Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 5 19:23:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9l_2871/10_2023/3j9l_2871_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9l_2871/10_2023/3j9l_2871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9l_2871/10_2023/3j9l_2871.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9l_2871/10_2023/3j9l_2871.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9l_2871/10_2023/3j9l_2871_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9l_2871/10_2023/3j9l_2871_neut_updated.pdb" } resolution = 4.0 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= 0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 45 5.49 5 S 368 5.16 5 C 70681 2.51 5 N 20476 2.21 5 O 21381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 20": "OE1" <-> "OE2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A ARG 267": "NH1" <-> "NH2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C ARG 267": "NH1" <-> "NH2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "C GLU 434": "OE1" <-> "OE2" Residue "C GLU 479": "OE1" <-> "OE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D GLU 43": "OE1" <-> "OE2" Residue "D GLU 44": "OE1" <-> "OE2" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D ARG 229": "NH1" <-> "NH2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D ARG 267": "NH1" <-> "NH2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D GLU 434": "OE1" <-> "OE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E GLU 43": "OE1" <-> "OE2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E GLU 70": "OE1" <-> "OE2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E ARG 104": "NH1" <-> "NH2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "E ARG 267": "NH1" <-> "NH2" Residue "E GLU 361": "OE1" <-> "OE2" Residue "E GLU 434": "OE1" <-> "OE2" Residue "E GLU 479": "OE1" <-> "OE2" Residue "F GLU 20": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 44": "OE1" <-> "OE2" Residue "F GLU 70": "OE1" <-> "OE2" Residue "F GLU 79": "OE1" <-> "OE2" Residue "F ARG 104": "NH1" <-> "NH2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "F ARG 229": "NH1" <-> "NH2" Residue "F GLU 238": "OE1" <-> "OE2" Residue "F ARG 267": "NH1" <-> "NH2" Residue "F GLU 361": "OE1" <-> "OE2" Residue "F GLU 434": "OE1" <-> "OE2" Residue "F GLU 479": "OE1" <-> "OE2" Residue "G GLU 20": "OE1" <-> "OE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G GLU 79": "OE1" <-> "OE2" Residue "G ARG 104": "NH1" <-> "NH2" Residue "G GLU 190": "OE1" <-> "OE2" Residue "G GLU 227": "OE1" <-> "OE2" Residue "G ARG 229": "NH1" <-> "NH2" Residue "G GLU 238": "OE1" <-> "OE2" Residue "G ARG 267": "NH1" <-> "NH2" Residue "G GLU 361": "OE1" <-> "OE2" Residue "G GLU 434": "OE1" <-> "OE2" Residue "G GLU 479": "OE1" <-> "OE2" Residue "H GLU 20": "OE1" <-> "OE2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H GLU 44": "OE1" <-> "OE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H GLU 79": "OE1" <-> "OE2" Residue "H ARG 104": "NH1" <-> "NH2" Residue "H GLU 190": "OE1" <-> "OE2" Residue "H GLU 227": "OE1" <-> "OE2" Residue "H ARG 229": "NH1" <-> "NH2" Residue "H GLU 238": "OE1" <-> "OE2" Residue "H ARG 267": "NH1" <-> "NH2" Residue "H GLU 361": "OE1" <-> "OE2" Residue "H GLU 434": "OE1" <-> "OE2" Residue "H GLU 479": "OE1" <-> "OE2" Residue "I GLU 20": "OE1" <-> "OE2" Residue "I GLU 43": "OE1" <-> "OE2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I GLU 70": "OE1" <-> "OE2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I ARG 104": "NH1" <-> "NH2" Residue "I GLU 190": "OE1" <-> "OE2" Residue "I GLU 227": "OE1" <-> "OE2" Residue "I ARG 229": "NH1" <-> "NH2" Residue "I GLU 238": "OE1" <-> "OE2" Residue "I ARG 267": "NH1" <-> "NH2" Residue "I GLU 361": "OE1" <-> "OE2" Residue "I GLU 434": "OE1" <-> "OE2" Residue "I GLU 479": "OE1" <-> "OE2" Residue "J GLU 20": "OE1" <-> "OE2" Residue "J GLU 43": "OE1" <-> "OE2" Residue "J GLU 44": "OE1" <-> "OE2" Residue "J GLU 70": "OE1" <-> "OE2" Residue "J GLU 79": "OE1" <-> "OE2" Residue "J ARG 104": "NH1" <-> "NH2" Residue "J GLU 190": "OE1" <-> "OE2" Residue "J GLU 227": "OE1" <-> "OE2" Residue "J ARG 229": "NH1" <-> "NH2" Residue "J GLU 238": "OE1" <-> "OE2" Residue "J ARG 267": "NH1" <-> "NH2" Residue "J GLU 361": "OE1" <-> "OE2" Residue "J GLU 434": "OE1" <-> "OE2" Residue "J GLU 479": "OE1" <-> "OE2" Residue "K GLU 20": "OE1" <-> "OE2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K GLU 44": "OE1" <-> "OE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "K GLU 79": "OE1" <-> "OE2" Residue "K ARG 104": "NH1" <-> "NH2" Residue "K GLU 190": "OE1" <-> "OE2" Residue "K GLU 227": "OE1" <-> "OE2" Residue "K ARG 229": "NH1" <-> "NH2" Residue "K GLU 238": "OE1" <-> "OE2" Residue "K ARG 267": "NH1" <-> "NH2" Residue "K GLU 361": "OE1" <-> "OE2" Residue "K GLU 434": "OE1" <-> "OE2" Residue "K GLU 479": "OE1" <-> "OE2" Residue "L GLU 20": "OE1" <-> "OE2" Residue "L GLU 43": "OE1" <-> "OE2" Residue "L GLU 44": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "L ARG 104": "NH1" <-> "NH2" Residue "L GLU 190": "OE1" <-> "OE2" Residue "L GLU 227": "OE1" <-> "OE2" Residue "L ARG 229": "NH1" <-> "NH2" Residue "L GLU 238": "OE1" <-> "OE2" Residue "L ARG 267": "NH1" <-> "NH2" Residue "L GLU 361": "OE1" <-> "OE2" Residue "L GLU 434": "OE1" <-> "OE2" Residue "L GLU 479": "OE1" <-> "OE2" Residue "M GLU 20": "OE1" <-> "OE2" Residue "M GLU 43": "OE1" <-> "OE2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M GLU 70": "OE1" <-> "OE2" Residue "M GLU 79": "OE1" <-> "OE2" Residue "M ARG 104": "NH1" <-> "NH2" Residue "M GLU 190": "OE1" <-> "OE2" Residue "M GLU 227": "OE1" <-> "OE2" Residue "M ARG 229": "NH1" <-> "NH2" Residue "M GLU 238": "OE1" <-> "OE2" Residue "M ARG 267": "NH1" <-> "NH2" Residue "M GLU 361": "OE1" <-> "OE2" Residue "M GLU 434": "OE1" <-> "OE2" Residue "M GLU 479": "OE1" <-> "OE2" Residue "N GLU 20": "OE1" <-> "OE2" Residue "N GLU 43": "OE1" <-> "OE2" Residue "N GLU 44": "OE1" <-> "OE2" Residue "N GLU 70": "OE1" <-> "OE2" Residue "N GLU 79": "OE1" <-> "OE2" Residue "N ARG 104": "NH1" <-> "NH2" Residue "N GLU 190": "OE1" <-> "OE2" Residue "N GLU 227": "OE1" <-> "OE2" Residue "N ARG 229": "NH1" <-> "NH2" Residue "N GLU 238": "OE1" <-> "OE2" Residue "N ARG 267": "NH1" <-> "NH2" Residue "N GLU 361": "OE1" <-> "OE2" Residue "N GLU 434": "OE1" <-> "OE2" Residue "N GLU 479": "OE1" <-> "OE2" Residue "O GLU 20": "OE1" <-> "OE2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O GLU 44": "OE1" <-> "OE2" Residue "O GLU 70": "OE1" <-> "OE2" Residue "O GLU 79": "OE1" <-> "OE2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O GLU 190": "OE1" <-> "OE2" Residue "O GLU 227": "OE1" <-> "OE2" Residue "O ARG 229": "NH1" <-> "NH2" Residue "O GLU 238": "OE1" <-> "OE2" Residue "O ARG 267": "NH1" <-> "NH2" Residue "O GLU 361": "OE1" <-> "OE2" Residue "O GLU 434": "OE1" <-> "OE2" Residue "O GLU 479": "OE1" <-> "OE2" Residue "P GLU 20": "OE1" <-> "OE2" Residue "P GLU 43": "OE1" <-> "OE2" Residue "P GLU 44": "OE1" <-> "OE2" Residue "P GLU 70": "OE1" <-> "OE2" Residue "P GLU 79": "OE1" <-> "OE2" Residue "P ARG 104": "NH1" <-> "NH2" Residue "P GLU 190": "OE1" <-> "OE2" Residue "P GLU 227": "OE1" <-> "OE2" Residue "P ARG 229": "NH1" <-> "NH2" Residue "P GLU 238": "OE1" <-> "OE2" Residue "P ARG 267": "NH1" <-> "NH2" Residue "P GLU 361": "OE1" <-> "OE2" Residue "P GLU 434": "OE1" <-> "OE2" Residue "P GLU 479": "OE1" <-> "OE2" Residue "Q GLU 20": "OE1" <-> "OE2" Residue "Q GLU 43": "OE1" <-> "OE2" Residue "Q GLU 44": "OE1" <-> "OE2" Residue "Q GLU 70": "OE1" <-> "OE2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "Q ARG 104": "NH1" <-> "NH2" Residue "Q GLU 190": "OE1" <-> "OE2" Residue "Q GLU 227": "OE1" <-> "OE2" Residue "Q ARG 229": "NH1" <-> "NH2" Residue "Q GLU 238": "OE1" <-> "OE2" Residue "Q ARG 267": "NH1" <-> "NH2" Residue "Q GLU 361": "OE1" <-> "OE2" Residue "Q GLU 434": "OE1" <-> "OE2" Residue "Q GLU 479": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 112951 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 7031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 7031 Classifications: {'peptide': 1062} Incomplete info: {'backbone_only': 20, 'truncation_to_alanine': 515} Link IDs: {'CIS': 2, 'PTRANS': 25, 'TRANS': 1034} Chain breaks: 42 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1107 Unresolved non-hydrogen angles: 1660 Unresolved non-hydrogen dihedrals: 557 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'UNK:plan-1': 519, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 546 Chain: "C" Number of atoms: 7031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 7031 Classifications: {'peptide': 1062} Incomplete info: {'backbone_only': 20, 'truncation_to_alanine': 515} Link IDs: {'CIS': 2, 'PTRANS': 25, 'TRANS': 1034} Chain breaks: 42 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1107 Unresolved non-hydrogen angles: 1660 Unresolved non-hydrogen dihedrals: 557 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'UNK:plan-1': 519, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 546 Chain: "D" Number of atoms: 7031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 7031 Classifications: {'peptide': 1062} Incomplete info: {'backbone_only': 20, 'truncation_to_alanine': 515} Link IDs: {'CIS': 2, 'PTRANS': 25, 'TRANS': 1034} Chain breaks: 42 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1107 Unresolved non-hydrogen angles: 1660 Unresolved non-hydrogen dihedrals: 557 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'UNK:plan-1': 519, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 546 Chain: "E" Number of atoms: 7031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 7031 Classifications: {'peptide': 1062} Incomplete info: {'backbone_only': 20, 'truncation_to_alanine': 515} Link IDs: {'CIS': 2, 'PTRANS': 25, 'TRANS': 1034} Chain breaks: 42 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1107 Unresolved non-hydrogen angles: 1660 Unresolved non-hydrogen dihedrals: 557 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'UNK:plan-1': 519, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 546 Chain: "F" Number of atoms: 7031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 7031 Classifications: {'peptide': 1062} Incomplete info: {'backbone_only': 20, 'truncation_to_alanine': 515} Link IDs: {'CIS': 2, 'PTRANS': 25, 'TRANS': 1034} Chain breaks: 42 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1107 Unresolved non-hydrogen angles: 1660 Unresolved non-hydrogen dihedrals: 557 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'UNK:plan-1': 519, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 546 Chain: "G" Number of atoms: 7031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 7031 Classifications: {'peptide': 1062} Incomplete info: {'backbone_only': 20, 'truncation_to_alanine': 515} Link IDs: {'CIS': 2, 'PTRANS': 25, 'TRANS': 1034} Chain breaks: 42 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1107 Unresolved non-hydrogen angles: 1660 Unresolved non-hydrogen dihedrals: 557 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'UNK:plan-1': 519, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 546 Chain: "H" Number of atoms: 7031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 7031 Classifications: {'peptide': 1062} Incomplete info: {'backbone_only': 20, 'truncation_to_alanine': 515} Link IDs: {'CIS': 2, 'PTRANS': 25, 'TRANS': 1034} Chain breaks: 42 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1107 Unresolved non-hydrogen angles: 1660 Unresolved non-hydrogen dihedrals: 557 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'UNK:plan-1': 519, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 546 Chain: "I" Number of atoms: 7031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 7031 Classifications: {'peptide': 1062} Incomplete info: {'backbone_only': 20, 'truncation_to_alanine': 515} Link IDs: {'CIS': 2, 'PTRANS': 25, 'TRANS': 1034} Chain breaks: 42 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1107 Unresolved non-hydrogen angles: 1660 Unresolved non-hydrogen dihedrals: 557 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'UNK:plan-1': 519, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 546 Chain: "J" Number of atoms: 7031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 7031 Classifications: {'peptide': 1062} Incomplete info: {'backbone_only': 20, 'truncation_to_alanine': 515} Link IDs: {'CIS': 2, 'PTRANS': 25, 'TRANS': 1034} Chain breaks: 42 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1107 Unresolved non-hydrogen angles: 1660 Unresolved non-hydrogen dihedrals: 557 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'UNK:plan-1': 519, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 546 Chain: "K" Number of atoms: 7031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 7031 Classifications: {'peptide': 1062} Incomplete info: {'backbone_only': 20, 'truncation_to_alanine': 515} Link IDs: {'CIS': 2, 'PTRANS': 25, 'TRANS': 1034} Chain breaks: 42 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1107 Unresolved non-hydrogen angles: 1660 Unresolved non-hydrogen dihedrals: 557 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'UNK:plan-1': 519, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 546 Chain: "L" Number of atoms: 7031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 7031 Classifications: {'peptide': 1062} Incomplete info: {'backbone_only': 20, 'truncation_to_alanine': 515} Link IDs: {'CIS': 2, 'PTRANS': 25, 'TRANS': 1034} Chain breaks: 42 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1107 Unresolved non-hydrogen angles: 1660 Unresolved non-hydrogen dihedrals: 557 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'UNK:plan-1': 519, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 546 Chain: "M" Number of atoms: 7031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 7031 Classifications: {'peptide': 1062} Incomplete info: {'backbone_only': 20, 'truncation_to_alanine': 515} Link IDs: {'CIS': 2, 'PTRANS': 25, 'TRANS': 1034} Chain breaks: 42 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1107 Unresolved non-hydrogen angles: 1660 Unresolved non-hydrogen dihedrals: 557 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'UNK:plan-1': 519, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 546 Chain: "N" Number of atoms: 7031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 7031 Classifications: {'peptide': 1062} Incomplete info: {'backbone_only': 20, 'truncation_to_alanine': 515} Link IDs: {'CIS': 2, 'PTRANS': 25, 'TRANS': 1034} Chain breaks: 42 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1107 Unresolved non-hydrogen angles: 1660 Unresolved non-hydrogen dihedrals: 557 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'UNK:plan-1': 519, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 546 Chain: "O" Number of atoms: 7031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 7031 Classifications: {'peptide': 1062} Incomplete info: {'backbone_only': 20, 'truncation_to_alanine': 515} Link IDs: {'CIS': 2, 'PTRANS': 25, 'TRANS': 1034} Chain breaks: 42 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1107 Unresolved non-hydrogen angles: 1660 Unresolved non-hydrogen dihedrals: 557 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'UNK:plan-1': 519, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 546 Chain: "P" Number of atoms: 7031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 7031 Classifications: {'peptide': 1062} Incomplete info: {'backbone_only': 20, 'truncation_to_alanine': 515} Link IDs: {'CIS': 2, 'PTRANS': 25, 'TRANS': 1034} Chain breaks: 42 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1107 Unresolved non-hydrogen angles: 1660 Unresolved non-hydrogen dihedrals: 557 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'UNK:plan-1': 519, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 546 Chain: "Q" Number of atoms: 7036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 7036 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 20, 'truncation_to_alanine': 516} Link IDs: {'CIS': 2, 'PTRANS': 25, 'TRANS': 1035} Chain breaks: 41 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1109 Unresolved non-hydrogen angles: 1663 Unresolved non-hydrogen dihedrals: 558 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'UNK:plan-1': 520, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 547 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 41.52, per 1000 atoms: 0.37 Number of scatterers: 112951 At special positions: 0 Unit cell: (290.78, 290.78, 170.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 368 16.00 P 45 15.00 O 21381 8.00 N 20476 7.00 C 70681 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=15, symmetry=0 Number of additional bonds: simple=15, symmetry=0 Coordination: Other bonds: Time building additional restraints: 32.27 Conformation dependent library (CDL) restraints added in 7.7 seconds 16928 Ramachandran restraints generated. 8464 Oldfield, 0 Emsley, 8464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 33186 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 512 helices and 16 sheets defined 71.5% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.61 Creating SS restraints... Processing helix chain 'A' and resid 11 through 20 removed outlier: 4.306A pdb=" N SER A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL A 18 " --> pdb=" O ASP A 14 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 27 removed outlier: 3.726A pdb=" N ASP A 25 " --> pdb=" O ASP A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 51 removed outlier: 3.841A pdb=" N ILE A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET A 50 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 51 " --> pdb=" O HIS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 69 removed outlier: 3.974A pdb=" N GLY A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLN A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 85 removed outlier: 4.431A pdb=" N GLN A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A 79 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL A 80 " --> pdb=" O PHE A 76 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 98 removed outlier: 3.534A pdb=" N SER A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Proline residue: A 91 - end of helix removed outlier: 3.751A pdb=" N GLU A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 118 removed outlier: 3.566A pdb=" N ARG A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 141 removed outlier: 3.636A pdb=" N GLN A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 140 " --> pdb=" O GLN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 168 removed outlier: 3.566A pdb=" N VAL A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N TYR A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 175 removed outlier: 3.695A pdb=" N LYS A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 204 removed outlier: 4.517A pdb=" N VAL A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 193 " --> pdb=" O PRO A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 233 removed outlier: 3.679A pdb=" N ILE A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 257 removed outlier: 3.709A pdb=" N TRP A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 removed outlier: 5.781A pdb=" N SER A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 removed outlier: 5.362A pdb=" N LEU A 292 " --> pdb=" O HIS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 306 removed outlier: 3.916A pdb=" N VAL A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 298 " --> pdb=" O PRO A 294 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 removed outlier: 3.589A pdb=" N ASP A 311 " --> pdb=" O CYS A 307 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU A 312 " --> pdb=" O ARG A 308 " (cutoff:3.500A) Proline residue: A 313 - end of helix No H-bonds generated for 'chain 'A' and resid 307 through 314' Processing helix chain 'A' and resid 320 through 333 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.842A pdb=" N LYS A 342 " --> pdb=" O TRP A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 359 removed outlier: 3.680A pdb=" N LEU A 357 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 373 removed outlier: 3.642A pdb=" N MET A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU A 372 " --> pdb=" O MET A 368 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 389 removed outlier: 3.791A pdb=" N LEU A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 409 removed outlier: 3.506A pdb=" N SER A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 435 removed outlier: 3.810A pdb=" N LEU A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN A 435 " --> pdb=" O VAL A 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 429 through 435' Processing helix chain 'A' and resid 438 through 454 Proline residue: A 450 - end of helix removed outlier: 4.748A pdb=" N ASP A 454 " --> pdb=" O PRO A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 479 removed outlier: 5.209A pdb=" N TYR A 468 " --> pdb=" O ASP A 464 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLY A 472 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N HIS A 473 " --> pdb=" O SER A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 487 Processing helix chain 'A' and resid 491 through 503 removed outlier: 4.764A pdb=" N ARG A 495 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN A 499 " --> pdb=" O ARG A 495 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS A 503 " --> pdb=" O GLN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 528 removed outlier: 3.788A pdb=" N GLN A 520 " --> pdb=" O ASN A 516 " (cutoff:3.500A) Proline residue: A 526 - end of helix Processing helix chain 'A' and resid 532 through 549 removed outlier: 3.788A pdb=" N LEU A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Proline residue: A 547 - end of helix Processing helix chain 'A' and resid 558 through 568 removed outlier: 4.283A pdb=" N LEU A 562 " --> pdb=" O TYR A 558 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET A 567 " --> pdb=" O ARG A 563 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 583 removed outlier: 3.619A pdb=" N GLU A 575 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 20 removed outlier: 4.306A pdb=" N SER C 17 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL C 18 " --> pdb=" O ASP C 14 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 27 removed outlier: 3.725A pdb=" N ASP C 25 " --> pdb=" O ASP C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 51 removed outlier: 3.841A pdb=" N ILE C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET C 50 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER C 51 " --> pdb=" O HIS C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 69 removed outlier: 3.973A pdb=" N GLY C 57 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU C 59 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 66 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLN C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 85 removed outlier: 4.431A pdb=" N GLN C 74 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU C 79 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL C 80 " --> pdb=" O PHE C 76 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU C 81 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 98 removed outlier: 3.534A pdb=" N SER C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Proline residue: C 91 - end of helix removed outlier: 3.751A pdb=" N GLU C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG C 97 " --> pdb=" O LYS C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 118 removed outlier: 3.565A pdb=" N ARG C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 141 removed outlier: 3.637A pdb=" N GLN C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA C 137 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU C 140 " --> pdb=" O GLN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 168 removed outlier: 3.566A pdb=" N VAL C 160 " --> pdb=" O GLY C 156 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR C 168 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 175 removed outlier: 3.694A pdb=" N LYS C 173 " --> pdb=" O LYS C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 204 removed outlier: 4.518A pdb=" N VAL C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU C 193 " --> pdb=" O PRO C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 233 removed outlier: 3.679A pdb=" N ILE C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS C 222 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 257 removed outlier: 3.710A pdb=" N TRP C 253 " --> pdb=" O ASN C 249 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 276 removed outlier: 5.781A pdb=" N SER C 276 " --> pdb=" O THR C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 292 removed outlier: 5.362A pdb=" N LEU C 292 " --> pdb=" O HIS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 306 removed outlier: 3.915A pdb=" N VAL C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS C 298 " --> pdb=" O PRO C 294 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 314 removed outlier: 3.589A pdb=" N ASP C 311 " --> pdb=" O CYS C 307 