 6.9990 chunk 381 optimal weight: 4.9990 chunk 558 optimal weight: 0.9980 chunk 842 optimal weight: 0.7980 chunk 775 optimal weight: 1.9990 chunk 671 optimal weight: 1.9990 chunk 69 optimal weight: 40.0000 chunk 518 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN I 146 GLN R 126 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 1.0587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 61092 Z= 0.215 Angle : 0.548 10.498 82962 Z= 0.276 Chirality : 0.042 0.155 10206 Planarity : 0.003 0.040 10674 Dihedral : 5.779 54.776 9486 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.84 % Allowed : 24.14 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.00 (0.09), residues: 8226 helix: 0.32 (0.08), residues: 4302 sheet: 1.87 (0.17), residues: 900 loop : -0.94 (0.10), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 199 HIS 0.004 0.001 HIS E 126 PHE 0.005 0.001 PHE K 489 TYR 0.026 0.001 TYR Q 122 ARG 0.011 0.000 ARG M 388 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 6786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 697 time to evaluate : 5.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 GLN cc_start: 0.7160 (tp40) cc_final: 0.6633 (tp-100) REVERT: B 239 ARG cc_start: 0.7069 (ttm110) cc_final: 0.6175 (mmt-90) REVERT: B 496 MET cc_start: 0.8241 (mmm) cc_final: 0.7565 (mmm) REVERT: C 95 GLN cc_start: 0.7569 (tp40) cc_final: 0.7162 (tp-100) REVERT: C 496 MET cc_start: 0.8268 (mmm) cc_final: 0.7611 (mmm) REVERT: D 239 ARG cc_start: 0.6264 (mmm160) cc_final: 0.6030 (mmt-90) REVERT: E 496 MET cc_start: 0.8351 (mmm) cc_final: 0.8109 (mmp) REVERT: F 421 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6578 (mm-30) REVERT: G 95 GLN cc_start: 0.7236 (tp-100) cc_final: 0.6824 (tp40) REVERT: H 496 MET cc_start: 0.8388 (mmm) cc_final: 0.7967 (mmm) REVERT: I 90 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8375 (tm-30) REVERT: J 484 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7873 (m-10) REVERT: J 496 MET cc_start: 0.8391 (mmm) cc_final: 0.8172 (mmp) REVERT: L 496 MET cc_start: 0.8365 (mmm) cc_final: 0.7907 (mmm) REVERT: N 73 THR cc_start: 0.8459 (p) cc_final: 0.8258 (m) REVERT: N 517 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7107 (tt0) REVERT: P 81 GLN cc_start: 0.6889 (pm20) cc_final: 0.6670 (pm20) REVERT: P 87 LEU cc_start: 0.7126 (pp) cc_final: 0.6889 (mp) REVERT: P 95 GLN cc_start: 0.7641 (tp40) cc_final: 0.7105 (tp-100) REVERT: P 484 TYR cc_start: 0.8230 (OUTLIER) cc_final: 0.7061 (t80) REVERT: P 517 GLU cc_start: 0.7111 (tt0) cc_final: 0.6896 (tt0) REVERT: Q 502 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8607 (mm) REVERT: R 496 MET cc_start: 0.8501 (mmm) cc_final: 0.7975 (mmp) REVERT: R 521 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8392 (mp) outliers start: 100 outliers final: 82 residues processed: 774 average time/residue: 0.5288 time to fit residues: 714.1873 Evaluate side-chains 763 residues out of total 6786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 676 time to evaluate : 4.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 450 ILE Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 421 GLU Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 450 ILE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 490 THR Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 450 ILE Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 199 TRP Chi-restraints excluded: chain J residue 484 TYR Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 450 ILE Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 484 TYR Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 191 VAL Chi-restraints excluded: chain O residue 201 VAL Chi-restraints excluded: chain O residue 450 ILE Chi-restraints excluded: chain O residue 484 TYR Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 191 VAL Chi-restraints excluded: chain P residue 420 VAL Chi-restraints excluded: chain P residue 450 ILE Chi-restraints excluded: chain P residue 484 TYR Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 450 ILE Chi-restraints excluded: chain Q residue 502 ILE Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 521 LEU Chi-restraints excluded: chain R residue 527 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 411 optimal weight: 0.9980 chunk 533 optimal weight: 0.0000 chunk 714 optimal weight: 0.4980 chunk 205 optimal weight: 6.9990 chunk 618 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 186 optimal weight: 0.7980 chunk 672 optimal weight: 5.9990 chunk 281 optimal weight: 3.9990 chunk 690 optimal weight: 5.9990 chunk 85 optimal weight: 0.1980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 GLN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 GLN L 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.226347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.177792 restraints weight = 74938.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.176873 restraints weight = 88095.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.177917 restraints weight = 79878.638| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 1.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 61092 Z= 0.144 Angle : 0.506 11.080 82962 Z= 0.257 Chirality : 0.041 0.178 10206 Planarity : 0.003 0.038 10674 Dihedral : 5.453 57.816 9486 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.51 % Allowed : 24.82 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.32 (0.09), residues: 8226 helix: 0.62 (0.08), residues: 4302 sheet: 1.94 (0.18), residues: 900 loop : -0.84 (0.10), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 199 HIS 0.002 0.000 HIS H 126 PHE 0.003 0.000 PHE K 489 TYR 0.026 0.001 TYR Q 122 ARG 0.010 0.000 ARG M 388 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13096.65 seconds wall clock time: 230 minutes 13.96 seconds (13813.96 seconds total)