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Proline residue: C 313 - end of helix No H-bonds generated for 'chain 'C' and resid 307 through 314' Processing helix chain 'C' and resid 320 through 333 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.843A pdb=" N LYS C 342 " --> pdb=" O TRP C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 359 removed outlier: 3.680A pdb=" N LEU C 357 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 373 removed outlier: 3.641A pdb=" N MET C 368 " --> pdb=" O GLU C 364 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU C 372 " --> pdb=" O MET C 368 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 389 removed outlier: 3.791A pdb=" N LEU C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE C 389 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 409 removed outlier: 3.506A pdb=" N SER C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 removed outlier: 3.810A pdb=" N LEU C 433 " --> pdb=" O LEU C 429 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU C 434 " --> pdb=" O LYS C 430 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN C 435 " --> pdb=" O VAL C 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 429 through 435' Processing helix chain 'C' and resid 438 through 454 Proline residue: C 450 - end of helix removed outlier: 4.749A pdb=" N ASP C 454 " --> pdb=" O PRO C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 479 removed outlier: 5.208A pdb=" N TYR C 468 " --> pdb=" O ASP C 464 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY C 472 " --> pdb=" O TYR C 468 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N HIS C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 487 Processing helix chain 'C' and resid 491 through 503 removed outlier: 4.764A pdb=" N ARG C 495 " --> pdb=" O PHE C 491 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN C 499 " --> pdb=" O ARG C 495 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS C 503 " --> pdb=" O GLN C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 528 removed outlier: 3.788A pdb=" N GLN C 520 " --> pdb=" O ASN C 516 " (cutoff:3.500A) Proline residue: C 526 - end of helix Processing helix chain 'C' and resid 532 through 549 removed outlier: 3.788A pdb=" N LEU C 538 " --> pdb=" O LYS C 534 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) Proline residue: C 547 - end of helix Processing helix chain 'C' and resid 558 through 568 removed outlier: 4.283A pdb=" N LEU C 562 " --> pdb=" O TYR C 558 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET C 567 " --> pdb=" O ARG C 563 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA C 568 " --> pdb=" O ILE C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 583 removed outlier: 3.620A pdb=" N GLU C 575 " --> pdb=" O GLU C 571 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS C 579 " --> pdb=" O GLU C 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 20 removed outlier: 4.306A pdb=" N SER D 17 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL D 18 " --> pdb=" O ASP D 14 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 27 removed outlier: 3.726A pdb=" N ASP D 25 " --> pdb=" O ASP D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 51 removed outlier: 3.841A pdb=" N ILE D 49 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER D 51 " --> pdb=" O HIS D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 69 removed outlier: 3.974A pdb=" N GLY D 57 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 66 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLN D 69 " --> pdb=" O LEU D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 85 removed outlier: 4.431A pdb=" N GLN D 74 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL D 80 " --> pdb=" O PHE D 76 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU D 81 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN D 84 " --> pdb=" O VAL D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 98 removed outlier: 3.534A pdb=" N SER D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Proline residue: D 91 - end of helix removed outlier: 3.751A pdb=" N GLU D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG D 97 " --> pdb=" O LYS D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 118 removed outlier: 3.566A pdb=" N ARG D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 141 removed outlier: 3.636A pdb=" N GLN D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 140 " --> pdb=" O GLN D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 168 removed outlier: 3.566A pdb=" N VAL D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N TYR D 168 " --> pdb=" O VAL D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 175 removed outlier: 3.695A pdb=" N LYS D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 204 removed outlier: 4.517A pdb=" N VAL D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU D 193 " --> pdb=" O PRO D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 233 removed outlier: 3.679A pdb=" N ILE D 221 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS D 222 " --> pdb=" O LYS D 218 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 257 removed outlier: 3.709A pdb=" N TRP D 253 " --> pdb=" O ASN D 249 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 276 removed outlier: 5.781A pdb=" N SER D 276 " --> pdb=" O THR D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 292 removed outlier: 5.362A pdb=" N LEU D 292 " --> pdb=" O HIS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 306 removed outlier: 3.916A pdb=" N VAL D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS D 298 " --> pdb=" O PRO D 294 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS D 303 " --> pdb=" O SER D 299 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 314 removed outlier: 3.589A pdb=" N ASP D 311 " --> pdb=" O CYS D 307 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU D 312 " --> pdb=" O ARG D 308 " (cutoff:3.500A) Proline residue: D 313 - end of helix No H-bonds generated for 'chain 'D' and resid 307 through 314' Processing helix chain 'D' and resid 320 through 333 Processing helix chain 'D' and resid 338 through 343 removed outlier: 3.842A pdb=" N LYS D 342 " --> pdb=" O TRP D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 359 removed outlier: 3.680A pdb=" N LEU D 357 " --> pdb=" O ILE D 353 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 373 removed outlier: 3.642A pdb=" N MET D 368 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU D 372 " --> pdb=" O MET D 368 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 389 removed outlier: 3.791A pdb=" N LEU D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 409 removed outlier: 3.506A pdb=" N SER D 409 " --> pdb=" O LEU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 435 removed outlier: 3.810A pdb=" N LEU D 433 " --> pdb=" O LEU D 429 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU D 434 " --> pdb=" O LYS D 430 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN D 435 " --> pdb=" O VAL D 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 429 through 435' Processing helix chain 'D' and resid 438 through 454 Proline residue: D 450 - end of helix removed outlier: 4.748A pdb=" N ASP D 454 " --> pdb=" O PRO D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 479 removed outlier: 5.209A pdb=" N TYR D 468 " --> pdb=" O ASP D 464 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLY D 472 " --> pdb=" O TYR D 468 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N HIS D 473 " --> pdb=" O SER D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 487 Processing helix chain 'D' and resid 491 through 503 removed outlier: 4.764A pdb=" N ARG D 495 " --> pdb=" O PHE D 491 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN D 499 " --> pdb=" O ARG D 495 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS D 503 " --> pdb=" O GLN D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 528 removed outlier: 3.788A pdb=" N GLN D 520 " --> pdb=" O ASN D 516 " (cutoff:3.500A) Proline residue: D 526 - end of helix Processing helix chain 'D' and resid 532 through 549 removed outlier: 3.788A pdb=" N LEU D 538 " --> pdb=" O LYS D 534 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) Proline residue: D 547 - end of helix Processing helix chain 'D' and resid 558 through 568 removed outlier: 4.283A pdb=" N LEU D 562 " --> pdb=" O TYR D 558 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET D 567 " --> pdb=" O ARG D 563 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA D 568 " --> pdb=" O ILE D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 583 removed outlier: 3.619A pdb=" N GLU D 575 " --> pdb=" O GLU D 571 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS D 579 " --> pdb=" O GLU D 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 20 removed outlier: 4.306A pdb=" N SER E 17 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL E 18 " --> pdb=" O ASP E 14 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU E 20 " --> pdb=" O LEU E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 27 removed outlier: 3.726A pdb=" N ASP E 25 " --> pdb=" O ASP E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 51 removed outlier: 3.841A pdb=" N ILE E 49 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER E 51 " --> pdb=" O HIS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 69 removed outlier: 3.973A pdb=" N GLY E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 66 " --> pdb=" O PHE E 62 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLN E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 85 removed outlier: 4.431A pdb=" N GLN E 74 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU E 79 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL E 80 " --> pdb=" O PHE E 76 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU E 81 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN E 84 " --> pdb=" O VAL E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 98 removed outlier: 3.534A pdb=" N SER E 90 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Proline residue: E 91 - end of helix removed outlier: 3.751A pdb=" N GLU E 95 " --> pdb=" O PRO E 91 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG E 97 " --> pdb=" O LYS E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 118 removed outlier: 3.565A pdb=" N ARG E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 141 removed outlier: 3.637A pdb=" N GLN E 136 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU E 140 " --> pdb=" O GLN E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 168 removed outlier: 3.566A pdb=" N VAL E 160 " --> pdb=" O GLY E 156 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR E 168 " --> pdb=" O VAL E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 175 removed outlier: 3.694A pdb=" N LYS E 173 " --> pdb=" O LYS E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 204 removed outlier: 4.518A pdb=" N VAL E 192 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU E 193 " --> pdb=" O PRO E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 233 removed outlier: 3.679A pdb=" N ILE E 221 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS E 222 " --> pdb=" O LYS E 218 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER E 223 " --> pdb=" O LEU E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 257 removed outlier: 3.710A pdb=" N TRP E 253 " --> pdb=" O ASN E 249 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 276 removed outlier: 5.781A pdb=" N SER E 276 " --> pdb=" O THR E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 292 removed outlier: 5.362A pdb=" N LEU E 292 " --> pdb=" O HIS E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 306 removed outlier: 3.915A pdb=" N VAL E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS E 298 " --> pdb=" O PRO E 294 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR E 304 " --> pdb=" O LEU E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 314 removed outlier: 3.589A pdb=" N ASP E 311 " --> pdb=" O CYS E 307 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU E 312 " --> pdb=" O ARG E 308 " (cutoff:3.500A) Proline residue: E 313 - end of helix No H-bonds generated for 'chain 'E' and resid 307 through 314' Processing helix chain 'E' and resid 320 through 333 Processing helix chain 'E' and resid 338 through 343 removed outlier: 3.843A pdb=" N LYS E 342 " --> pdb=" O TRP E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 359 removed outlier: 3.680A pdb=" N LEU E 357 " --> pdb=" O ILE E 353 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN E 358 " --> pdb=" O GLU E 354 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL E 359 " --> pdb=" O SER E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 373 removed outlier: 3.641A pdb=" N MET E 368 " --> pdb=" O GLU E 364 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU E 372 " --> pdb=" O MET E 368 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 389 removed outlier: 3.791A pdb=" N LEU E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE E 389 " --> pdb=" O LEU E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 409 removed outlier: 3.506A pdb=" N SER E 409 " --> pdb=" O LEU E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 435 removed outlier: 3.810A pdb=" N LEU E 433 " --> pdb=" O LEU E 429 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU E 434 " --> pdb=" O LYS E 430 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN E 435 " --> pdb=" O VAL E 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 429 through 435' Processing helix chain 'E' and resid 438 through 454 Proline residue: E 450 - end of helix removed outlier: 4.748A pdb=" N ASP E 454 " --> pdb=" O PRO E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 479 removed outlier: 5.208A pdb=" N TYR E 468 " --> pdb=" O ASP E 464 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY E 472 " --> pdb=" O TYR E 468 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N HIS E 473 " --> pdb=" O SER E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 487 Processing helix chain 'E' and resid 491 through 503 removed outlier: 4.764A pdb=" N ARG E 495 " --> pdb=" O PHE E 491 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN E 499 " --> pdb=" O ARG E 495 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS E 503 " --> pdb=" O GLN E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 528 removed outlier: 3.788A pdb=" N GLN E 520 " --> pdb=" O ASN E 516 " (cutoff:3.500A) Proline residue: E 526 - end of helix Processing helix chain 'E' and resid 532 through 549 removed outlier: 3.788A pdb=" N LEU E 538 " --> pdb=" O LYS E 534 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE E 545 " --> pdb=" O ALA E 541 " (cutoff:3.500A) Proline residue: E 547 - end of helix Processing helix chain 'E' and resid 558 through 568 removed outlier: 4.283A pdb=" N LEU E 562 " --> pdb=" O TYR E 558 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET E 567 " --> pdb=" O ARG E 563 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA E 568 " --> pdb=" O ILE E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 583 removed outlier: 3.620A pdb=" N GLU E 575 " --> pdb=" O GLU E 571 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS E 579 " --> pdb=" O GLU E 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 20 removed outlier: 4.306A pdb=" N SER F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL F 18 " --> pdb=" O ASP F 14 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 27 removed outlier: 3.726A pdb=" N ASP F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 51 removed outlier: 3.841A pdb=" N ILE F 49 " --> pdb=" O ILE F 45 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER F 51 " --> pdb=" O HIS F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 69 removed outlier: 3.974A pdb=" N GLY F 57 " --> pdb=" O ASP F 53 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU F 59 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU F 66 " --> pdb=" O PHE F 62 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLN F 69 " --> pdb=" O LEU F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 85 removed outlier: 4.431A pdb=" N GLN F 74 " --> pdb=" O GLU F 70 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU F 79 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL F 80 " --> pdb=" O PHE F 76 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU F 81 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN F 84 " --> pdb=" O VAL F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 98 removed outlier: 3.534A pdb=" N SER F 90 " --> pdb=" O LYS F 86 " (cutoff:3.500A) Proline residue: F 91 - end of helix removed outlier: 3.751A pdb=" N GLU F 95 " --> pdb=" O PRO F 91 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG F 97 " --> pdb=" O LYS F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 118 removed outlier: 3.566A pdb=" N ARG F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 141 removed outlier: 3.636A pdb=" N GLN F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA F 137 " --> pdb=" O LYS F 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU F 140 " --> pdb=" O GLN F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 168 removed outlier: 3.566A pdb=" N VAL F 160 " --> pdb=" O GLY F 156 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N TYR F 168 " --> pdb=" O VAL F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 175 removed outlier: 3.695A pdb=" N LYS F 173 " --> pdb=" O LYS F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 204 removed outlier: 4.517A pdb=" N VAL F 192 " --> pdb=" O SER F 188 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU F 193 " --> pdb=" O PRO F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 233 removed outlier: 3.679A pdb=" N ILE F 221 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS F 222 " --> pdb=" O LYS F 218 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER F 223 " --> pdb=" O LEU F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 257 removed outlier: 3.709A pdb=" N TRP F 253 " --> pdb=" O ASN F 249 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 276 removed outlier: 5.781A pdb=" N SER F 276 " --> pdb=" O THR F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 292 removed outlier: 5.362A pdb=" N LEU F 292 " --> pdb=" O HIS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 306 removed outlier: 3.916A pdb=" N VAL F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS F 298 " --> pdb=" O PRO F 294 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS F 303 " --> pdb=" O SER F 299 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR F 304 " --> pdb=" O LEU F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 314 removed outlier: 3.589A pdb=" N ASP F 311 " --> pdb=" O CYS F 307 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU F 312 " --> pdb=" O ARG F 308 " (cutoff:3.500A) Proline residue: F 313 - end of helix No H-bonds generated for 'chain 'F' and resid 307 through 314' Processing helix chain 'F' and resid 320 through 333 Processing helix chain 'F' and resid 338 through 343 removed outlier: 3.842A pdb=" N LYS F 342 " --> pdb=" O TRP F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 359 removed outlier: 3.680A pdb=" N LEU F 357 " --> pdb=" O ILE F 353 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN F 358 " --> pdb=" O GLU F 354 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL F 359 " --> pdb=" O SER F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 373 removed outlier: 3.642A pdb=" N MET F 368 " --> pdb=" O GLU F 364 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU F 372 " --> pdb=" O MET F 368 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 389 removed outlier: 3.791A pdb=" N LEU F 388 " --> pdb=" O ILE F 384 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE F 389 " --> pdb=" O LEU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 409 removed outlier: 3.506A pdb=" N SER F 409 " --> pdb=" O LEU F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 435 removed outlier: 3.810A pdb=" N LEU F 433 " --> pdb=" O LEU F 429 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU F 434 " --> pdb=" O LYS F 430 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN F 435 " --> pdb=" O VAL F 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 429 through 435' Processing helix chain 'F' and resid 438 through 454 Proline residue: F 450 - end of helix removed outlier: 4.748A pdb=" N ASP F 454 " --> pdb=" O PRO F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 479 removed outlier: 5.209A pdb=" N TYR F 468 " --> pdb=" O ASP F 464 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLY F 472 " --> pdb=" O TYR F 468 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N HIS F 473 " --> pdb=" O SER F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 487 Processing helix chain 'F' and resid 491 through 503 removed outlier: 4.764A pdb=" N ARG F 495 " --> pdb=" O PHE F 491 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN F 499 " --> pdb=" O ARG F 495 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS F 503 " --> pdb=" O GLN F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 528 removed outlier: 3.788A pdb=" N GLN F 520 " --> pdb=" O ASN F 516 " (cutoff:3.500A) Proline residue: F 526 - end of helix Processing helix chain 'F' and resid 532 through 549 removed outlier: 3.788A pdb=" N LEU F 538 " --> pdb=" O LYS F 534 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Proline residue: F 547 - end of helix Processing helix chain 'F' and resid 558 through 568 removed outlier: 4.283A pdb=" N LEU F 562 " --> pdb=" O TYR F 558 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET F 567 " --> pdb=" O ARG F 563 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA F 568 " --> pdb=" O ILE F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 583 removed outlier: 3.619A pdb=" N GLU F 575 " --> pdb=" O GLU F 571 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS F 579 " --> pdb=" O GLU F 575 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 20 removed outlier: 4.306A pdb=" N SER G 17 " --> pdb=" O LYS G 13 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL G 18 " --> pdb=" O ASP G 14 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU G 20 " --> pdb=" O LEU G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 27 removed outlier: 3.726A pdb=" N ASP G 25 " --> pdb=" O ASP G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 51 removed outlier: 3.841A pdb=" N ILE G 49 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET G 50 " --> pdb=" O ASP G 46 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER G 51 " --> pdb=" O HIS G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 69 removed outlier: 3.973A pdb=" N GLY G 57 " --> pdb=" O ASP G 53 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU G 59 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU G 66 " --> pdb=" O PHE G 62 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLN G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 85 removed outlier: 4.431A pdb=" N GLN G 74 " --> pdb=" O GLU G 70 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU G 79 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL G 80 " --> pdb=" O PHE G 76 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU G 81 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN G 84 " --> pdb=" O VAL G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 98 removed outlier: 3.534A pdb=" N SER G 90 " --> pdb=" O LYS G 86 " (cutoff:3.500A) Proline residue: G 91 - end of helix removed outlier: 3.751A pdb=" N GLU G 95 " --> pdb=" O PRO G 91 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG G 97 " --> pdb=" O LYS G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 118 removed outlier: 3.565A pdb=" N ARG G 112 " --> pdb=" O GLU G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 141 removed outlier: 3.637A pdb=" N GLN G 136 " --> pdb=" O LEU G 132 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA G 137 " --> pdb=" O LYS G 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU G 140 " --> pdb=" O GLN G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 168 removed outlier: 3.566A pdb=" N VAL G 160 " --> pdb=" O GLY G 156 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR G 168 " --> pdb=" O VAL G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 175 removed outlier: 3.694A pdb=" N LYS G 173 " --> pdb=" O LYS G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 204 removed outlier: 4.518A pdb=" N VAL G 192 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU G 193 " --> pdb=" O PRO G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 233 removed outlier: 3.679A pdb=" N ILE G 221 " --> pdb=" O ILE G 217 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS G 222 " --> pdb=" O LYS G 218 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 257 removed outlier: 3.710A pdb=" N TRP G 253 " --> pdb=" O ASN G 249 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA G 255 " --> pdb=" O LYS G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 276 removed outlier: 5.781A pdb=" N SER G 276 " --> pdb=" O THR G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 292 removed outlier: 5.362A pdb=" N LEU G 292 " --> pdb=" O HIS G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 306 removed outlier: 3.915A pdb=" N VAL G 297 " --> pdb=" O THR G 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS G 298 " --> pdb=" O PRO G 294 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS G 303 " --> pdb=" O SER G 299 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR G 304 " --> pdb=" O LEU G 300 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 314 removed outlier: 3.589A pdb=" N ASP G 311 " --> pdb=" O CYS G 307 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU G 312 " --> pdb=" O ARG G 308 " (cutoff:3.500A) Proline residue: G 313 - end of helix No H-bonds generated for 'chain 'G' and resid 307 through 314' Processing helix chain 'G' and resid 320 through 333 Processing helix chain 'G' and resid 338 through 343 removed outlier: 3.843A pdb=" N LYS G 342 " --> pdb=" O TRP G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 348 through 359 removed outlier: 3.680A pdb=" N LEU G 357 " --> pdb=" O ILE G 353 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN G 358 " --> pdb=" O GLU G 354 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL G 359 " --> pdb=" O SER G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 373 removed outlier: 3.641A pdb=" N MET G 368 " --> pdb=" O GLU G 364 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU G 372 " --> pdb=" O MET G 368 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER G 373 " --> pdb=" O PHE G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 389 removed outlier: 3.791A pdb=" N LEU G 388 " --> pdb=" O ILE G 384 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE G 389 " --> pdb=" O LEU G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 409 removed outlier: 3.506A pdb=" N SER G 409 " --> pdb=" O LEU G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 435 removed outlier: 3.810A pdb=" N LEU G 433 " --> pdb=" O LEU G 429 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU G 434 " --> pdb=" O LYS G 430 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN G 435 " --> pdb=" O VAL G 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 429 through 435' Processing helix chain 'G' and resid 438 through 454 Proline residue: G 450 - end of helix removed outlier: 4.748A pdb=" N ASP G 454 " --> pdb=" O PRO G 450 " (cutoff:3.500A) Processing helix chain 'G' and resid 464 through 479 removed outlier: 5.208A pdb=" N TYR G 468 " --> pdb=" O ASP G 464 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY G 472 " --> pdb=" O TYR G 468 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N HIS G 473 " --> pdb=" O SER G 469 " (cutoff:3.500A) Processing helix chain 'G' and resid 480 through 487 Processing helix chain 'G' and resid 491 through 503 removed outlier: 4.764A pdb=" N ARG G 495 " --> pdb=" O PHE G 491 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN G 499 " --> pdb=" O ARG G 495 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS G 503 " --> pdb=" O GLN G 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 516 through 528 removed outlier: 3.788A pdb=" N GLN G 520 " --> pdb=" O ASN G 516 " (cutoff:3.500A) Proline residue: G 526 - end of helix Processing helix chain 'G' and resid 532 through 549 removed outlier: 3.788A pdb=" N LEU G 538 " --> pdb=" O LYS G 534 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE G 545 " --> pdb=" O ALA G 541 " (cutoff:3.500A) Proline residue: G 547 - end of helix Processing helix chain 'G' and resid 558 through 568 removed outlier: 4.283A pdb=" N LEU G 562 " --> pdb=" O TYR G 558 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET G 567 " --> pdb=" O ARG G 563 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA G 568 " --> pdb=" O ILE G 564 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 583 removed outlier: 3.620A pdb=" N GLU G 575 " --> pdb=" O GLU G 571 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS G 579 " --> pdb=" O GLU G 575 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 20 removed outlier: 4.306A pdb=" N SER H 17 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL H 18 " --> pdb=" O ASP H 14 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE H 19 " --> pdb=" O ILE H 15 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU H 20 " --> pdb=" O LEU H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 27 removed outlier: 3.726A pdb=" N ASP H 25 " --> pdb=" O ASP H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 51 removed outlier: 3.841A pdb=" N ILE H 49 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET H 50 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER H 51 " --> pdb=" O HIS H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 69 removed outlier: 3.974A pdb=" N GLY H 57 " --> pdb=" O ASP H 53 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU H 59 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU H 66 " --> pdb=" O PHE H 62 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLN H 69 " --> pdb=" O LEU H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 85 removed outlier: 4.431A pdb=" N GLN H 74 " --> pdb=" O GLU H 70 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU H 79 " --> pdb=" O LYS H 75 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL H 80 " --> pdb=" O PHE H 76 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU H 81 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN H 84 " --> pdb=" O VAL H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 98 removed outlier: 3.534A pdb=" N SER H 90 " --> pdb=" O LYS H 86 " (cutoff:3.500A) Proline residue: H 91 - end of helix removed outlier: 3.751A pdb=" N GLU H 95 " --> pdb=" O PRO H 91 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG H 97 " --> pdb=" O LYS H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 118 removed outlier: 3.566A pdb=" N ARG H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 141 removed outlier: 3.636A pdb=" N GLN H 136 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA H 137 " --> pdb=" O LYS H 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU H 140 " --> pdb=" O GLN H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 168 removed outlier: 3.566A pdb=" N VAL H 160 " --> pdb=" O GLY H 156 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N TYR H 168 " --> pdb=" O VAL H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 175 removed outlier: 3.695A pdb=" N LYS H 173 " --> pdb=" O LYS H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 204 removed outlier: 4.517A pdb=" N VAL H 192 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU H 193 " --> pdb=" O PRO H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 233 removed outlier: 3.679A pdb=" N ILE H 221 " --> pdb=" O ILE H 217 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS H 222 " --> pdb=" O LYS H 218 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER H 223 " --> pdb=" O LEU H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 257 removed outlier: 3.709A pdb=" N TRP H 253 " --> pdb=" O ASN H 249 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA H 255 " --> pdb=" O LYS H 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 276 removed outlier: 5.781A pdb=" N SER H 276 " --> pdb=" O THR H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 292 removed outlier: 5.362A pdb=" N LEU H 292 " --> pdb=" O HIS H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 306 removed outlier: 3.916A pdb=" N VAL H 297 " --> pdb=" O THR H 293 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS H 298 " --> pdb=" O PRO H 294 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS H 303 " --> pdb=" O SER H 299 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR H 304 " --> pdb=" O LEU H 300 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 314 removed outlier: 3.589A pdb=" N ASP H 311 " --> pdb=" O CYS H 307 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU H 312 " --> pdb=" O ARG H 308 " (cutoff:3.500A) Proline residue: H 313 - end of helix No H-bonds generated for 'chain 'H' and resid 307 through 314' Processing helix chain 'H' and resid 320 through 333 Processing helix chain 'H' and resid 338 through 343 removed outlier: 3.842A pdb=" N LYS H 342 " --> pdb=" O TRP H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 348 through 359 removed outlier: 3.680A pdb=" N LEU H 357 " --> pdb=" O ILE H 353 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN H 358 " --> pdb=" O GLU H 354 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL H 359 " --> pdb=" O SER H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 364 through 373 removed outlier: 3.642A pdb=" N MET H 368 " --> pdb=" O GLU H 364 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU H 372 " --> pdb=" O MET H 368 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER H 373 " --> pdb=" O PHE H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 382 through 389 removed outlier: 3.791A pdb=" N LEU H 388 " --> pdb=" O ILE H 384 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE H 389 " --> pdb=" O LEU H 385 " (cutoff:3.500A) Processing helix chain 'H' and resid 396 through 409 removed outlier: 3.506A pdb=" N SER H 409 " --> pdb=" O LEU H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 429 through 435 removed outlier: 3.810A pdb=" N LEU H 433 " --> pdb=" O LEU H 429 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN H 435 " --> pdb=" O VAL H 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 429 through 435' Processing helix chain 'H' and resid 438 through 454 Proline residue: H 450 - end of helix removed outlier: 4.748A pdb=" N ASP H 454 " --> pdb=" O PRO H 450 " (cutoff:3.500A) Processing helix chain 'H' and resid 464 through 479 removed outlier: 5.209A pdb=" N TYR H 468 " --> pdb=" O ASP H 464 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLY H 472 " --> pdb=" O TYR H 468 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N HIS H 473 " --> pdb=" O SER H 469 " (cutoff:3.500A) Processing helix chain 'H' and resid 480 through 487 Processing helix chain 'H' and resid 491 through 503 removed outlier: 4.764A pdb=" N ARG H 495 " --> pdb=" O PHE H 491 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN H 499 " --> pdb=" O ARG H 495 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS H 503 " --> pdb=" O GLN H 499 " (cutoff:3.500A) Processing helix chain 'H' and resid 516 through 528 removed outlier: 3.788A pdb=" N GLN H 520 " --> pdb=" O ASN H 516 " (cutoff:3.500A) Proline residue: H 526 - end of helix Processing helix chain 'H' and resid 532 through 549 removed outlier: 3.788A pdb=" N LEU H 538 " --> pdb=" O LYS H 534 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE H 545 " --> pdb=" O ALA H 541 " (cutoff:3.500A) Proline residue: H 547 - end of helix Processing helix chain 'H' and resid 558 through 568 removed outlier: 4.283A pdb=" N LEU H 562 " --> pdb=" O TYR H 558 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET H 567 " --> pdb=" O ARG H 563 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA H 568 " --> pdb=" O ILE H 564 " (cutoff:3.500A) Processing helix chain 'H' and resid 571 through 583 removed outlier: 3.619A pdb=" N GLU H 575 " --> pdb=" O GLU H 571 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS H 579 " --> pdb=" O GLU H 575 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 20 removed outlier: 4.306A pdb=" N SER I 17 " --> pdb=" O LYS I 13 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL I 18 " --> pdb=" O ASP I 14 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE I 19 " --> pdb=" O ILE I 15 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU I 20 " --> pdb=" O LEU I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 27 removed outlier: 3.726A pdb=" N ASP I 25 " --> pdb=" O ASP I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 51 removed outlier: 3.841A pdb=" N ILE I 49 " --> pdb=" O ILE I 45 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET I 50 " --> pdb=" O ASP I 46 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER I 51 " --> pdb=" O HIS I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 69 removed outlier: 3.973A pdb=" N GLY I 57 " --> pdb=" O ASP I 53 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU I 59 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU I 66 " --> pdb=" O PHE I 62 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLN I 69 " --> pdb=" O LEU I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 85 removed outlier: 4.431A pdb=" N GLN I 74 " --> pdb=" O GLU I 70 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS I 75 " --> pdb=" O GLU I 71 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU I 79 " --> pdb=" O LYS I 75 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL I 80 " --> pdb=" O PHE I 76 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN I 84 " --> pdb=" O VAL I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 98 removed outlier: 3.534A pdb=" N SER I 90 " --> pdb=" O LYS I 86 " (cutoff:3.500A) Proline residue: I 91 - end of helix removed outlier: 3.751A pdb=" N GLU I 95 " --> pdb=" O PRO I 91 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG I 97 " --> pdb=" O LYS I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 118 removed outlier: 3.565A pdb=" N ARG I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 141 removed outlier: 3.637A pdb=" N GLN I 136 " --> pdb=" O LEU I 132 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA I 137 " --> pdb=" O LYS I 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU I 140 " --> pdb=" O GLN I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 168 removed outlier: 3.566A pdb=" N VAL I 160 " --> pdb=" O GLY I 156 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR I 168 " --> pdb=" O VAL I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 175 removed outlier: 3.694A pdb=" N LYS I 173 " --> pdb=" O LYS I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 204 removed outlier: 4.518A pdb=" N VAL I 192 " --> pdb=" O SER I 188 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU I 193 " --> pdb=" O PRO I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 233 removed outlier: 3.679A pdb=" N ILE I 221 " --> pdb=" O ILE I 217 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS I 222 " --> pdb=" O LYS I 218 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER I 223 " --> pdb=" O LEU I 219 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 257 removed outlier: 3.710A pdb=" N TRP I 253 " --> pdb=" O ASN I 249 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA I 255 " --> pdb=" O LYS I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 276 removed outlier: 5.781A pdb=" N SER I 276 " --> pdb=" O THR I 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 292 removed outlier: 5.362A pdb=" N LEU I 292 " --> pdb=" O HIS I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 306 removed outlier: 3.915A pdb=" N VAL I 297 " --> pdb=" O THR I 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS I 298 " --> pdb=" O PRO I 294 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS I 303 " --> pdb=" O SER I 299 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR I 304 " --> pdb=" O LEU I 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 307 through 314 removed outlier: 3.589A pdb=" N ASP I 311 " --> pdb=" O CYS I 307 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU I 312 " --> pdb=" O ARG I 308 " (cutoff:3.500A) Proline residue: I 313 - end of helix No H-bonds generated for 'chain 'I' and resid 307 through 314' Processing helix chain 'I' and resid 320 through 333 Processing helix chain 'I' and resid 338 through 343 removed outlier: 3.843A pdb=" N LYS I 342 " --> pdb=" O TRP I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 348 through 359 removed outlier: 3.680A pdb=" N LEU I 357 " --> pdb=" O ILE I 353 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN I 358 " --> pdb=" O GLU I 354 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL I 359 " --> pdb=" O SER I 355 " (cutoff:3.500A) Processing helix chain 'I' and resid 364 through 373 removed outlier: 3.641A pdb=" N MET I 368 " --> pdb=" O GLU I 364 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU I 372 " --> pdb=" O MET I 368 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER I 373 " --> pdb=" O PHE I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 382 through 389 removed outlier: 3.791A pdb=" N LEU I 388 " --> pdb=" O ILE I 384 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE I 389 " --> pdb=" O LEU I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 396 through 409 removed outlier: 3.506A pdb=" N SER I 409 " --> pdb=" O LEU I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 429 through 435 removed outlier: 3.810A pdb=" N LEU I 433 " --> pdb=" O LEU I 429 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU I 434 " --> pdb=" O LYS I 430 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN I 435 " --> pdb=" O VAL I 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 429 through 435' Processing helix chain 'I' and resid 438 through 454 Proline residue: I 450 - end of helix removed outlier: 4.748A pdb=" N ASP I 454 " --> pdb=" O PRO I 450 " (cutoff:3.500A) Processing helix chain 'I' and resid 464 through 479 removed outlier: 5.208A pdb=" N TYR I 468 " --> pdb=" O ASP I 464 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY I 472 " --> pdb=" O TYR I 468 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N HIS I 473 " --> pdb=" O SER I 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 480 through 487 Processing helix chain 'I' and resid 491 through 503 removed outlier: 4.764A pdb=" N ARG I 495 " --> pdb=" O PHE I 491 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN I 499 " --> pdb=" O ARG I 495 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS I 503 " --> pdb=" O GLN I 499 " (cutoff:3.500A) Processing helix chain 'I' and resid 516 through 528 removed outlier: 3.788A pdb=" N GLN I 520 " --> pdb=" O ASN I 516 " (cutoff:3.500A) Proline residue: I 526 - end of helix Processing helix chain 'I' and resid 532 through 549 removed outlier: 3.788A pdb=" N LEU I 538 " --> pdb=" O LYS I 534 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE I 545 " --> pdb=" O ALA I 541 " (cutoff:3.500A) Proline residue: I 547 - end of helix Processing helix chain 'I' and resid 558 through 568 removed outlier: 4.283A pdb=" N LEU I 562 " --> pdb=" O TYR I 558 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET I 567 " --> pdb=" O ARG I 563 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA I 568 " --> pdb=" O ILE I 564 " (cutoff:3.500A) Processing helix chain 'I' and resid 571 through 583 removed outlier: 3.620A pdb=" N GLU I 575 " --> pdb=" O GLU I 571 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS I 579 " --> pdb=" O GLU I 575 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 20 removed outlier: 4.306A pdb=" N SER J 17 " --> pdb=" O LYS J 13 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL J 18 " --> pdb=" O ASP J 14 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE J 19 " --> pdb=" O ILE J 15 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU J 20 " --> pdb=" O LEU J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 27 removed outlier: 3.726A pdb=" N ASP J 25 " --> pdb=" O ASP J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 51 removed outlier: 3.841A pdb=" N ILE J 49 " --> pdb=" O ILE J 45 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET J 50 " --> pdb=" O ASP J 46 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER J 51 " --> pdb=" O HIS J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 69 removed outlier: 3.974A pdb=" N GLY J 57 " --> pdb=" O ASP J 53 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU J 59 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU J 66 " --> pdb=" O PHE J 62 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLN J 69 " --> pdb=" O LEU J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 85 removed outlier: 4.431A pdb=" N GLN J 74 " --> pdb=" O GLU J 70 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU J 79 " --> pdb=" O LYS J 75 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL J 80 " --> pdb=" O PHE J 76 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU J 81 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN J 84 " --> pdb=" O VAL J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 98 removed outlier: 3.534A pdb=" N SER J 90 " --> pdb=" O LYS J 86 " (cutoff:3.500A) Proline residue: J 91 - end of helix removed outlier: 3.751A pdb=" N GLU J 95 " --> pdb=" O PRO J 91 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG J 97 " --> pdb=" O LYS J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 118 removed outlier: 3.566A pdb=" N ARG J 112 " --> pdb=" O GLU J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 141 removed outlier: 3.636A pdb=" N GLN J 136 " --> pdb=" O LEU J 132 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA J 137 " --> pdb=" O LYS J 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU J 140 " --> pdb=" O GLN J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 168 removed outlier: 3.566A pdb=" N VAL J 160 " --> pdb=" O GLY J 156 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N TYR J 168 " --> pdb=" O VAL J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 175 removed outlier: 3.695A pdb=" N LYS J 173 " --> pdb=" O LYS J 169 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 204 removed outlier: 4.517A pdb=" N VAL J 192 " --> pdb=" O SER J 188 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU J 193 " --> pdb=" O PRO J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 233 removed outlier: 3.679A pdb=" N ILE J 221 " --> pdb=" O ILE J 217 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS J 222 " --> pdb=" O LYS J 218 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER J 223 " --> pdb=" O LEU J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 257 removed outlier: 3.709A pdb=" N TRP J 253 " --> pdb=" O ASN J 249 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA J 255 " --> pdb=" O LYS J 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 276 removed outlier: 5.781A pdb=" N SER J 276 " --> pdb=" O THR J 272 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 292 removed outlier: 5.362A pdb=" N LEU J 292 " --> pdb=" O HIS J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 306 removed outlier: 3.916A pdb=" N VAL J 297 " --> pdb=" O THR J 293 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS J 298 " --> pdb=" O PRO J 294 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS J 303 " --> pdb=" O SER J 299 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR J 304 " --> pdb=" O LEU J 300 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 314 removed outlier: 3.589A pdb=" N ASP J 311 " --> pdb=" O CYS J 307 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU J 312 " --> pdb=" O ARG J 308 " (cutoff:3.500A) Proline residue: J 313 - end of helix No H-bonds generated for 'chain 'J' and resid 307 through 314' Processing helix chain 'J' and resid 320 through 333 Processing helix chain 'J' and resid 338 through 343 removed outlier: 3.842A pdb=" N LYS J 342 " --> pdb=" O TRP J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 348 through 359 removed outlier: 3.680A pdb=" N LEU J 357 " --> pdb=" O ILE J 353 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN J 358 " --> pdb=" O GLU J 354 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL J 359 " --> pdb=" O SER J 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 364 through 373 removed outlier: 3.642A pdb=" N MET J 368 " --> pdb=" O GLU J 364 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU J 372 " --> pdb=" O MET J 368 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER J 373 " --> pdb=" O PHE J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 382 through 389 removed outlier: 3.791A pdb=" N LEU J 388 " --> pdb=" O ILE J 384 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE J 389 " --> pdb=" O LEU J 385 " (cutoff:3.500A) Processing helix chain 'J' and resid 396 through 409 removed outlier: 3.506A pdb=" N SER J 409 " --> pdb=" O LEU J 405 " (cutoff:3.500A) Processing helix chain 'J' and resid 429 through 435 removed outlier: 3.810A pdb=" N LEU J 433 " --> pdb=" O LEU J 429 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU J 434 " --> pdb=" O LYS J 430 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN J 435 " --> pdb=" O VAL J 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 429 through 435' Processing helix chain 'J' and resid 438 through 454 Proline residue: J 450 - end of helix removed outlier: 4.748A pdb=" N ASP J 454 " --> pdb=" O PRO J 450 " (cutoff:3.500A) Processing helix chain 'J' and resid 464 through 479 removed outlier: 5.209A pdb=" N TYR J 468 " --> pdb=" O ASP J 464 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLY J 472 " --> pdb=" O TYR J 468 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N HIS J 473 " --> pdb=" O SER J 469 " (cutoff:3.500A) Processing helix chain 'J' and resid 480 through 487 Processing helix chain 'J' and resid 491 through 503 removed outlier: 4.764A pdb=" N ARG J 495 " --> pdb=" O PHE J 491 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN J 499 " --> pdb=" O ARG J 495 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS J 503 " --> pdb=" O GLN J 499 " (cutoff:3.500A) Processing helix chain 'J' and resid 516 through 528 removed outlier: 3.788A pdb=" N GLN J 520 " --> pdb=" O ASN J 516 " (cutoff:3.500A) Proline residue: J 526 - end of helix Processing helix chain 'J' and resid 532 through 549 removed outlier: 3.788A pdb=" N LEU J 538 " --> pdb=" O LYS J 534 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE J 545 " --> pdb=" O ALA J 541 " (cutoff:3.500A) Proline residue: J 547 - end of helix Processing helix chain 'J' and resid 558 through 568 removed outlier: 4.283A pdb=" N LEU J 562 " --> pdb=" O TYR J 558 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET J 567 " --> pdb=" O ARG J 563 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA J 568 " --> pdb=" O ILE J 564 " (cutoff:3.500A) Processing helix chain 'J' and resid 571 through 583 removed outlier: 3.619A pdb=" N GLU J 575 " --> pdb=" O GLU J 571 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS J 579 " --> pdb=" O GLU J 575 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 20 removed outlier: 4.306A pdb=" N SER K 17 " --> pdb=" O LYS K 13 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL K 18 " --> pdb=" O ASP K 14 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE K 19 " --> pdb=" O ILE K 15 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU K 20 " --> pdb=" O LEU K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 27 removed outlier: 3.726A pdb=" N ASP K 25 " --> pdb=" O ASP K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 51 removed outlier: 3.841A pdb=" N ILE K 49 " --> pdb=" O ILE K 45 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET K 50 " --> pdb=" O ASP K 46 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER K 51 " --> pdb=" O HIS K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 69 removed outlier: 3.973A pdb=" N GLY K 57 " --> pdb=" O ASP K 53 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU K 59 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU K 66 " --> pdb=" O PHE K 62 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLN K 69 " --> pdb=" O LEU K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 85 removed outlier: 4.431A pdb=" N GLN K 74 " --> pdb=" O GLU K 70 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS K 75 " --> pdb=" O GLU K 71 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU K 79 " --> pdb=" O LYS K 75 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL K 80 " --> pdb=" O PHE K 76 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU K 81 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN K 84 " --> pdb=" O VAL K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 98 removed outlier: 3.534A pdb=" N SER K 90 " --> pdb=" O LYS K 86 " (cutoff:3.500A) Proline residue: K 91 - end of helix removed outlier: 3.751A pdb=" N GLU K 95 " --> pdb=" O PRO K 91 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG K 97 " --> pdb=" O LYS K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 118 removed outlier: 3.565A pdb=" N ARG K 112 " --> pdb=" O GLU K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 141 removed outlier: 3.637A pdb=" N GLN K 136 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA K 137 " --> pdb=" O LYS K 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU K 140 " --> pdb=" O GLN K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 168 removed outlier: 3.566A pdb=" N VAL K 160 " --> pdb=" O GLY K 156 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR K 168 " --> pdb=" O VAL K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 169 through 175 removed outlier: 3.694A pdb=" N LYS K 173 " --> pdb=" O LYS K 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 204 removed outlier: 4.518A pdb=" N VAL K 192 " --> pdb=" O SER K 188 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU K 193 " --> pdb=" O PRO K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 216 through 233 removed outlier: 3.679A pdb=" N ILE K 221 " --> pdb=" O ILE K 217 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS K 222 " --> pdb=" O LYS K 218 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER K 223 " --> pdb=" O LEU K 219 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 257 removed outlier: 3.710A pdb=" N TRP K 253 " --> pdb=" O ASN K 249 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA K 255 " --> pdb=" O LYS K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 268 through 276 removed outlier: 5.781A pdb=" N SER K 276 " --> pdb=" O THR K 272 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 292 removed outlier: 5.362A pdb=" N LEU K 292 " --> pdb=" O HIS K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 293 through 306 removed outlier: 3.915A pdb=" N VAL K 297 " --> pdb=" O THR K 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS K 298 " --> pdb=" O PRO K 294 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS K 303 " --> pdb=" O SER K 299 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR K 304 " --> pdb=" O LEU K 300 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 314 removed outlier: 3.589A pdb=" N ASP K 311 " --> pdb=" O CYS K 307 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU K 312 " --> pdb=" O ARG K 308 " (cutoff:3.500A) Proline residue: K 313 - end of helix No H-bonds generated for 'chain 'K' and resid 307 through 314' Processing helix chain 'K' and resid 320 through 333 Processing helix chain 'K' and resid 338 through 343 removed outlier: 3.843A pdb=" N LYS K 342 " --> pdb=" O TRP K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 348 through 359 removed outlier: 3.680A pdb=" N LEU K 357 " --> pdb=" O ILE K 353 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN K 358 " --> pdb=" O GLU K 354 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL K 359 " --> pdb=" O SER K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 364 through 373 removed outlier: 3.641A pdb=" N MET K 368 " --> pdb=" O GLU K 364 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU K 372 " --> pdb=" O MET K 368 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER K 373 " --> pdb=" O PHE K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 382 through 389 removed outlier: 3.791A pdb=" N LEU K 388 " --> pdb=" O ILE K 384 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE K 389 " --> pdb=" O LEU K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 396 through 409 removed outlier: 3.506A pdb=" N SER K 409 " --> pdb=" O LEU K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 429 through 435 removed outlier: 3.810A pdb=" N LEU K 433 " --> pdb=" O LEU K 429 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU K 434 " --> pdb=" O LYS K 430 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN K 435 " --> pdb=" O VAL K 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 429 through 435' Processing helix chain 'K' and resid 438 through 454 Proline residue: K 450 - end of helix removed outlier: 4.748A pdb=" N ASP K 454 " --> pdb=" O PRO K 450 " (cutoff:3.500A) Processing helix chain 'K' and resid 464 through 479 removed outlier: 5.209A pdb=" N TYR K 468 " --> pdb=" O ASP K 464 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY K 472 " --> pdb=" O TYR K 468 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N HIS K 473 " --> pdb=" O SER K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 480 through 487 Processing helix chain 'K' and resid 491 through 503 removed outlier: 4.764A pdb=" N ARG K 495 " --> pdb=" O PHE K 491 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN K 499 " --> pdb=" O ARG K 495 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS K 503 " --> pdb=" O GLN K 499 " (cutoff:3.500A) Processing helix chain 'K' and resid 516 through 528 removed outlier: 3.788A pdb=" N GLN K 520 " --> pdb=" O ASN K 516 " (cutoff:3.500A) Proline residue: K 526 - end of helix Processing helix chain 'K' and resid 532 through 549 removed outlier: 3.788A pdb=" N LEU K 538 " --> pdb=" O LYS K 534 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE K 545 " --> pdb=" O ALA K 541 " (cutoff:3.500A) Proline residue: K 547 - end of helix Processing helix chain 'K' and resid 558 through 568 removed outlier: 4.283A pdb=" N LEU K 562 " --> pdb=" O TYR K 558 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET K 567 " --> pdb=" O ARG K 563 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA K 568 " --> pdb=" O ILE K 564 " (cutoff:3.500A) Processing helix chain 'K' and resid 571 through 583 removed outlier: 3.620A pdb=" N GLU K 575 " --> pdb=" O GLU K 571 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS K 579 " --> pdb=" O GLU K 575 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 20 removed outlier: 4.306A pdb=" N SER L 17 " --> pdb=" O LYS L 13 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL L 18 " --> pdb=" O ASP L 14 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE L 19 " --> pdb=" O ILE L 15 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU L 20 " --> pdb=" O LEU L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 27 removed outlier: 3.726A pdb=" N ASP L 25 " --> pdb=" O ASP L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 51 removed outlier: 3.841A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET L 50 " --> pdb=" O ASP L 46 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER L 51 " --> pdb=" O HIS L 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 69 removed outlier: 3.974A pdb=" N GLY L 57 " --> pdb=" O ASP L 53 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU L 59 " --> pdb=" O VAL L 55 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU L 66 " --> pdb=" O PHE L 62 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLN L 69 " --> pdb=" O LEU L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 85 removed outlier: 4.431A pdb=" N GLN L 74 " --> pdb=" O GLU L 70 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS L 75 " --> pdb=" O GLU L 71 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU L 79 " --> pdb=" O LYS L 75 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL L 80 " --> pdb=" O PHE L 76 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU L 81 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN L 84 " --> pdb=" O VAL L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 98 removed outlier: 3.534A pdb=" N SER L 90 " --> pdb=" O LYS L 86 " (cutoff:3.500A) Proline residue: L 91 - end of helix removed outlier: 3.751A pdb=" N GLU L 95 " --> pdb=" O PRO L 91 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG L 97 " --> pdb=" O LYS L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 118 removed outlier: 3.566A pdb=" N ARG L 112 " --> pdb=" O GLU L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 141 removed outlier: 3.636A pdb=" N GLN L 136 " --> pdb=" O LEU L 132 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA L 137 " --> pdb=" O LYS L 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU L 140 " --> pdb=" O GLN L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 168 removed outlier: 3.566A pdb=" N VAL L 160 " --> pdb=" O GLY L 156 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N TYR L 168 " --> pdb=" O VAL L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 169 through 175 removed outlier: 3.695A pdb=" N LYS L 173 " --> pdb=" O LYS L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 204 removed outlier: 4.517A pdb=" N VAL L 192 " --> pdb=" O SER L 188 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU L 193 " --> pdb=" O PRO L 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 216 through 233 removed outlier: 3.679A pdb=" N ILE L 221 " --> pdb=" O ILE L 217 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS L 222 " --> pdb=" O LYS L 218 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER L 223 " --> pdb=" O LEU L 219 " (cutoff:3.500A) Processing helix chain 'L' and resid 249 through 257 removed outlier: 3.709A pdb=" N TRP L 253 " --> pdb=" O ASN L 249 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA L 255 " --> pdb=" O LYS L 251 " (cutoff:3.500A) Processing helix chain 'L' and resid 268 through 276 removed outlier: 5.781A pdb=" N SER L 276 " --> pdb=" O THR L 272 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 292 removed outlier: 5.362A pdb=" N LEU L 292 " --> pdb=" O HIS L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 306 removed outlier: 3.916A pdb=" N VAL L 297 " --> pdb=" O THR L 293 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS L 298 " --> pdb=" O PRO L 294 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS L 303 " --> pdb=" O SER L 299 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR L 304 " --> pdb=" O LEU L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 314 removed outlier: 3.589A pdb=" N ASP L 311 " --> pdb=" O CYS L 307 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU L 312 " --> pdb=" O ARG L 308 " (cutoff:3.500A) Proline residue: L 313 - end of helix No H-bonds generated for 'chain 'L' and resid 307 through 314' Processing helix chain 'L' and resid 320 through 333 Processing helix chain 'L' and resid 338 through 343 removed outlier: 3.842A pdb=" N LYS L 342 " --> pdb=" O TRP L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 348 through 359 removed outlier: 3.680A pdb=" N LEU L 357 " --> pdb=" O ILE L 353 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN L 358 " --> pdb=" O GLU L 354 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL L 359 " --> pdb=" O SER L 355 " (cutoff:3.500A) Processing helix chain 'L' and resid 364 through 373 removed outlier: 3.642A pdb=" N MET L 368 " --> pdb=" O GLU L 364 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU L 372 " --> pdb=" O MET L 368 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER L 373 " --> pdb=" O PHE L 369 " (cutoff:3.500A) Processing helix chain 'L' and resid 382 through 389 removed outlier: 3.791A pdb=" N LEU L 388 " --> pdb=" O ILE L 384 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE L 389 " --> pdb=" O LEU L 385 " (cutoff:3.500A) Processing helix chain 'L' and resid 396 through 409 removed outlier: 3.506A pdb=" N SER L 409 " --> pdb=" O LEU L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 429 through 435 removed outlier: 3.810A pdb=" N LEU L 433 " --> pdb=" O LEU L 429 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU L 434 " --> pdb=" O LYS L 430 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN L 435 " --> pdb=" O VAL L 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 429 through 435' Processing helix chain 'L' and resid 438 through 454 Proline residue: L 450 - end of helix removed outlier: 4.748A pdb=" N ASP L 454 " --> pdb=" O PRO L 450 " (cutoff:3.500A) Processing helix chain 'L' and resid 464 through 479 removed outlier: 5.209A pdb=" N TYR L 468 " --> pdb=" O ASP L 464 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLY L 472 " --> pdb=" O TYR L 468 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N HIS L 473 " --> pdb=" O SER L 469 " (cutoff:3.500A) Processing helix chain 'L' and resid 480 through 487 Processing helix chain 'L' and resid 491 through 503 removed outlier: 4.764A pdb=" N ARG L 495 " --> pdb=" O PHE L 491 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN L 499 " --> pdb=" O ARG L 495 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS L 503 " --> pdb=" O GLN L 499 " (cutoff:3.500A) Processing helix chain 'L' and resid 516 through 528 removed outlier: 3.788A pdb=" N GLN L 520 " --> pdb=" O ASN L 516 " (cutoff:3.500A) Proline residue: L 526 - end of helix Processing helix chain 'L' and resid 532 through 549 removed outlier: 3.788A pdb=" N LEU L 538 " --> pdb=" O LYS L 534 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE L 545 " --> pdb=" O ALA L 541 " (cutoff:3.500A) Proline residue: L 547 - end of helix Processing helix chain 'L' and resid 558 through 568 removed outlier: 4.283A pdb=" N LEU L 562 " --> pdb=" O TYR L 558 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET L 567 " --> pdb=" O ARG L 563 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA L 568 " --> pdb=" O ILE L 564 " (cutoff:3.500A) Processing helix chain 'L' and resid 571 through 583 removed outlier: 3.619A pdb=" N GLU L 575 " --> pdb=" O GLU L 571 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS L 579 " --> pdb=" O GLU L 575 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 20 removed outlier: 4.306A pdb=" N SER M 17 " --> pdb=" O LYS M 13 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL M 18 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE M 19 " --> pdb=" O ILE M 15 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU M 20 " --> pdb=" O LEU M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 27 removed outlier: 3.726A pdb=" N ASP M 25 " --> pdb=" O ASP M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 51 removed outlier: 3.841A pdb=" N ILE M 49 " --> pdb=" O ILE M 45 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET M 50 " --> pdb=" O ASP M 46 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER M 51 " --> pdb=" O HIS M 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 69 removed outlier: 3.973A pdb=" N GLY M 57 " --> pdb=" O ASP M 53 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU M 59 " --> pdb=" O VAL M 55 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU M 66 " --> pdb=" O PHE M 62 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLN M 69 " --> pdb=" O LEU M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 85 removed outlier: 4.431A pdb=" N GLN M 74 " --> pdb=" O GLU M 70 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS M 75 " --> pdb=" O GLU M 71 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU M 79 " --> pdb=" O LYS M 75 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL M 80 " --> pdb=" O PHE M 76 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU M 81 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN M 84 " --> pdb=" O VAL M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 98 removed outlier: 3.534A pdb=" N SER M 90 " --> pdb=" O LYS M 86 " (cutoff:3.500A) Proline residue: M 91 - end of helix removed outlier: 3.751A pdb=" N GLU M 95 " --> pdb=" O PRO M 91 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG M 97 " --> pdb=" O LYS M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 118 removed outlier: 3.565A pdb=" N ARG M 112 " --> pdb=" O GLU M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 141 removed outlier: 3.637A pdb=" N GLN M 136 " --> pdb=" O LEU M 132 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA M 137 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU M 140 " --> pdb=" O GLN M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 168 removed outlier: 3.566A pdb=" N VAL M 160 " --> pdb=" O GLY M 156 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR M 168 " --> pdb=" O VAL M 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 169 through 175 removed outlier: 3.694A pdb=" N LYS M 173 " --> pdb=" O LYS M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 204 removed outlier: 4.518A pdb=" N VAL M 192 " --> pdb=" O SER M 188 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU M 193 " --> pdb=" O PRO M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 233 removed outlier: 3.679A pdb=" N ILE M 221 " --> pdb=" O ILE M 217 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS M 222 " --> pdb=" O LYS M 218 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER M 223 " --> pdb=" O LEU M 219 " (cutoff:3.500A) Processing helix chain 'M' and resid 249 through 257 removed outlier: 3.710A pdb=" N TRP M 253 " --> pdb=" O ASN M 249 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA M 255 " --> pdb=" O LYS M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 268 through 276 removed outlier: 5.781A pdb=" N SER M 276 " --> pdb=" O THR M 272 " (cutoff:3.500A) Processing helix chain 'M' and resid 287 through 292 removed outlier: 5.362A pdb=" N LEU M 292 " --> pdb=" O HIS M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 306 removed outlier: 3.915A pdb=" N VAL M 297 " --> pdb=" O THR M 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS M 298 " --> pdb=" O PRO M 294 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS M 303 " --> pdb=" O SER M 299 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR M 304 " --> pdb=" O LEU M 300 " (cutoff:3.500A) Processing helix chain 'M' and resid 307 through 314 removed outlier: 3.589A pdb=" N ASP M 311 " --> pdb=" O CYS M 307 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU M 312 " --> pdb=" O ARG M 308 " (cutoff:3.500A) Proline residue: M 313 - end of helix No H-bonds generated for 'chain 'M' and resid 307 through 314' Processing helix chain 'M' and resid 320 through 333 Processing helix chain 'M' and resid 338 through 343 removed outlier: 3.843A pdb=" N LYS M 342 " --> pdb=" O TRP M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 359 removed outlier: 3.680A pdb=" N LEU M 357 " --> pdb=" O ILE M 353 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN M 358 " --> pdb=" O GLU M 354 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL M 359 " --> pdb=" O SER M 355 " (cutoff:3.500A) Processing helix chain 'M' and resid 364 through 373 removed outlier: 3.641A pdb=" N MET M 368 " --> pdb=" O GLU M 364 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU M 372 " --> pdb=" O MET M 368 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER M 373 " --> pdb=" O PHE M 369 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 389 removed outlier: 3.791A pdb=" N LEU M 388 " --> pdb=" O ILE M 384 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE M 389 " --> pdb=" O LEU M 385 " (cutoff:3.500A) Processing helix chain 'M' and resid 396 through 409 removed outlier: 3.506A pdb=" N SER M 409 " --> pdb=" O LEU M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 429 through 435 removed outlier: 3.810A pdb=" N LEU M 433 " --> pdb=" O LEU M 429 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU M 434 " --> pdb=" O LYS M 430 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN M 435 " --> pdb=" O VAL M 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 429 through 435' Processing helix chain 'M' and resid 438 through 454 Proline residue: M 450 - end of helix removed outlier: 4.748A pdb=" N ASP M 454 " --> pdb=" O PRO M 450 " (cutoff:3.500A) Processing helix chain 'M' and resid 464 through 479 removed outlier: 5.208A pdb=" N TYR M 468 " --> pdb=" O ASP M 464 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY M 472 " --> pdb=" O TYR M 468 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N HIS M 473 " --> pdb=" O SER M 469 " (cutoff:3.500A) Processing helix chain 'M' and resid 480 through 487 Processing helix chain 'M' and resid 491 through 503 removed outlier: 4.764A pdb=" N ARG M 495 " --> pdb=" O PHE M 491 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN M 499 " --> pdb=" O ARG M 495 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS M 503 " --> pdb=" O GLN M 499 " (cutoff:3.500A) Processing helix chain 'M' and resid 516 through 528 removed outlier: 3.788A pdb=" N GLN M 520 " --> pdb=" O ASN M 516 " (cutoff:3.500A) Proline residue: M 526 - end of helix Processing helix chain 'M' and resid 532 through 549 removed outlier: 3.788A pdb=" N LEU M 538 " --> pdb=" O LYS M 534 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE M 545 " --> pdb=" O ALA M 541 " (cutoff:3.500A) Proline residue: M 547 - end of helix Processing helix chain 'M' and resid 558 through 568 removed outlier: 4.283A pdb=" N LEU M 562 " --> pdb=" O TYR M 558 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET M 567 " --> pdb=" O ARG M 563 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA M 568 " --> pdb=" O ILE M 564 " (cutoff:3.500A) Processing helix chain 'M' and resid 571 through 583 removed outlier: 3.620A pdb=" N GLU M 575 " --> pdb=" O GLU M 571 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS M 579 " --> pdb=" O GLU M 575 " (cutoff:3.500A) Processing helix chain 'N' and resid 11 through 20 removed outlier: 4.306A pdb=" N SER N 17 " --> pdb=" O LYS N 13 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL N 18 " --> pdb=" O ASP N 14 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE N 19 " --> pdb=" O ILE N 15 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU N 20 " --> pdb=" O LEU N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 21 through 27 removed outlier: 3.726A pdb=" N ASP N 25 " --> pdb=" O ASP N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 51 removed outlier: 3.841A pdb=" N ILE N 49 " --> pdb=" O ILE N 45 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET N 50 " --> pdb=" O ASP N 46 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER N 51 " --> pdb=" O HIS N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 69 removed outlier: 3.974A pdb=" N GLY N 57 " --> pdb=" O ASP N 53 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU N 59 " --> pdb=" O VAL N 55 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU N 66 " --> pdb=" O PHE N 62 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLN N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 85 removed outlier: 4.431A pdb=" N GLN N 74 " --> pdb=" O GLU N 70 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS N 75 " --> pdb=" O GLU N 71 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU N 79 " --> pdb=" O LYS N 75 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL N 80 " --> pdb=" O PHE N 76 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU N 81 " --> pdb=" O VAL N 77 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN N 84 " --> pdb=" O VAL N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 98 removed outlier: 3.534A pdb=" N SER N 90 " --> pdb=" O LYS N 86 " (cutoff:3.500A) Proline residue: N 91 - end of helix removed outlier: 3.751A pdb=" N GLU N 95 " --> pdb=" O PRO N 91 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG N 97 " --> pdb=" O LYS N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 118 removed outlier: 3.566A pdb=" N ARG N 112 " --> pdb=" O GLU N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 141 removed outlier: 3.636A pdb=" N GLN N 136 " --> pdb=" O LEU N 132 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA N 137 " --> pdb=" O LYS N 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU N 140 " --> pdb=" O GLN N 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 156 through 168 removed outlier: 3.566A pdb=" N VAL N 160 " --> pdb=" O GLY N 156 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N TYR N 168 " --> pdb=" O VAL N 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 169 through 175 removed outlier: 3.695A pdb=" N LYS N 173 " --> pdb=" O LYS N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 204 removed outlier: 4.517A pdb=" N VAL N 192 " --> pdb=" O SER N 188 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU N 193 " --> pdb=" O PRO N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 216 through 233 removed outlier: 3.679A pdb=" N ILE N 221 " --> pdb=" O ILE N 217 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS N 222 " --> pdb=" O LYS N 218 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER N 223 " --> pdb=" O LEU N 219 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 257 removed outlier: 3.709A pdb=" N TRP N 253 " --> pdb=" O ASN N 249 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA N 255 " --> pdb=" O LYS N 251 " (cutoff:3.500A) Processing helix chain 'N' and resid 268 through 276 removed outlier: 5.781A pdb=" N SER N 276 " --> pdb=" O THR N 272 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 292 removed outlier: 5.362A pdb=" N LEU N 292 " --> pdb=" O HIS N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 293 through 306 removed outlier: 3.916A pdb=" N VAL N 297 " --> pdb=" O THR N 293 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS N 298 " --> pdb=" O PRO N 294 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS N 303 " --> pdb=" O SER N 299 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR N 304 " --> pdb=" O LEU N 300 " (cutoff:3.500A) Processing helix chain 'N' and resid 307 through 314 removed outlier: 3.589A pdb=" N ASP N 311 " --> pdb=" O CYS N 307 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU N 312 " --> pdb=" O ARG N 308 " (cutoff:3.500A) Proline residue: N 313 - end of helix No H-bonds generated for 'chain 'N' and resid 307 through 314' Processing helix chain 'N' and resid 320 through 333 Processing helix chain 'N' and resid 338 through 343 removed outlier: 3.842A pdb=" N LYS N 342 " --> pdb=" O TRP N 338 " (cutoff:3.500A) Processing helix chain 'N' and resid 348 through 359 removed outlier: 3.680A pdb=" N LEU N 357 " --> pdb=" O ILE N 353 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN N 358 " --> pdb=" O GLU N 354 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL N 359 " --> pdb=" O SER N 355 " (cutoff:3.500A) Processing helix chain 'N' and resid 364 through 373 removed outlier: 3.642A pdb=" N MET N 368 " --> pdb=" O GLU N 364 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU N 372 " --> pdb=" O MET N 368 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER N 373 " --> pdb=" O PHE N 369 " (cutoff:3.500A) Processing helix chain 'N' and resid 382 through 389 removed outlier: 3.791A pdb=" N LEU N 388 " --> pdb=" O ILE N 384 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE N 389 " --> pdb=" O LEU N 385 " (cutoff:3.500A) Processing helix chain 'N' and resid 396 through 409 removed outlier: 3.506A pdb=" N SER N 409 " --> pdb=" O LEU N 405 " (cutoff:3.500A) Processing helix chain 'N' and resid 429 through 435 removed outlier: 3.810A pdb=" N LEU N 433 " --> pdb=" O LEU N 429 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU N 434 " --> pdb=" O LYS N 430 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN N 435 " --> pdb=" O VAL N 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 429 through 435' Processing helix chain 'N' and resid 438 through 454 Proline residue: N 450 - end of helix removed outlier: 4.748A pdb=" N ASP N 454 " --> pdb=" O PRO N 450 " (cutoff:3.500A) Processing helix chain 'N' and resid 464 through 479 removed outlier: 5.209A pdb=" N TYR N 468 " --> pdb=" O ASP N 464 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLY N 472 " --> pdb=" O TYR N 468 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N HIS N 473 " --> pdb=" O SER N 469 " (cutoff:3.500A) Processing helix chain 'N' and resid 480 through 487 Processing helix chain 'N' and resid 491 through 503 removed outlier: 4.764A pdb=" N ARG N 495 " --> pdb=" O PHE N 491 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN N 499 " --> pdb=" O ARG N 495 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS N 503 " --> pdb=" O GLN N 499 " (cutoff:3.500A) Processing helix chain 'N' and resid 516 through 528 removed outlier: 3.788A pdb=" N GLN N 520 " --> pdb=" O ASN N 516 " (cutoff:3.500A) Proline residue: N 526 - end of helix Processing helix chain 'N' and resid 532 through 549 removed outlier: 3.788A pdb=" N LEU N 538 " --> pdb=" O LYS N 534 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE N 545 " --> pdb=" O ALA N 541 " (cutoff:3.500A) Proline residue: N 547 - end of helix Processing helix chain 'N' and resid 558 through 568 removed outlier: 4.283A pdb=" N LEU N 562 " --> pdb=" O TYR N 558 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET N 567 " --> pdb=" O ARG N 563 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA N 568 " --> pdb=" O ILE N 564 " (cutoff:3.500A) Processing helix chain 'N' and resid 571 through 583 removed outlier: 3.619A pdb=" N GLU N 575 " --> pdb=" O GLU N 571 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS N 579 " --> pdb=" O GLU N 575 " (cutoff:3.500A) Processing helix chain 'O' and resid 11 through 20 removed outlier: 4.306A pdb=" N SER O 17 " --> pdb=" O LYS O 13 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL O 18 " --> pdb=" O ASP O 14 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE O 19 " --> pdb=" O ILE O 15 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU O 20 " --> pdb=" O LEU O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 27 removed outlier: 3.726A pdb=" N ASP O 25 " --> pdb=" O ASP O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 51 removed outlier: 3.841A pdb=" N ILE O 49 " --> pdb=" O ILE O 45 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET O 50 " --> pdb=" O ASP O 46 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER O 51 " --> pdb=" O HIS O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 53 through 69 removed outlier: 3.973A pdb=" N GLY O 57 " --> pdb=" O ASP O 53 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU O 59 " --> pdb=" O VAL O 55 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU O 66 " --> pdb=" O PHE O 62 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLN O 69 " --> pdb=" O LEU O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 85 removed outlier: 4.431A pdb=" N GLN O 74 " --> pdb=" O GLU O 70 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS O 75 " --> pdb=" O GLU O 71 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU O 79 " --> pdb=" O LYS O 75 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL O 80 " --> pdb=" O PHE O 76 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU O 81 " --> pdb=" O VAL O 77 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN O 84 " --> pdb=" O VAL O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 98 removed outlier: 3.534A pdb=" N SER O 90 " --> pdb=" O LYS O 86 " (cutoff:3.500A) Proline residue: O 91 - end of helix removed outlier: 3.751A pdb=" N GLU O 95 " --> pdb=" O PRO O 91 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG O 97 " --> pdb=" O LYS O 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 118 removed outlier: 3.565A pdb=" N ARG O 112 " --> pdb=" O GLU O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 141 removed outlier: 3.637A pdb=" N GLN O 136 " --> pdb=" O LEU O 132 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA O 137 " --> pdb=" O LYS O 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU O 140 " --> pdb=" O GLN O 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 156 through 168 removed outlier: 3.566A pdb=" N VAL O 160 " --> pdb=" O GLY O 156 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR O 168 " --> pdb=" O VAL O 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 169 through 175 removed outlier: 3.694A pdb=" N LYS O 173 " --> pdb=" O LYS O 169 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 204 removed outlier: 4.518A pdb=" N VAL O 192 " --> pdb=" O SER O 188 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU O 193 " --> pdb=" O PRO O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 216 through 233 removed outlier: 3.679A pdb=" N ILE O 221 " --> pdb=" O ILE O 217 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS O 222 " --> pdb=" O LYS O 218 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER O 223 " --> pdb=" O LEU O 219 " (cutoff:3.500A) Processing helix chain 'O' and resid 249 through 257 removed outlier: 3.710A pdb=" N TRP O 253 " --> pdb=" O ASN O 249 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA O 255 " --> pdb=" O LYS O 251 " (cutoff:3.500A) Processing helix chain 'O' and resid 268 through 276 removed outlier: 5.781A pdb=" N SER O 276 " --> pdb=" O THR O 272 " (cutoff:3.500A) Processing helix chain 'O' and resid 287 through 292 removed outlier: 5.362A pdb=" N LEU O 292 " --> pdb=" O HIS O 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 293 through 306 removed outlier: 3.915A pdb=" N VAL O 297 " --> pdb=" O THR O 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS O 298 " --> pdb=" O PRO O 294 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS O 303 " --> pdb=" O SER O 299 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR O 304 " --> pdb=" O LEU O 300 " (cutoff:3.500A) Processing helix chain 'O' and resid 307 through 314 removed outlier: 3.589A pdb=" N ASP O 311 " --> pdb=" O CYS O 307 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU O 312 " --> pdb=" O ARG O 308 " (cutoff:3.500A) Proline residue: O 313 - end of helix No H-bonds generated for 'chain 'O' and resid 307 through 314' Processing helix chain 'O' and resid 320 through 333 Processing helix chain 'O' and resid 338 through 343 removed outlier: 3.843A pdb=" N LYS O 342 " --> pdb=" O TRP O 338 " (cutoff:3.500A) Processing helix chain 'O' and resid 348 through 359 removed outlier: 3.680A pdb=" N LEU O 357 " --> pdb=" O ILE O 353 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN O 358 " --> pdb=" O GLU O 354 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL O 359 " --> pdb=" O SER O 355 " (cutoff:3.500A) Processing helix chain 'O' and resid 364 through 373 removed outlier: 3.641A pdb=" N MET O 368 " --> pdb=" O GLU O 364 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU O 372 " --> pdb=" O MET O 368 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER O 373 " --> pdb=" O PHE O 369 " (cutoff:3.500A) Processing helix chain 'O' and resid 382 through 389 removed outlier: 3.791A pdb=" N LEU O 388 " --> pdb=" O ILE O 384 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE O 389 " --> pdb=" O LEU O 385 " (cutoff:3.500A) Processing helix chain 'O' and resid 396 through 409 removed outlier: 3.506A pdb=" N SER O 409 " --> pdb=" O LEU O 405 " (cutoff:3.500A) Processing helix chain 'O' and resid 429 through 435 removed outlier: 3.810A pdb=" N LEU O 433 " --> pdb=" O LEU O 429 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU O 434 " --> pdb=" O LYS O 430 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN O 435 " --> pdb=" O VAL O 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 429 through 435' Processing helix chain 'O' and resid 438 through 454 Proline residue: O 450 - end of helix removed outlier: 4.748A pdb=" N ASP O 454 " --> pdb=" O PRO O 450 " (cutoff:3.500A) Processing helix chain 'O' and resid 464 through 479 removed outlier: 5.208A pdb=" N TYR O 468 " --> pdb=" O ASP O 464 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY O 472 " --> pdb=" O TYR O 468 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N HIS O 473 " --> pdb=" O SER O 469 " (cutoff:3.500A) Processing helix chain 'O' and resid 480 through 487 Processing helix chain 'O' and resid 491 through 503 removed outlier: 4.764A pdb=" N ARG O 495 " --> pdb=" O PHE O 491 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN O 499 " --> pdb=" O ARG O 495 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS O 503 " --> pdb=" O GLN O 499 " (cutoff:3.500A) Processing helix chain 'O' and resid 516 through 528 removed outlier: 3.788A pdb=" N GLN O 520 " --> pdb=" O ASN O 516 " (cutoff:3.500A) Proline residue: O 526 - end of helix Processing helix chain 'O' and resid 532 through 549 removed outlier: 3.788A pdb=" N LEU O 538 " --> pdb=" O LYS O 534 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE O 545 " --> pdb=" O ALA O 541 " (cutoff:3.500A) Proline residue: O 547 - end of helix Processing helix chain 'O' and resid 558 through 568 removed outlier: 4.283A pdb=" N LEU O 562 " --> pdb=" O TYR O 558 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET O 567 " --> pdb=" O ARG O 563 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA O 568 " --> pdb=" O ILE O 564 " (cutoff:3.500A) Processing helix chain 'O' and resid 571 through 583 removed outlier: 3.620A pdb=" N GLU O 575 " --> pdb=" O GLU O 571 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS O 579 " --> pdb=" O GLU O 575 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 20 removed outlier: 4.306A pdb=" N SER P 17 " --> pdb=" O LYS P 13 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL P 18 " --> pdb=" O ASP P 14 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE P 19 " --> pdb=" O ILE P 15 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU P 20 " --> pdb=" O LEU P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 27 removed outlier: 3.726A pdb=" N ASP P 25 " --> pdb=" O ASP P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 51 removed outlier: 3.841A pdb=" N ILE P 49 " --> pdb=" O ILE P 45 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET P 50 " --> pdb=" O ASP P 46 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER P 51 " --> pdb=" O HIS P 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 69 removed outlier: 3.974A pdb=" N GLY P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU P 59 " --> pdb=" O VAL P 55 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU P 66 " --> pdb=" O PHE P 62 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLN P 69 " --> pdb=" O LEU P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 85 removed outlier: 4.431A pdb=" N GLN P 74 " --> pdb=" O GLU P 70 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS P 75 " --> pdb=" O GLU P 71 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU P 79 " --> pdb=" O LYS P 75 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL P 80 " --> pdb=" O PHE P 76 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU P 81 " --> pdb=" O VAL P 77 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN P 84 " --> pdb=" O VAL P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 98 removed outlier: 3.534A pdb=" N SER P 90 " --> pdb=" O LYS P 86 " (cutoff:3.500A) Proline residue: P 91 - end of helix removed outlier: 3.751A pdb=" N GLU P 95 " --> pdb=" O PRO P 91 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG P 97 " --> pdb=" O LYS P 93 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 118 removed outlier: 3.566A pdb=" N ARG P 112 " --> pdb=" O GLU P 108 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 141 removed outlier: 3.636A pdb=" N GLN P 136 " --> pdb=" O LEU P 132 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA P 137 " --> pdb=" O LYS P 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU P 140 " --> pdb=" O GLN P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 168 removed outlier: 3.566A pdb=" N VAL P 160 " --> pdb=" O GLY P 156 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N TYR P 168 " --> pdb=" O VAL P 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 169 through 175 removed outlier: 3.695A pdb=" N LYS P 173 " --> pdb=" O LYS P 169 " (cutoff:3.500A) Processing helix chain 'P' and resid 188 through 204 removed outlier: 4.517A pdb=" N VAL P 192 " --> pdb=" O SER P 188 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU P 193 " --> pdb=" O PRO P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 216 through 233 removed outlier: 3.679A pdb=" N ILE P 221 " --> pdb=" O ILE P 217 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS P 222 " --> pdb=" O LYS P 218 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER P 223 " --> pdb=" O LEU P 219 " (cutoff:3.500A) Processing helix chain 'P' and resid 249 through 257 removed outlier: 3.709A pdb=" N TRP P 253 " --> pdb=" O ASN P 249 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA P 255 " --> pdb=" O LYS P 251 " (cutoff:3.500A) Processing helix chain 'P' and resid 268 through 276 removed outlier: 5.781A pdb=" N SER P 276 " --> pdb=" O THR P 272 " (cutoff:3.500A) Processing helix chain 'P' and resid 287 through 292 removed outlier: 5.362A pdb=" N LEU P 292 " --> pdb=" O HIS P 288 " (cutoff:3.500A) Processing helix chain 'P' and resid 293 through 306 removed outlier: 3.916A pdb=" N VAL P 297 " --> pdb=" O THR P 293 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS P 298 " --> pdb=" O PRO P 294 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS P 303 " --> pdb=" O SER P 299 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR P 304 " --> pdb=" O LEU P 300 " (cutoff:3.500A) Processing helix chain 'P' and resid 307 through 314 removed outlier: 3.589A pdb=" N ASP P 311 " --> pdb=" O CYS P 307 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU P 312 " --> pdb=" O ARG P 308 " (cutoff:3.500A) Proline residue: P 313 - end of helix No H-bonds generated for 'chain 'P' and resid 307 through 314' Processing helix chain 'P' and resid 320 through 333 Processing helix chain 'P' and resid 338 through 343 removed outlier: 3.842A pdb=" N LYS P 342 " --> pdb=" O TRP P 338 " (cutoff:3.500A) Processing helix chain 'P' and resid 348 through 359 removed outlier: 3.680A pdb=" N LEU P 357 " --> pdb=" O ILE P 353 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN P 358 " --> pdb=" O GLU P 354 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL P 359 " --> pdb=" O SER P 355 " (cutoff:3.500A) Processing helix chain 'P' and resid 364 through 373 removed outlier: 3.642A pdb=" N MET P 368 " --> pdb=" O GLU P 364 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU P 372 " --> pdb=" O MET P 368 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER P 373 " --> pdb=" O PHE P 369 " (cutoff:3.500A) Processing helix chain 'P' and resid 382 through 389 removed outlier: 3.791A pdb=" N LEU P 388 " --> pdb=" O ILE P 384 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE P 389 " --> pdb=" O LEU P 385 " (cutoff:3.500A) Processing helix chain 'P' and resid 396 through 409 removed outlier: 3.506A pdb=" N SER P 409 " --> pdb=" O LEU P 405 " (cutoff:3.500A) Processing helix chain 'P' and resid 429 through 435 removed outlier: 3.810A pdb=" N LEU P 433 " --> pdb=" O LEU P 429 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU P 434 " --> pdb=" O LYS P 430 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN P 435 " --> pdb=" O VAL P 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 429 through 435' Processing helix chain 'P' and resid 438 through 454 Proline residue: P 450 - end of helix removed outlier: 4.748A pdb=" N ASP P 454 " --> pdb=" O PRO P 450 " (cutoff:3.500A) Processing helix chain 'P' and resid 464 through 479 removed outlier: 5.209A pdb=" N TYR P 468 " --> pdb=" O ASP P 464 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLY P 472 " --> pdb=" O TYR P 468 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N HIS P 473 " --> pdb=" O SER P 469 " (cutoff:3.500A) Processing helix chain 'P' and resid 480 through 487 Processing helix chain 'P' and resid 491 through 503 removed outlier: 4.764A pdb=" N ARG P 495 " --> pdb=" O PHE P 491 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN P 499 " --> pdb=" O ARG P 495 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS P 503 " --> pdb=" O GLN P 499 " (cutoff:3.500A) Processing helix chain 'P' and resid 516 through 528 removed outlier: 3.788A pdb=" N GLN P 520 " --> pdb=" O ASN P 516 " (cutoff:3.500A) Proline residue: P 526 - end of helix Processing helix chain 'P' and resid 532 through 549 removed outlier: 3.788A pdb=" N LEU P 538 " --> pdb=" O LYS P 534 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE P 545 " --> pdb=" O ALA P 541 " (cutoff:3.500A) Proline residue: P 547 - end of helix Processing helix chain 'P' and resid 558 through 568 removed outlier: 4.283A pdb=" N LEU P 562 " --> pdb=" O TYR P 558 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET P 567 " --> pdb=" O ARG P 563 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA P 568 " --> pdb=" O ILE P 564 " (cutoff:3.500A) Processing helix chain 'P' and resid 571 through 583 removed outlier: 3.619A pdb=" N GLU P 575 " --> pdb=" O GLU P 571 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS P 579 " --> pdb=" O GLU P 575 " (cutoff:3.500A) Processing helix chain 'Q' and resid 11 through 20 removed outlier: 4.306A pdb=" N SER Q 17 " --> pdb=" O LYS Q 13 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL Q 18 " --> pdb=" O ASP Q 14 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE Q 19 " --> pdb=" O ILE Q 15 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU Q 20 " --> pdb=" O LEU Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 27 removed outlier: 3.726A pdb=" N ASP Q 25 " --> pdb=" O ASP Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 51 removed outlier: 3.841A pdb=" N ILE Q 49 " --> pdb=" O ILE Q 45 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET Q 50 " --> pdb=" O ASP Q 46 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER Q 51 " --> pdb=" O HIS Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 69 removed outlier: 3.973A pdb=" N GLY Q 57 " --> pdb=" O ASP Q 53 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU Q 59 " --> pdb=" O VAL Q 55 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU Q 66 " --> pdb=" O PHE Q 62 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLN Q 69 " --> pdb=" O LEU Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 85 removed outlier: 4.431A pdb=" N GLN Q 74 " --> pdb=" O GLU Q 70 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS Q 75 " --> pdb=" O GLU Q 71 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU Q 79 " --> pdb=" O LYS Q 75 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL Q 80 " --> pdb=" O PHE Q 76 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU Q 81 " --> pdb=" O VAL Q 77 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN Q 84 " --> pdb=" O VAL Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 98 removed outlier: 3.534A pdb=" N SER Q 90 " --> pdb=" O LYS Q 86 " (cutoff:3.500A) Proline residue: Q 91 - end of helix removed outlier: 3.751A pdb=" N GLU Q 95 " --> pdb=" O PRO Q 91 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG Q 97 " --> pdb=" O LYS Q 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 118 removed outlier: 3.565A pdb=" N ARG Q 112 " --> pdb=" O GLU Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 141 removed outlier: 3.637A pdb=" N GLN Q 136 " --> pdb=" O LEU Q 132 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA Q 137 " --> pdb=" O LYS Q 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU Q 140 " --> pdb=" O GLN Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 156 through 168 removed outlier: 3.566A pdb=" N VAL Q 160 " --> pdb=" O GLY Q 156 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR Q 168 " --> pdb=" O VAL Q 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 169 through 175 removed outlier: 3.694A pdb=" N LYS Q 173 " --> pdb=" O LYS Q 169 " (cutoff:3.500A) Processing helix chain 'Q' and resid 188 through 204 removed outlier: 4.518A pdb=" N VAL Q 192 " --> pdb=" O SER Q 188 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU Q 193 " --> pdb=" O PRO Q 189 " (cutoff:3.500A) Processing helix chain 'Q' and resid 216 through 233 removed outlier: 3.679A pdb=" N ILE Q 221 " --> pdb=" O ILE Q 217 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS Q 222 " --> pdb=" O LYS Q 218 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER Q 223 " --> pdb=" O LEU Q 219 " (cutoff:3.500A) Processing helix chain 'Q' and resid 249 through 257 removed outlier: 3.710A pdb=" N TRP Q 253 " --> pdb=" O ASN Q 249 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA Q 255 " --> pdb=" O LYS Q 251 " (cutoff:3.500A) Processing helix chain 'Q' and resid 268 through 276 removed outlier: 5.781A pdb=" N SER Q 276 " --> pdb=" O THR Q 272 " (cutoff:3.500A) Processing helix chain 'Q' and resid 287 through 292 removed outlier: 5.362A pdb=" N LEU Q 292 " --> pdb=" O HIS Q 288 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 306 removed outlier: 3.915A pdb=" N VAL Q 297 " --> pdb=" O THR Q 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS Q 298 " --> pdb=" O PRO Q 294 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS Q 303 " --> pdb=" O SER Q 299 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR Q 304 " --> pdb=" O LEU Q 300 " (cutoff:3.500A) Processing helix chain 'Q' and resid 307 through 314 removed outlier: 3.589A pdb=" N ASP Q 311 " --> pdb=" O CYS Q 307 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU Q 312 " --> pdb=" O ARG Q 308 " (cutoff:3.500A) Proline residue: Q 313 - end of helix No H-bonds generated for 'chain 'Q' and resid 307 through 314' Processing helix chain 'Q' and resid 320 through 333 Processing helix chain 'Q' and resid 338 through 343 removed outlier: 3.843A pdb=" N LYS Q 342 " --> pdb=" O TRP Q 338 " (cutoff:3.500A) Processing helix chain 'Q' and resid 348 through 359 removed outlier: 3.680A pdb=" N LEU Q 357 " --> pdb=" O ILE Q 353 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN Q 358 " --> pdb=" O GLU Q 354 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL Q 359 " --> pdb=" O SER Q 355 " (cutoff:3.500A) Processing helix chain 'Q' and resid 364 through 373 removed outlier: 3.641A pdb=" N MET Q 368 " --> pdb=" O GLU Q 364 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU Q 372 " --> pdb=" O MET Q 368 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER Q 373 " --> pdb=" O PHE Q 369 " (cutoff:3.500A) Processing helix chain 'Q' and resid 382 through 389 removed outlier: 3.791A pdb=" N LEU Q 388 " --> pdb=" O ILE Q 384 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE Q 389 " --> pdb=" O LEU Q 385 " (cutoff:3.500A) Processing helix chain 'Q' and resid 396 through 409 removed outlier: 3.506A pdb=" N SER Q 409 " --> pdb=" O LEU Q 405 " (cutoff:3.500A) Processing helix chain 'Q' and resid 429 through 435 removed outlier: 3.810A pdb=" N LEU Q 433 " --> pdb=" O LEU Q 429 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU Q 434 " --> pdb=" O LYS Q 430 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN Q 435 " --> pdb=" O VAL Q 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 429 through 435' Processing helix chain 'Q' and resid 438 through 454 Proline residue: Q 450 - end of helix removed outlier: 4.748A pdb=" N ASP Q 454 " --> pdb=" O PRO Q 450 " (cutoff:3.500A) Processing helix chain 'Q' and resid 464 through 479 removed outlier: 5.208A pdb=" N TYR Q 468 " --> pdb=" O ASP Q 464 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY Q 472 " --> pdb=" O TYR Q 468 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N HIS Q 473 " --> pdb=" O SER Q 469 " (cutoff:3.500A) Processing helix chain 'Q' and resid 480 through 487 Processing helix chain 'Q' and resid 491 through 503 removed outlier: 4.764A pdb=" N ARG Q 495 " --> pdb=" O PHE Q 491 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN Q 499 " --> pdb=" O ARG Q 495 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS Q 503 " --> pdb=" O GLN Q 499 " (cutoff:3.500A) Processing helix chain 'Q' and resid 516 through 528 removed outlier: 3.788A pdb=" N GLN Q 520 " --> pdb=" O ASN Q 516 " (cutoff:3.500A) Proline residue: Q 526 - end of helix Processing helix chain 'Q' and resid 532 through 549 removed outlier: 3.788A pdb=" N LEU Q 538 " --> pdb=" O LYS Q 534 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE Q 545 " --> pdb=" O ALA Q 541 " (cutoff:3.500A) Proline residue: Q 547 - end of helix Processing helix chain 'Q' and resid 558 through 568 removed outlier: 4.283A pdb=" N LEU Q 562 " --> pdb=" O TYR Q 558 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET Q 567 " --> pdb=" O ARG Q 563 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA Q 568 " --> pdb=" O ILE Q 564 " (cutoff:3.500A) Processing helix chain 'Q' and resid 571 through 583 removed outlier: 3.620A pdb=" N GLU Q 575 " --> pdb=" O GLU Q 571 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS Q 579 " --> pdb=" O GLU Q 575 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 177 through 182 removed outlier: 3.771A pdb=" N LEU A 241 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE A 179 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 243 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 181 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS A 261 " --> pdb=" O CYS A 240 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 242 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 262 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY A 151 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR A 281 " --> pdb=" O ASN A 146 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 177 through 182 removed outlier: 3.812A pdb=" N LEU C 241 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE C 179 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 243 " --> pdb=" O PHE C 179 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS C 261 " --> pdb=" O CYS C 240 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU C 242 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE C 262 " --> pdb=" O LYS C 145 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY C 151 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR C 281 " --> pdb=" O ASN C 146 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 177 through 182 removed outlier: 3.812A pdb=" N LEU D 241 " --> pdb=" O LYS D 177 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE D 179 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL D 243 " --> pdb=" O PHE D 179 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 181 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS D 261 " --> pdb=" O CYS D 240 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU D 242 " --> pdb=" O LYS D 261 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE D 262 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY D 151 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR D 281 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'E' and resid 177 through 182 removed outlier: 3.812A pdb=" N LEU E 241 " --> pdb=" O LYS E 177 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE E 179 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL E 243 " --> pdb=" O PHE E 179 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS E 261 " --> pdb=" O CYS E 240 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU E 242 " --> pdb=" O LYS E 261 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE E 262 " --> pdb=" O LYS E 145 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY E 151 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR E 281 " --> pdb=" O ASN E 146 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'F' and resid 177 through 182 removed outlier: 3.812A pdb=" N LEU F 241 " --> pdb=" O LYS F 177 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE F 179 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL F 243 " --> pdb=" O PHE F 179 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU F 181 " --> pdb=" O VAL F 243 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS F 261 " --> pdb=" O CYS F 240 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU F 242 " --> pdb=" O LYS F 261 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE F 262 " --> pdb=" O LYS F 145 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY F 151 " --> pdb=" O THR F 266 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR F 281 " --> pdb=" O ASN F 146 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'G' and resid 177 through 182 removed outlier: 3.812A pdb=" N LEU G 241 " --> pdb=" O LYS G 177 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE G 179 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL G 243 " --> pdb=" O PHE G 179 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS G 261 " --> pdb=" O CYS G 240 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU G 242 " --> pdb=" O LYS G 261 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE G 262 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY G 151 " --> pdb=" O THR G 266 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR G 281 " --> pdb=" O ASN G 146 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'H' and resid 177 through 182 removed outlier: 3.812A pdb=" N LEU H 241 " --> pdb=" O LYS H 177 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE H 179 " --> pdb=" O LEU H 241 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL H 243 " --> pdb=" O PHE H 179 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU H 181 " --> pdb=" O VAL H 243 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS H 261 " --> pdb=" O CYS H 240 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU H 242 " --> pdb=" O LYS H 261 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE H 262 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY H 151 " --> pdb=" O THR H 266 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR H 281 " --> pdb=" O ASN H 146 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'I' and resid 177 through 182 removed outlier: 3.812A pdb=" N LEU I 241 " --> pdb=" O LYS I 177 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE I 179 " --> pdb=" O LEU I 241 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL I 243 " --> pdb=" O PHE I 179 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS I 261 " --> pdb=" O CYS I 240 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU I 242 " --> pdb=" O LYS I 261 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE I 262 " --> pdb=" O LYS I 145 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY I 151 " --> pdb=" O THR I 266 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR I 281 " --> pdb=" O ASN I 146 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'J' and resid 177 through 182 removed outlier: 3.812A pdb=" N LEU J 241 " --> pdb=" O LYS J 177 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE J 179 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL J 243 " --> pdb=" O PHE J 179 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU J 181 " --> pdb=" O VAL J 243 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS J 261 " --> pdb=" O CYS J 240 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU J 242 " --> pdb=" O LYS J 261 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE J 262 " --> pdb=" O LYS J 145 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY J 151 " --> pdb=" O THR J 266 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR J 281 " --> pdb=" O ASN J 146 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'K' and resid 177 through 182 removed outlier: 3.812A pdb=" N LEU K 241 " --> pdb=" O LYS K 177 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE K 179 " --> pdb=" O LEU K 241 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL K 243 " --> pdb=" O PHE K 179 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS K 261 " --> pdb=" O CYS K 240 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU K 242 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE K 262 " --> pdb=" O LYS K 145 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY K 151 " --> pdb=" O THR K 266 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR K 281 " --> pdb=" O ASN K 146 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'L' and resid 177 through 182 removed outlier: 3.812A pdb=" N LEU L 241 " --> pdb=" O LYS L 177 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE L 179 " --> pdb=" O LEU L 241 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL L 243 " --> pdb=" O PHE L 179 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU L 181 " --> pdb=" O VAL L 243 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS L 261 " --> pdb=" O CYS L 240 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU L 242 " --> pdb=" O LYS L 261 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE L 262 " --> pdb=" O LYS L 145 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY L 151 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR L 281 " --> pdb=" O ASN L 146 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'M' and resid 177 through 182 removed outlier: 3.812A pdb=" N LEU M 241 " --> pdb=" O LYS M 177 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE M 179 " --> pdb=" O LEU M 241 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL M 243 " --> pdb=" O PHE M 179 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS M 261 " --> pdb=" O CYS M 240 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU M 242 " --> pdb=" O LYS M 261 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE M 262 " --> pdb=" O LYS M 145 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY M 151 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR M 281 " --> pdb=" O ASN M 146 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'N' and resid 177 through 182 removed outlier: 3.812A pdb=" N LEU N 241 " --> pdb=" O LYS N 177 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE N 179 " --> pdb=" O LEU N 241 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL N 243 " --> pdb=" O PHE N 179 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU N 181 " --> pdb=" O VAL N 243 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS N 261 " --> pdb=" O CYS N 240 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU N 242 " --> pdb=" O LYS N 261 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE N 262 " --> pdb=" O LYS N 145 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY N 151 " --> pdb=" O THR N 266 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR N 281 " --> pdb=" O ASN N 146 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'O' and resid 177 through 182 removed outlier: 3.812A pdb=" N LEU O 241 " --> pdb=" O LYS O 177 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE O 179 " --> pdb=" O LEU O 241 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL O 243 " --> pdb=" O PHE O 179 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS O 261 " --> pdb=" O CYS O 240 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU O 242 " --> pdb=" O LYS O 261 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE O 262 " --> pdb=" O LYS O 145 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY O 151 " --> pdb=" O THR O 266 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR O 281 " --> pdb=" O ASN O 146 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'P' and resid 177 through 182 removed outlier: 3.812A pdb=" N LEU P 241 " --> pdb=" O LYS P 177 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE P 179 " --> pdb=" O LEU P 241 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL P 243 " --> pdb=" O PHE P 179 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU P 181 " --> pdb=" O VAL P 243 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS P 261 " --> pdb=" O CYS P 240 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU P 242 " --> pdb=" O LYS P 261 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE P 262 " --> pdb=" O LYS P 145 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY P 151 " --> pdb=" O THR P 266 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR P 281 " --> pdb=" O ASN P 146 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'Q' and resid 177 through 182 removed outlier: 3.812A pdb=" N LEU Q 241 " --> pdb=" O LYS Q 177 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE Q 179 " --> pdb=" O LEU Q 241 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL Q 243 " --> pdb=" O PHE Q 179 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS Q 261 " --> pdb=" O CYS Q 240 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU Q 242 " --> pdb=" O LYS Q 261 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE Q 262 " --> pdb=" O LYS Q 145 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY Q 151 " --> pdb=" O THR Q 266 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR Q 281 " --> pdb=" O ASN Q 146 " (cutoff:3.500A) 3000 hydrogen bonds defined for protein. 9000 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: 33.54 Time building geometry restraints manager: 35.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.44 - 0.93: 1 0.93 - 1.41: 45643 1.41 - 1.90: 68218 1.90 - 2.39: 0 2.39 - 2.87: 16 Warning: very small bond lengths. Bond restraints: 113878 Sorted by residual: bond pdb=" C UNK K 835 " pdb=" N UNK K 836 " ideal model delta sigma weight residual 1.329 2.875 -1.546 1.40e-02 5.10e+03 1.22e+04 bond pdb=" C UNK Q 835 " pdb=" N UNK Q 836 " ideal model delta sigma weight residual 1.329 2.875 -1.546 1.40e-02 5.10e+03 1.22e+04 bond pdb=" C UNK O 835 " pdb=" N UNK O 836 " ideal model delta sigma weight residual 1.329 2.875 -1.546 1.40e-02 5.10e+03 1.22e+04 bond pdb=" C UNK M 835 " pdb=" N UNK M 836 " ideal model delta sigma weight residual 1.329 2.875 -1.546 1.40e-02 5.10e+03 1.22e+04 bond pdb=" C UNK C 835 " pdb=" N UNK C 836 " ideal model delta sigma weight residual 1.329 2.875 -1.546 1.40e-02 5.10e+03 1.22e+04 ... (remaining 113873 not shown) Histogram of bond angle deviations from ideal: 55.42 - 77.33: 2 77.33 - 99.24: 128 99.24 - 121.14: 120840 121.14 - 143.05: 33933 143.05 - 164.95: 1 Bond angle restraints: 154904 Sorted by residual: angle pdb=" C UNK Q 615 " pdb=" N UNK Q 616 " pdb=" CA UNK Q 616 " ideal model delta sigma weight residual 121.70 63.42 58.28 1.80e+00 3.09e-01 1.05e+03 angle pdb=" CA UNK Q 615 " pdb=" C UNK Q 615 " pdb=" N UNK Q 616 " ideal model delta sigma weight residual 116.20 55.42 60.78 2.00e+00 2.50e-01 9.23e+02 angle pdb=" O UNK Q 615 " pdb=" C UNK Q 615 " pdb=" N UNK Q 616 " ideal model delta sigma weight residual 123.00 164.95 -41.95 1.60e+00 3.91e-01 6.87e+02 angle pdb=" N VAL G 411 " pdb=" CA VAL G 411 " pdb=" CB VAL G 411 " ideal model delta sigma weight residual 112.40 88.48 23.92 1.17e+00 7.31e-01 4.18e+02 angle pdb=" N VAL E 411 " pdb=" CA VAL E 411 " pdb=" CB VAL E 411 " ideal model delta sigma weight residual 112.40 88.48 23.92 1.17e+00 7.31e-01 4.18e+02 ... (remaining 154899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.12: 63985 31.12 - 62.24: 4209 62.24 - 93.36: 184 93.36 - 124.48: 0 124.48 - 155.60: 7 Dihedral angle restraints: 68385 sinusoidal: 18525 harmonic: 49860 Sorted by residual: dihedral pdb=" C UNK L1222 " pdb=" N UNK L1222 " pdb=" CA UNK L1222 " pdb=" CB UNK L1222 " ideal model delta harmonic sigma weight residual -122.60 -159.76 37.16 0 2.50e+00 1.60e-01 2.21e+02 dihedral pdb=" C UNK H1222 " pdb=" N UNK H1222 " pdb=" CA UNK H1222 " pdb=" CB UNK H1222 " ideal model delta harmonic sigma weight residual -122.60 -159.76 37.16 0 2.50e+00 1.60e-01 2.21e+02 dihedral pdb=" C UNK N1222 " pdb=" N UNK N1222 " pdb=" CA UNK N1222 " pdb=" CB UNK N1222 " ideal model delta harmonic sigma weight residual -122.60 -159.76 37.16 0 2.50e+00 1.60e-01 2.21e+02 ... (remaining 68382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.317: 19046 0.317 - 0.634: 200 0.634 - 0.951: 16 0.951 - 1.269: 0 1.269 - 1.586: 32 Chirality restraints: 19294 Sorted by residual: chirality pdb=" CA UNK L1222 " pdb=" N UNK L1222 " pdb=" C UNK L1222 " pdb=" CB UNK L1222 " both_signs ideal model delta sigma weight residual False 2.52 0.93 1.59 2.00e-01 2.50e+01 6.29e+01 chirality pdb=" CA UNK N1222 " pdb=" N UNK N1222 " pdb=" C UNK N1222 " pdb=" CB UNK N1222 " both_signs ideal model delta sigma weight residual False 2.52 0.93 1.59 2.00e-01 2.50e+01 6.29e+01 chirality pdb=" CA UNK H1222 " pdb=" N UNK H1222 " pdb=" C UNK H1222 " pdb=" CB UNK H1222 " both_signs ideal model delta sigma weight residual False 2.52 0.93 1.59 2.00e-01 2.50e+01 6.29e+01 ... (remaining 19291 not shown) Planarity restraints: 20033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA UNK Q 835 " -0.105 2.00e-02 2.50e+03 2.07e-01 4.29e+02 pdb=" C UNK Q 835 " 0.348 2.00e-02 2.50e+03 pdb=" O UNK Q 835 " -0.193 2.00e-02 2.50e+03 pdb=" N UNK Q 836 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK M 835 " 0.105 2.00e-02 2.50e+03 2.07e-01 4.29e+02 pdb=" C UNK M 835 " -0.348 2.00e-02 2.50e+03 pdb=" O UNK M 835 " 0.193 2.00e-02 2.50e+03 pdb=" N UNK M 836 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK G 835 " -0.105 2.00e-02 2.50e+03 2.07e-01 4.29e+02 pdb=" C UNK G 835 " 0.348 2.00e-02 2.50e+03 pdb=" O UNK G 835 " -0.193 2.00e-02 2.50e+03 pdb=" N UNK G 836 " -0.050 2.00e-02 2.50e+03 ... (remaining 20030 not shown) Histogram of nonbonded interaction distances: 1.06 - 1.83: 305 1.83 - 2.59: 4516 2.59 - 3.36: 153416 3.36 - 4.13: 251640 4.13 - 4.90: 430693 Nonbonded interactions: 840570 Sorted by model distance: nonbonded pdb=" CB UNK J 808 " pdb=" C UNK J 850 " model vdw 1.058 3.670 nonbonded pdb=" CB UNK N 808 " pdb=" C UNK N 850 " model vdw 1.058 3.670 nonbonded pdb=" CB UNK L 808 " pdb=" C UNK L 850 " model vdw 1.058 3.670 nonbonded pdb=" CB UNK H 808 " pdb=" C UNK H 850 " model vdw 1.058 3.670 nonbonded pdb=" CB UNK P 808 " pdb=" C UNK P 850 " model vdw 1.058 3.670 ... (remaining 840565 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 627 or (resid 628 and (name N or name CA or nam \ e C or name O )) or resid 629 through 634 or (resid 635 and (name N or name CA o \ r name C or name O )) or resid 636 through 647 or (resid 648 and (name N or name \ CA or name C or name O )) or resid 649 through 689 or (resid 690 and (name N or \ name CA or name C or name O )) or resid 691 through 719 or (resid 720 and (name \ N or name CA or name C or name O )) or resid 721 through 765 or (resid 766 and \ (name N or name CA or name C or name O )) or resid 767 through 810 or (resid 811 \ and (name N or name CA or name C or name O )) or resid 812 through 830 or (resi \ d 831 and (name N or name CA or name C or name O )) or resid 832 through 880 or \ (resid 881 and (name N or name CA or name C or name O )) or resid 882 through 88 \ 7 or (resid 888 and (name N or name CA or name C or name O )) or resid 889 throu \ gh 894 or (resid 895 and (name N or name CA or name C or name O )) or resid 896 \ through 951 or (resid 952 and (name N or name CA or name C or name O )) or resid \ 955 through 979 or (resid 980 and (name N or name CA or name C or name O )) or \ resid 981 through 999 or (resid 1000 and (name N or name CA or name C or name O \ )) or resid 1007 through 1065 or (resid 1066 and (name N or name CA or name C or \ name O )) or resid 1067 through 1125 or (resid 1126 and (name N or name CA or n \ ame C or name O )) or resid 1127 through 1145 or (resid 1146 and (name N or name \ CA or name C or name O )) or resid 1147 through 1149 or (resid 1150 and (name N \ or name CA or name C or name O )) or resid 1151 through 1218 or (resid 1219 and \ (name N or name CA or name C or name O )) or resid 1220 through 1240 or (resid \ 1241 and (name N or name CA or name C or name O )) or resid 1242 through 1246)) selection = (chain 'C' and (resid 10 through 627 or (resid 628 and (name N or name CA or nam \ e C or name O )) or resid 629 through 634 or (resid 635 and (name N or name CA o \ r name C or name O )) or resid 636 through 647 or (resid 648 and (name N or name \ CA or name C or name O )) or resid 649 through 689 or (resid 690 and (name N or \ name CA or name C or name O )) or resid 691 through 719 or (resid 720 and (name \ N or name CA or name C or name O )) or resid 721 through 765 or (resid 766 and \ (name N or name CA or name C or name O )) or resid 767 through 810 or (resid 811 \ and (name N or name CA or name C or name O )) or resid 812 through 830 or (resi \ d 831 and (name N or name CA or name C or name O )) or resid 832 through 880 or \ (resid 881 and (name N or name CA or name C or name O )) or resid 882 through 88 \ 7 or (resid 888 and (name N or name CA or name C or name O )) or resid 889 throu \ gh 894 or (resid 895 and (name N or name CA or name C or name O )) or resid 896 \ through 951 or (resid 952 and (name N or name CA or name C or name O )) or resid \ 955 through 979 or (resid 980 and (name N or name CA or name C or name O )) or \ resid 981 through 999 or (resid 1000 and (name N or name CA or name C or name O \ )) or resid 1007 through 1065 or (resid 1066 and (name N or name CA or name C or \ name O )) or resid 1067 through 1125 or (resid 1126 and (name N or name CA or n \ ame C or name O )) or resid 1127 through 1145 or (resid 1146 and (name N or name \ CA or name C or name O )) or resid 1147 through 1149 or (resid 1150 and (name N \ or name CA or name C or name O )) or resid 1151 through 1218 or (resid 1219 and \ (name N or name CA or name C or name O )) or resid 1220 through 1240 or (resid \ 1241 and (name N or name CA or name C or name O )) or resid 1242 through 1246)) selection = (chain 'D' and (resid 10 through 627 or (resid 628 and (name N or name CA or nam \ e C or name O )) or resid 629 through 634 or (resid 635 and (name N or name CA o \ r name C or name O )) or resid 636 through 647 or (resid 648 and (name N or name \ CA or name C or name O )) or resid 649 through 689 or (resid 690 and (name N or \ name CA or name C or name O )) or resid 691 through 719 or (resid 720 and (name \ N or name CA or name C or name O )) or resid 721 through 765 or (resid 766 and \ (name N or name CA or name C or name O )) or resid 767 through 810 or (resid 811 \ and (name N or name CA or name C or name O )) or resid 812 through 830 or (resi \ d 831 and (name N or name CA or name C or name O )) or resid 832 through 880 or \ (resid 881 and (name N or name CA or name C or name O )) or resid 882 through 88 \ 7 or (resid 888 and (name N or name CA or name C or name O )) or resid 889 throu \ gh 894 or (resid 895 and (name N or name CA or name C or name O )) or resid 896 \ through 951 or (resid 952 and (name N or name CA or name C or name O )) or resid \ 955 through 979 or (resid 980 and (name N or name CA or name C or name O )) or \ resid 981 through 999 or (resid 1000 and (name N or name CA or name C or name O \ )) or resid 1007 through 1065 or (resid 1066 and (name N or name CA or name C or \ name O )) or resid 1067 through 1125 or (resid 1126 and (name N or name CA or n \ ame C or name O )) or resid 1127 through 1145 or (resid 1146 and (name N or name \ CA or name C or name O )) or resid 1147 through 1149 or (resid 1150 and (name N \ or name CA or name C or name O )) or resid 1151 through 1218 or (resid 1219 and \ (name N or name CA or name C or name O )) or resid 1220 through 1240 or (resid \ 1241 and (name N or name CA or name C or name O )) or resid 1242 through 1246)) selection = (chain 'E' and (resid 10 through 627 or (resid 628 and (name N or name CA or nam \ e C or name O )) or resid 629 through 634 or (resid 635 and (name N or name CA o \ r name C or name O )) or resid 636 through 647 or (resid 648 and (name N or name \ CA or name C or name O )) or resid 649 through 689 or (resid 690 and (name N or \ name CA or name C or name O )) or resid 691 through 719 or (resid 720 and (name \ N or name CA or name C or name O )) or resid 721 through 765 or (resid 766 and \ (name N or name CA or name C or name O )) or resid 767 through 810 or (resid 811 \ and (name N or name CA or name C or name O )) or resid 812 through 830 or (resi \ d 831 and (name N or name CA or name C or name O )) or resid 832 through 880 or \ (resid 881 and (name N or name CA or name C or name O )) or resid 882 through 88 \ 7 or (resid 888 and (name N or name CA or name C or name O )) or resid 889 throu \ gh 894 or (resid 895 and (name N or name CA or name C or name O )) or resid 896 \ through 951 or (resid 952 and (name N or name CA or name C or name O )) or resid \ 955 through 979 or (resid 980 and (name N or name CA or name C or name O )) or \ resid 981 through 999 or (resid 1000 and (name N or name CA or name C or name O \ )) or resid 1007 through 1065 or (resid 1066 and (name N or name CA or name C or \ name O )) or resid 1067 through 1125 or (resid 1126 and (name N or name CA or n \ ame C or name O )) or resid 1127 through 1145 or (resid 1146 and (name N or name \ CA or name C or name O )) or resid 1147 through 1149 or (resid 1150 and (name N \ or name CA or name C or name O )) or resid 1151 through 1218 or (resid 1219 and \ (name N or name CA or name C or name O )) or resid 1220 through 1240 or (resid \ 1241 and (name N or name CA or name C or name O )) or resid 1242 through 1246)) selection = (chain 'F' and (resid 10 through 627 or (resid 628 and (name N or name CA or nam \ e C or name O )) or resid 629 through 634 or (resid 635 and (name N or name CA o \ r name C or name O )) or resid 636 through 647 or (resid 648 and (name N or name \ CA or name C or name O )) or resid 649 through 689 or (resid 690 and (name N or \ name CA or name C or name O )) or resid 691 through 719 or (resid 720 and (name \ N or name CA or name C or name O )) or resid 721 through 765 or (resid 766 and \ (name N or name CA or name C or name O )) or resid 767 through 810 or (resid 811 \ and (name N or name CA or name C or name O )) or resid 812 through 830 or (resi \ d 831 and (name N or name CA or name C or name O )) or resid 832 through 880 or \ (resid 881 and (name N or name CA or name C or name O )) or resid 882 through 88 \ 7 or (resid 888 and (name N or name CA or name C or name O )) or resid 889 throu \ gh 894 or (resid 895 and (name N or name CA or name C or name O )) or resid 896 \ through 951 or (resid 952 and (name N or name CA or name C or name O )) or resid \ 955 through 979 or (resid 980 and (name N or name CA or name C or name O )) or \ resid 981 through 999 or (resid 1000 and (name N or name CA or name C or name O \ )) or resid 1007 through 1065 or (resid 1066 and (name N or name CA or name C or \ name O )) or resid 1067 through 1125 or (resid 1126 and (name N or name CA or n \ ame C or name O )) or resid 1127 through 1145 or (resid 1146 and (name N or name \ CA or name C or name O )) or resid 1147 through 1149 or (resid 1150 and (name N \ or name CA or name C or name O )) or resid 1151 through 1218 or (resid 1219 and \ (name N or name CA or name C or name O )) or resid 1220 through 1240 or (resid \ 1241 and (name N or name CA or name C or name O )) or resid 1242 through 1246)) selection = (chain 'G' and (resid 10 through 627 or (resid 628 and (name N or name CA or nam \ e C or name O )) or resid 629 through 634 or (resid 635 and (name N or name CA o \ r name C or name O )) or resid 636 through 647 or (resid 648 and (name N or name \ CA or name C or name O )) or resid 649 through 689 or (resid 690 and (name N or \ name CA or name C or name O )) or resid 691 through 719 or (resid 720 and (name \ N or name CA or name C or name O )) or resid 721 through 765 or (resid 766 and \ (name N or name CA or name C or name O )) or resid 767 through 810 or (resid 811 \ and (name N or name CA or name C or name O )) or resid 812 through 830 or (resi \ d 831 and (name N or name CA or name C or name O )) or resid 832 through 880 or \ (resid 881 and (name N or name CA or name C or name O )) or resid 882 through 88 \ 7 or (resid 888 and (name N or name CA or name C or name O )) or resid 889 throu \ gh 894 or (resid 895 and (name N or name CA or name C or name O )) or resid 896 \ through 951 or (resid 952 and (name N or name CA or name C or name O )) or resid \ 955 through 979 or (resid 980 and (name N or name CA or name C or name O )) or \ resid 981 through 999 or (resid 1000 and (name N or name CA or name C or name O \ )) or resid 1007 through 1065 or (resid 1066 and (name N or name CA or name C or \ name O )) or resid 1067 through 1125 or (resid 1126 and (name N or name CA or n \ ame C or name O )) or resid 1127 through 1145 or (resid 1146 and (name N or name \ CA or name C or name O )) or resid 1147 through 1149 or (resid 1150 and (name N \ or name CA or name C or name O )) or resid 1151 through 1218 or (resid 1219 and \ (name N or name CA or name C or name O )) or resid 1220 through 1240 or (resid \ 1241 and (name N or name CA or name C or name O )) or resid 1242 through 1246)) selection = (chain 'H' and (resid 10 through 627 or (resid 628 and (name N or name CA or nam \ e C or name O )) or resid 629 through 634 or (resid 635 and (name N or name CA o \ r name C or name O )) or resid 636 through 647 or (resid 648 and (name N or name \ CA or name C or name O )) or resid 649 through 689 or (resid 690 and (name N or \ name CA or name C or name O )) or resid 691 through 719 or (resid 720 and (name \ N or name CA or name C or name O )) or resid 721 through 765 or (resid 766 and \ (name N or name CA or name C or name O )) or resid 767 through 810 or (resid 811 \ and (name N or name CA or name C or name O )) or resid 812 through 830 or (resi \ d 831 and (name N or name CA or name C or name O )) or resid 832 through 880 or \ (resid 881 and (name N or name CA or name C or name O )) or resid 882 through 88 \ 7 or (resid 888 and (name N or name CA or name C or name O )) or resid 889 throu \ gh 894 or (resid 895 and (name N or name CA or name C or name O )) or resid 896 \ through 951 or (resid 952 and (name N or name CA or name C or name O )) or resid \ 955 through 979 or (resid 980 and (name N or name CA or name C or name O )) or \ resid 981 through 999 or (resid 1000 and (name N or name CA or name C or name O \ )) or resid 1007 through 1065 or (resid 1066 and (name N or name CA or name C or \ name O )) or resid 1067 through 1125 or (resid 1126 and (name N or name CA or n \ ame C or name O )) or resid 1127 through 1145 or (resid 1146 and (name N or name \ CA or name C or name O )) or resid 1147 through 1149 or (resid 1150 and (name N \ or name CA or name C or name O )) or resid 1151 through 1218 or (resid 1219 and \ (name N or name CA or name C or name O )) or resid 1220 through 1240 or (resid \ 1241 and (name N or name CA or name C or name O )) or resid 1242 through 1246)) selection = (chain 'I' and (resid 10 through 627 or (resid 628 and (name N or name CA or nam \ e C or name O )) or resid 629 through 634 or (resid 635 and (name N or name CA o \ r name C or name O )) or resid 636 through 647 or (resid 648 and (name N or name \ CA or name C or name O )) or resid 649 through 689 or (resid 690 and (name N or \ name CA or name C or name O )) or resid 691 through 719 or (resid 720 and (name \ N or name CA or name C or name O )) or resid 721 through 765 or (resid 766 and \ (name N or name CA or name C or name O )) or resid 767 through 810 or (resid 811 \ and (name N or name CA or name C or name O )) or resid 812 through 830 or (resi \ d 831 and (name N or name CA or name C or name O )) or resid 832 through 880 or \ (resid 881 and (name N or name CA or name C or name O )) or resid 882 through 88 \ 7 or (resid 888 and (name N or name CA or name C or name O )) or resid 889 throu \ gh 894 or (resid 895 and (name N or name CA or name C or name O )) or resid 896 \ through 951 or (resid 952 and (name N or name CA or name C or name O )) or resid \ 955 through 979 or (resid 980 and (name N or name CA or name C or name O )) or \ resid 981 through 999 or (resid 1000 and (name N or name CA or name C or name O \ )) or resid 1007 through 1065 or (resid 1066 and (name N or name CA or name C or \ name O )) or resid 1067 through 1125 or (resid 1126 and (name N or name CA or n \ ame C or name O )) or resid 1127 through 1145 or (resid 1146 and (name N or name \ CA or name C or name O )) or resid 1147 through 1149 or (resid 1150 and (name N \ or name CA or name C or name O )) or resid 1151 through 1218 or (resid 1219 and \ (name N or name CA or name C or name O )) or resid 1220 through 1240 or (resid \ 1241 and (name N or name CA or name C or name O )) or resid 1242 through 1246)) selection = (chain 'J' and (resid 10 through 627 or (resid 628 and (name N or name CA or nam \ e C or name O )) or resid 629 through 634 or (resid 635 and (name N or name CA o \ r name C or name O )) or resid 636 through 647 or (resid 648 and (name N or name \ CA or name C or name O )) or resid 649 through 689 or (resid 690 and (name N or \ name CA or name C or name O )) or resid 691 through 719 or (resid 720 and (name \ N or name CA or name C or name O )) or resid 721 through 765 or (resid 766 and \ (name N or name CA or name C or name O )) or resid 767 through 810 or (resid 811 \ and (name N or name CA or name C or name O )) or resid 812 through 830 or (resi \ d 831 and (name N or name CA or name C or name O )) or resid 832 through 880 or \ (resid 881 and (name N or name CA or name C or name O )) or resid 882 through 88 \ 7 or (resid 888 and (name N or name CA or name C or name O )) or resid 889 throu \ gh 894 or (resid 895 and (name N or name CA or name C or name O )) or resid 896 \ through 951 or (resid 952 and (name N or name CA or name C or name O )) or resid \ 955 through 979 or (resid 980 and (name N or name CA or name C or name O )) or \ resid 981 through 999 or (resid 1000 and (name N or name CA or name C or name O \ )) or resid 1007 through 1065 or (resid 1066 and (name N or name CA or name C or \ name O )) or resid 1067 through 1125 or (resid 1126 and (name N or name CA or n \ ame C or name O )) or resid 1127 through 1145 or (resid 1146 and (name N or name \ CA or name C or name O )) or resid 1147 through 1149 or (resid 1150 and (name N \ or name CA or name C or name O )) or resid 1151 through 1218 or (resid 1219 and \ (name N or name CA or name C or name O )) or resid 1220 through 1240 or (resid \ 1241 and (name N or name CA or name C or name O )) or resid 1242 through 1246)) selection = (chain 'K' and (resid 10 through 627 or (resid 628 and (name N or name CA or nam \ e C or name O )) or resid 629 through 634 or (resid 635 and (name N or name CA o \ r name C or name O )) or resid 636 through 647 or (resid 648 and (name N or name \ CA or name C or name O )) or resid 649 through 689 or (resid 690 and (name N or \ name CA or name C or name O )) or resid 691 through 719 or (resid 720 and (name \ N or name CA or name C or name O )) or resid 721 through 765 or (resid 766 and \ (name N or name CA or name C or name O )) or resid 767 through 810 or (resid 811 \ and (name N or name CA or name C or name O )) or resid 812 through 830 or (resi \ d 831 and (name N or name CA or name C or name O )) or resid 832 through 880 or \ (resid 881 and (name N or name CA or name C or name O )) or resid 882 through 88 \ 7 or (resid 888 and (name N or name CA or name C or name O )) or resid 889 throu \ gh 894 or (resid 895 and (name N or name CA or name C or name O )) or resid 896 \ through 951 or (resid 952 and (name N or name CA or name C or name O )) or resid \ 955 through 979 or (resid 980 and (name N or name CA or name C or name O )) or \ resid 981 through 999 or (resid 1000 and (name N or name CA or name C or name O \ )) or resid 1007 through 1065 or (resid 1066 and (name N or name CA or name C or \ name O )) or resid 1067 through 1125 or (resid 1126 and (name N or name CA or n \ ame C or name O )) or resid 1127 through 1145 or (resid 1146 and (name N or name \ CA or name C or name O )) or resid 1147 through 1149 or (resid 1150 and (name N \ or name CA or name C or name O )) or resid 1151 through 1218 or (resid 1219 and \ (name N or name CA or name C or name O )) or resid 1220 through 1240 or (resid \ 1241 and (name N or name CA or name C or name O )) or resid 1242 through 1246)) selection = (chain 'L' and (resid 10 through 627 or (resid 628 and (name N or name CA or nam \ e C or name O )) or resid 629 through 634 or (resid 635 and (name N or name CA o \ r name C or name O )) or resid 636 through 647 or (resid 648 and (name N or name \ CA or name C or name O )) or resid 649 through 689 or (resid 690 and (name N or \ name CA or name C or name O )) or resid 691 through 719 or (resid 720 and (name \ N or name CA or name C or name O )) or resid 721 through 765 or (resid 766 and \ (name N or name CA or name C or name O )) or resid 767 through 810 or (resid 811 \ and (name N or name CA or name C or name O )) or resid 812 through 830 or (resi \ d 831 and (name N or name CA or name C or name O )) or resid 832 through 880 or \ (resid 881 and (name N or name CA or name C or name O )) or resid 882 through 88 \ 7 or (resid 888 and (name N or name CA or name C or name O )) or resid 889 throu \ gh 894 or (resid 895 and (name N or name CA or name C or name O )) or resid 896 \ through 951 or (resid 952 and (name N or name CA or name C or name O )) or resid \ 955 through 979 or (resid 980 and (name N or name CA or name C or name O )) or \ resid 981 through 999 or (resid 1000 and (name N or name CA or name C or name O \ )) or resid 1007 through 1065 or (resid 1066 and (name N or name CA or name C or \ name O )) or resid 1067 through 1125 or (resid 1126 and (name N or name CA or n \ ame C or name O )) or resid 1127 through 1145 or (resid 1146 and (name N or name \ CA or name C or name O )) or resid 1147 through 1149 or (resid 1150 and (name N \ or name CA or name C or name O )) or resid 1151 through 1218 or (resid 1219 and \ (name N or name CA or name C or name O )) or resid 1220 through 1240 or (resid \ 1241 and (name N or name CA or name C or name O )) or resid 1242 through 1246)) selection = (chain 'M' and (resid 10 through 627 or (resid 628 and (name N or name CA or nam \ e C or name O )) or resid 629 through 634 or (resid 635 and (name N or name CA o \ r name C or name O )) or resid 636 through 647 or (resid 648 and (name N or name \ CA or name C or name O )) or resid 649 through 689 or (resid 690 and (name N or \ name CA or name C or name O )) or resid 691 through 719 or (resid 720 and (name \ N or name CA or name C or name O )) or resid 721 through 765 or (resid 766 and \ (name N or name CA or name C or name O )) or resid 767 through 810 or (resid 811 \ and (name N or name CA or name C or name O )) or resid 812 through 830 or (resi \ d 831 and (name N or name CA or name C or name O )) or resid 832 through 880 or \ (resid 881 and (name N or name CA or name C or name O )) or resid 882 through 88 \ 7 or (resid 888 and (name N or name CA or name C or name O )) or resid 889 throu \ gh 894 or (resid 895 and (name N or name CA or name C or name O )) or resid 896 \ through 951 or (resid 952 and (name N or name CA or name C or name O )) or resid \ 955 through 979 or (resid 980 and (name N or name CA or name C or name O )) or \ resid 981 through 999 or (resid 1000 and (name N or name CA or name C or name O \ )) or resid 1007 through 1065 or (resid 1066 and (name N or name CA or name C or \ name O )) or resid 1067 through 1125 or (resid 1126 and (name N or name CA or n \ ame C or name O )) or resid 1127 through 1145 or (resid 1146 and (name N or name \ CA or name C or name O )) or resid 1147 through 1149 or (resid 1150 and (name N \ or name CA or name C or name O )) or resid 1151 through 1218 or (resid 1219 and \ (name N or name CA or name C or name O )) or resid 1220 through 1240 or (resid \ 1241 and (name N or name CA or name C or name O )) or resid 1242 through 1246)) selection = (chain 'N' and (resid 10 through 627 or (resid 628 and (name N or name CA or nam \ e C or name O )) or resid 629 through 634 or (resid 635 and (name N or name CA o \ r name C or name O )) or resid 636 through 647 or (resid 648 and (name N or name \ CA or name C or name O )) or resid 649 through 689 or (resid 690 and (name N or \ name CA or name C or name O )) or resid 691 through 719 or (resid 720 and (name \ N or name CA or name C or name O )) or resid 721 through 765 or (resid 766 and \ (name N or name CA or name C or name O )) or resid 767 through 810 or (resid 811 \ and (name N or name CA or name C or name O )) or resid 812 through 830 or (resi \ d 831 and (name N or name CA or name C or name O )) or resid 832 through 880 or \ (resid 881 and (name N or name CA or name C or name O )) or resid 882 through 88 \ 7 or (resid 888 and (name N or name CA or name C or name O )) or resid 889 throu \ gh 894 or (resid 895 and (name N or name CA or name C or name O )) or resid 896 \ through 951 or (resid 952 and (name N or name CA or name C or name O )) or resid \ 955 through 979 or (resid 980 and (name N or name CA or name C or name O )) or \ resid 981 through 999 or (resid 1000 and (name N or name CA or name C or name O \ )) or resid 1007 through 1065 or (resid 1066 and (name N or name CA or name C or \ name O )) or resid 1067 through 1125 or (resid 1126 and (name N or name CA or n \ ame C or name O )) or resid 1127 through 1145 or (resid 1146 and (name N or name \ CA or name C or name O )) or resid 1147 through 1149 or (resid 1150 and (name N \ or name CA or name C or name O )) or resid 1151 through 1218 or (resid 1219 and \ (name N or name CA or name C or name O )) or resid 1220 through 1240 or (resid \ 1241 and (name N or name CA or name C or name O )) or resid 1242 through 1246)) selection = (chain 'O' and (resid 10 through 627 or (resid 628 and (name N or name CA or nam \ e C or name O )) or resid 629 through 634 or (resid 635 and (name N or name CA o \ r name C or name O )) or resid 636 through 647 or (resid 648 and (name N or name \ CA or name C or name O )) or resid 649 through 689 or (resid 690 and (name N or \ name CA or name C or name O )) or resid 691 through 719 or (resid 720 and (name \ N or name CA or name C or name O )) or resid 721 through 765 or (resid 766 and \ (name N or name CA or name C or name O )) or resid 767 through 810 or (resid 811 \ and (name N or name CA or name C or name O )) or resid 812 through 830 or (resi \ d 831 and (name N or name CA or name C or name O )) or resid 832 through 880 or \ (resid 881 and (name N or name CA or name C or name O )) or resid 882 through 88 \ 7 or (resid 888 and (name N or name CA or name C or name O )) or resid 889 throu \ gh 894 or (resid 895 and (name N or name CA or name C or name O )) or resid 896 \ through 951 or (resid 952 and (name N or name CA or name C or name O )) or resid \ 955 through 979 or (resid 980 and (name N or name CA or name C or name O )) or \ resid 981 through 999 or (resid 1000 and (name N or name CA or name C or name O \ )) or resid 1007 through 1065 or (resid 1066 and (name N or name CA or name C or \ name O )) or resid 1067 through 1125 or (resid 1126 and (name N or name CA or n \ ame C or name O )) or resid 1127 through 1145 or (resid 1146 and (name N or name \ CA or name C or name O )) or resid 1147 through 1149 or (resid 1150 and (name N \ or name CA or name C or name O )) or resid 1151 through 1218 or (resid 1219 and \ (name N or name CA or name C or name O )) or resid 1220 through 1240 or (resid \ 1241 and (name N or name CA or name C or name O )) or resid 1242 through 1246)) selection = (chain 'P' and (resid 10 through 627 or (resid 628 and (name N or name CA or nam \ e C or name O )) or resid 629 through 634 or (resid 635 and (name N or name CA o \ r name C or name O )) or resid 636 through 647 or (resid 648 and (name N or name \ CA or name C or name O )) or resid 649 through 689 or (resid 690 and (name N or \ name CA or name C or name O )) or resid 691 through 719 or (resid 720 and (name \ N or name CA or name C or name O )) or resid 721 through 765 or (resid 766 and \ (name N or name CA or name C or name O )) or resid 767 through 810 or (resid 811 \ and (name N or name CA or name C or name O )) or resid 812 through 830 or (resi \ d 831 and (name N or name CA or name C or name O )) or resid 832 through 880 or \ (resid 881 and (name N or name CA or name C or name O )) or resid 882 through 88 \ 7 or (resid 888 and (name N or name CA or name C or name O )) or resid 889 throu \ gh 894 or (resid 895 and (name N or name CA or name C or name O )) or resid 896 \ through 951 or (resid 952 and (name N or name CA or name C or name O )) or resid \ 955 through 979 or (resid 980 and (name N or name CA or name C or name O )) or \ resid 981 through 999 or (resid 1000 and (name N or name CA or name C or name O \ )) or resid 1007 through 1065 or (resid 1066 and (name N or name CA or name C or \ name O )) or resid 1067 through 1125 or (resid 1126 and (name N or name CA or n \ ame C or name O )) or resid 1127 through 1145 or (resid 1146 and (name N or name \ CA or name C or name O )) or resid 1147 through 1149 or (resid 1150 and (name N \ or name CA or name C or name O )) or resid 1151 through 1218 or (resid 1219 and \ (name N or name CA or name C or name O )) or resid 1220 through 1240 or (resid \ 1241 and (name N or name CA or name C or name O )) or resid 1242 through 1246)) selection = (chain 'Q' and (resid 10 through 625 or (resid 626 through 627 and (name N or na \ me CA or name C or name O )) or resid 628 through 632 or (resid 633 through 634 \ and (name N or name CA or name C or name O )) or resid 635 through 645 or (resid \ 646 through 647 and (name N or name CA or name C or name O )) or resid 648 thro \ ugh 686 or (resid 687 through 689 and (name N or name CA or name C or name O )) \ or resid 690 through 717 or (resid 718 through 719 and (name N or name CA or nam \ e C or name O )) or resid 720 through 763 or (resid 764 through 765 and (name N \ or name CA or name C or name O )) or resid 766 through 808 or (resid 809 through \ 810 and (name N or name CA or name C or name O )) or resid 811 through 828 or ( \ resid 829 through 830 and (name N or name CA or name C or name O )) or resid 831 \ through 878 or (resid 879 through 880 and (name N or name CA or name C or name \ O )) or resid 881 through 885 or (resid 886 through 887 and (name N or name CA o \ r name C or name O )) or resid 888 through 892 or (resid 893 through 894 and (na \ me N or name CA or name C or name O )) or resid 895 through 949 or (resid 950 th \ rough 951 and (name N or name CA or name C or name O )) or resid 952 through 977 \ or (resid 978 through 979 and (name N or name CA or name C or name O )) or resi \ d 980 through 997 or (resid 998 through 999 and (name N or name CA or name C or \ name O )) or resid 1000 through 1063 or (resid 1064 through 1065 and (name N or \ name CA or name C or name O )) or resid 1066 through 1123 or (resid 1124 through \ 1125 and (name N or name CA or name C or name O )) or resid 1126 through 1143 o \ r (resid 1144 through 1145 and (name N or name CA or name C or name O )) or resi \ d 1146 through 1147 or (resid 1148 through 1149 and (name N or name CA or name C \ or name O )) or resid 1150 through 1216 or (resid 1217 through 1218 and (name N \ or name CA or name C or name O )) or resid 1219 through 1238 or (resid 1239 thr \ ough 1240 and (name N or name CA or name C or name O )) or resid 1241 through 12 \ 45)) } 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 11.480 Check model and map are aligned: 1.220 Set scattering table: 0.750 Process input model: 201.470 Find NCS groups from input model: 8.530 Set up NCS constraints: 0.340 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 227.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 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 : 0.022 1.546 113878 Z= 1.355 Angle : 1.961 60.776 154904 Z= 1.163 Chirality : 0.119 1.586 19294 Planarity : 0.013 0.207 20033 Dihedral : 19.470 155.602 35199 Min Nonbonded Distance : 1.058 Molprobity Statistics. All-atom Clashscore : 81.48 Ramachandran Plot: Outliers : 0.95 % Allowed : 10.49 % Favored : 88.56 % Rotamer: Outliers : 27.30 % Allowed : 16.90 % Favored : 55.80 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.59 % 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: -4.09 (0.08), residues: 8464 helix: -2.89 (0.06), residues: 4304 sheet: -2.97 (0.23), residues: 480 loop : -2.26 (0.10), residues: 3680 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16928 Ramachandran restraints generated. 8464 Oldfield, 0 Emsley, 8464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16928 Ramachandran restraints generated. 8464 Oldfield, 0 Emsley, 8464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4656 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2184 poor density : 2472 time to evaluate : 7.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2184 outliers final: 710 residues processed: 3944 average time/residue: 0.9442 time to fit residues: 6393.7259 Evaluate side-chains 2066 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 710 poor density : 1356 time to evaluate : 7.279 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 710 outliers final: 80 residues processed: 710 average time/residue: 0.8881 time to fit residues: 1120.7251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 8.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 HIS A 287 HIS ** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 HIS C 287 HIS C 414 GLN ** C 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN ** D 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 HIS D 287 HIS ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 GLN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 HIS E 287 HIS E 414 GLN ** E 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 ASN ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 HIS F 287 HIS ** F 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 GLN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 GLN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 HIS G 287 HIS G 414 GLN ** G 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 239 ASN ** H 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 282 HIS ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** I 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 GLN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 282 HIS I 287 HIS I 414 GLN ** I 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 239 ASN ** J 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 282 HIS ** J 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 GLN ** K 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 GLN ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 282 HIS K 287 HIS K 414 GLN ** K 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 239 ASN ** L 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 282 HIS ** L 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN ** M 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 129 GLN ** M 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 282 HIS M 287 HIS M 414 GLN ** M 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 239 ASN ** N 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 282 HIS ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 109 GLN ** O 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 129 GLN ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 282 HIS O 287 HIS O 414 GLN ** O 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 239 ASN ** P 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 282 HIS ** P 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 109 GLN ** Q 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 129 GLN ** Q 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 282 HIS Q 287 HIS Q 414 GLN ** Q 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 1.0238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.040 0.288 113878 Z= 2.416 Angle : 3.031 33.496 154904 Z= 1.468 Chirality : 0.121 0.567 19294 Planarity : 0.020 0.189 20033 Dihedral : 13.305 173.756 17151 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 92.82 Ramachandran Plot: Outliers : 3.67 % Allowed : 22.48 % Favored : 73.84 % Rotamer: Outliers : 25.71 % Allowed : 23.09 % Favored : 51.20 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 3.66 % 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: -6.34 (0.07), residues: 8464 helix: -4.09 (0.05), residues: 4784 sheet: -4.19 (0.17), residues: 528 loop : -4.11 (0.10), residues: 3152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16928 Ramachandran restraints generated. 8464 Oldfield, 0 Emsley, 8464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16928 Ramachandran restraints generated. 8464 Oldfield, 0 Emsley, 8464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3191 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2057 poor density : 1134 time to evaluate : 7.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2057 outliers final: 1134 residues processed: 2896 average time/residue: 0.8854 time to fit residues: 4526.4941 Evaluate side-chains 2077 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1134 poor density : 943 time to evaluate : 7.362 Switching outliers to nearest non-outliers outliers start: 1134 outliers final: 8 residues processed: 1134 average time/residue: 0.7594 time to fit residues: 1627.4321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 8.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 HIS ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 HIS ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS ** C 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 HIS ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN ** D 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 HIS E 69 GLN ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 HIS ** E 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 GLN ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 HIS ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 GLN ** F 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 HIS G 69 GLN ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS ** G 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 GLN ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 HIS H 343 HIS ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN ** H 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 47 HIS I 69 GLN I 74 GLN ** I 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 343 HIS ** I 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 287 HIS J 343 HIS ** J 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 GLN ** J 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 HIS K 69 GLN K 74 GLN ** K 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 343 HIS ** K 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 287 HIS L 343 HIS ** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 465 GLN ** L 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 HIS M 69 GLN ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 343 HIS ** M 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 287 HIS N 343 HIS ** N 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 465 GLN ** N 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 47 HIS O 69 GLN ** O 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 343 HIS ** O 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 69 GLN ** P 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 287 HIS P 343 HIS ** P 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 465 GLN ** P 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS Q 69 GLN Q 74 GLN ** Q 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 343 HIS ** Q 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 1.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.039 0.291 113878 Z= 2.387 Angle : 2.866 32.189 154904 Z= 1.380 Chirality : 0.113 0.646 19294 Planarity : 0.018 0.222 20033 Dihedral : 13.359 171.389 17151 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 96.35 Ramachandran Plot: Outliers : 2.74 % Allowed : 30.48 % Favored : 66.78 % Rotamer: Outliers : 24.75 % Allowed : 25.79 % Favored : 49.46 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 4.00 % Twisted General : 4.04 % 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: -6.95 (0.06), residues: 8464 helix: -4.35 (0.04), residues: 4576 sheet: -4.62 (0.15), residues: 528 loop : -4.82 (0.09), residues: 3360 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16928 Ramachandran restraints generated. 8464 Oldfield, 0 Emsley, 8464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16928 Ramachandran restraints generated. 8464 Oldfield, 0 Emsley, 8464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2808 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1980 poor density : 828 time to evaluate : 7.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1980 outliers final: 1190 residues processed: 2607 average time/residue: 0.8736 time to fit residues: 4036.3102 Evaluate side-chains 1954 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1190 poor density : 764 time to evaluate : 7.343 Switching outliers to nearest non-outliers outliers start: 1190 outliers final: 14 residues processed: 1190 average time/residue: 0.7876 time to fit residues: 1753.4925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 8.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 HIS C 69 GLN C 74 GLN C 124 ASN ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 578 HIS E 74 GLN E 124 ASN ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 578 HIS G 74 GLN G 124 ASN G 136 GLN ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 578 HIS I 124 ASN ** I 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 578 HIS K 124 ASN ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 578 HIS M 74 GLN M 124 ASN ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 578 HIS O 74 GLN O 124 ASN ** O 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 578 HIS Q 124 ASN Q 136 GLN ** Q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 1.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.039 0.300 113878 Z= 2.406 Angle : 2.883 34.744 154904 Z= 1.384 Chirality : 0.112 0.596 19294 Planarity : 0.018 0.204 20033 Dihedral : 13.844 175.131 17151 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 99.66 Ramachandran Plot: Outliers : 2.46 % Allowed : 36.44 % Favored : 61.11 % Rotamer: Outliers : 23.14 % Allowed : 29.99 % Favored : 46.88 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 6.00 % Twisted General : 4.66 % 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: -7.34 (0.06), residues: 8464 helix: -4.57 (0.04), residues: 4704 sheet: -4.90 (0.14), residues: 528 loop : -5.11 (0.09), residues: 3232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16928 Ramachandran restraints generated. 8464 Oldfield, 0 Emsley, 8464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16928 Ramachandran restraints generated. 8464 Oldfield, 0 Emsley, 8464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2593 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1851 poor density : 742 time to evaluate : 7.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1851 outliers final: 1091 residues processed: 2434 average time/residue: 0.9247 time to fit residues: 3934.6574 Evaluate side-chains 1869 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1091 poor density : 778 time to evaluate : 7.392 Switching outliers to nearest non-outliers outliers start: 1091 outliers final: 32 residues processed: 1091 average time/residue: 0.8188 time to fit residues: 1661.3217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 8.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN ** H 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN ** J 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 582 GLN ** O 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 1.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.040 0.296 113878 Z= 2.422 Angle : 2.840 35.087 154904 Z= 1.371 Chirality : 0.112 0.601 19294 Planarity : 0.017 0.192 20033 Dihedral : 14.012 167.140 17151 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 99.59 Ramachandran Plot: Outliers : 2.08 % Allowed : 38.23 % Favored : 59.69 % Rotamer: Outliers : 18.69 % Allowed : 33.89 % Favored : 47.42 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 6.00 % Twisted General : 5.23 % 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: -7.41 (0.06), residues: 8464 helix: -4.65 (0.04), residues: 4528 sheet: -5.17 (0.12), residues: 528 loop : -5.12 (0.09), residues: 3408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16928 Ramachandran restraints generated. 8464 Oldfield, 0 Emsley, 8464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16928 Ramachandran restraints generated. 8464 Oldfield, 0 Emsley, 8464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2251 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1495 poor density : 756 time to evaluate : 7.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1495 outliers final: 949 residues processed: 2096 average time/residue: 0.9099 time to fit residues: 3349.7433 Evaluate side-chains 1679 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 949 poor density : 730 time to evaluate : 7.380 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 949 outliers final: 50 residues processed: 949 average time/residue: 0.8135 time to fit residues: 1465.0104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 8.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 136 GLN ** O 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 1.5860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.040 0.297 113878 Z= 2.421 Angle : 2.846 34.329 154904 Z= 1.372 Chirality : 0.114 0.606 19294 Planarity : 0.017 0.170 20033 Dihedral : 14.251 168.037 17151 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 98.61 Ramachandran Plot: Outliers : 1.68 % Allowed : 39.28 % Favored : 59.04 % Rotamer: Outliers : 18.40 % Allowed : 36.67 % Favored : 44.92 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 8.00 % Twisted General : 5.31 % 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: -7.46 (0.06), residues: 8464 helix: -4.72 (0.04), residues: 4576 sheet: -5.34 (0.11), residues: 528 loop : -5.06 (0.09), residues: 3360 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16928 Ramachandran restraints generated. 8464 Oldfield, 0 Emsley, 8464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16928 Ramachandran restraints generated. 8464 Oldfield, 0 Emsley, 8464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2190 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1472 poor density : 718 time to evaluate : 7.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1472 outliers final: 941 residues processed: 2024 average time/residue: 0.9519 time to fit residues: 3404.1354 Evaluate side-chains 1660 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 941 poor density : 719 time to evaluate : 7.395 Switching outliers to nearest non-outliers outliers start: 941 outliers final: 43 residues processed: 941 average time/residue: 0.8068 time to fit residues: 1416.5392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 7.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 GLN ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** I 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 GLN ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 582 GLN M 109 GLN ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 109 GLN ** O 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 1.6295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.040 0.293 113878 Z= 2.428 Angle : 2.860 34.766 154904 Z= 1.379 Chirality : 0.116 0.606 19294 Planarity : 0.017 0.176 20033 Dihedral : 14.332 168.391 17151 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 98.55 Ramachandran Plot: Outliers : 1.83 % Allowed : 39.95 % Favored : 58.22 % Rotamer: Outliers : 13.49 % Allowed : 39.17 % Favored : 47.34 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 6.00 % Twisted General : 5.42 % 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: -7.50 (0.06), residues: 8464 helix: -4.80 (0.03), residues: 4784 sheet: -5.36 (0.11), residues: 528 loop : -4.89 (0.10), residues: 3152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16928 Ramachandran restraints generated. 8464 Oldfield, 0 Emsley, 8464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16928 Ramachandran restraints generated. 8464 Oldfield, 0 Emsley, 8464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1772 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1079 poor density : 693 time to evaluate : 6.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1079 outliers final: 651 residues processed: 1672 average time/residue: 0.9125 time to fit residues: 2718.2792 Evaluate side-chains 1325 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 651 poor density : 674 time to evaluate : 7.396 Switching outliers to nearest non-outliers outliers start: 651 outliers final: 42 residues processed: 651 average time/residue: 0.8391 time to fit residues: 1030.0660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 7.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 GLN ** C 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 GLN ** G 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 225 GLN ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 225 GLN ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 225 GLN ** M 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 1.6639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.040 0.295 113878 Z= 2.427 Angle : 2.872 35.061 154904 Z= 1.381 Chirality : 0.116 0.597 19294 Planarity : 0.017 0.162 20033 Dihedral : 14.339 167.746 17151 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 98.95 Ramachandran Plot: Outliers : 1.97 % Allowed : 39.33 % Favored : 58.70 % Rotamer: Outliers : 9.56 % Allowed : 41.84 % Favored : 48.60 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 8.00 % Twisted General : 5.37 % 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: -7.65 (0.06), residues: 8464 helix: -4.83 (0.03), residues: 4656 sheet: -5.41 (0.11), residues: 512 loop : -5.20 (0.09), residues: 3296 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16928 Ramachandran restraints generated. 8464 Oldfield, 0 Emsley, 8464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16928 Ramachandran restraints generated. 8464 Oldfield, 0 Emsley, 8464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1443 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 765 poor density : 678 time to evaluate : 7.398 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 outliers start: 765 outliers final: 476 residues processed: 1344 average time/residue: 0.9100 time to fit residues: 2190.0254 Evaluate side-chains 1116 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 476 poor density : 640 time to evaluate : 7.322 Switching outliers to nearest non-outliers outliers start: 476 outliers final: 46 residues processed: 476 average time/residue: 0.8021 time to fit residues: 724.7284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 7.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 HIS ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 473 HIS ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 473 HIS ** G 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 473 HIS ** I 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 473 HIS ** K 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 473 HIS ** M 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 473 HIS ** O 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 225 GLN ** Q 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 473 HIS ** Q 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 1.7032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.040 0.292 113878 Z= 2.429 Angle : 2.889 34.668 154904 Z= 1.391 Chirality : 0.117 0.659 19294 Planarity : 0.017 0.221 20033 Dihedral : 14.424 167.416 17151 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 99.61 Ramachandran Plot: Outliers : 1.93 % Allowed : 39.92 % Favored : 58.15 % Rotamer: Outliers : 8.05 % Allowed : 43.14 % Favored : 48.81 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 6.00 % Twisted General : 5.80 % 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: -7.60 (0.06), residues: 8464 helix: -4.81 (0.03), residues: 4736 sheet: -5.44 (0.10), residues: 512 loop : -5.10 (0.09), residues: 3216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16928 Ramachandran restraints generated. 8464 Oldfield, 0 Emsley, 8464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16928 Ramachandran restraints generated. 8464 Oldfield, 0 Emsley, 8464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1336 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 644 poor density : 692 time to evaluate : 7.649 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 outliers start: 644 outliers final: 402 residues processed: 1266 average time/residue: 0.8964 time to fit residues: 2009.5774 Evaluate side-chains 1076 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 402 poor density : 674 time to evaluate : 7.380 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 402 outliers final: 49 residues processed: 402 average time/residue: 0.8225 time to fit residues: 630.7502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 8.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 GLN ** N 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 1.7342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.040 0.294 113878 Z= 2.432 Angle : 2.889 36.269 154904 Z= 1.392 Chirality : 0.118 0.649 19294 Planarity : 0.017 0.176 20033 Dihedral : 14.434 169.307 17151 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 100.98 Ramachandran Plot: Outliers : 1.90 % Allowed : 40.02 % Favored : 58.08 % Rotamer: Outliers : 4.24 % Allowed : 44.52 % Favored : 51.24 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 8.00 % Twisted General : 5.66 % 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: -7.70 (0.05), residues: 8464 helix: -4.86 (0.03), residues: 4832 sheet: -5.49 (0.10), residues: 512 loop : -5.17 (0.09), residues: 3120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16928 Ramachandran restraints generated. 8464 Oldfield, 0 Emsley, 8464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16928 Ramachandran restraints generated. 8464 Oldfield, 0 Emsley, 8464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 686 time to evaluate : 7.371 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 outliers start: 339 outliers final: 232 residues processed: 956 average time/residue: 0.9120 time to fit residues: 1539.1407 Evaluate side-chains 891 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 659 time to evaluate : 7.342 Switching outliers to nearest non-outliers outliers start: 232 outliers final: 49 residues processed: 232 average time/residue: 0.8388 time to fit residues: 363.9907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 7.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.123135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.088957 restraints weight = 341327.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.089607 restraints weight = 270686.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.089561 restraints weight = 222725.122| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 1.7715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.040 0.304 113878 Z= 2.430 Angle : 2.889 36.289 154904 Z= 1.393 Chirality : 0.117 0.679 19294 Planarity : 0.017 0.178 20033 Dihedral : 14.476 168.944 17151 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 99.40 Ramachandran Plot: Outliers : 1.91 % Allowed : 39.87 % Favored : 58.21 % Rotamer: Outliers : 4.20 % Allowed : 45.27 % Favored : 50.52 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 8.00 % Twisted General : 6.13 % 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: -7.71 (0.05), residues: 8464 helix: -4.86 (0.03), residues: 4768 sheet: -5.51 (0.10), residues: 512 loop : -5.22 (0.09), residues: 3184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 69406.44 seconds wall clock time: 1188 minutes 49.46 seconds (71329.46 seconds total)