Starting phenix.real_space_refine on Sun Feb 18 01:34:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rey_4860/02_2024/6rey_4860_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rey_4860/02_2024/6rey_4860.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rey_4860/02_2024/6rey_4860_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rey_4860/02_2024/6rey_4860_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rey_4860/02_2024/6rey_4860_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rey_4860/02_2024/6rey_4860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rey_4860/02_2024/6rey_4860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rey_4860/02_2024/6rey_4860_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rey_4860/02_2024/6rey_4860_neut_updated.pdb" } resolution = 3.0 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= 0.017 sd= 1.004 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 28 5.49 5 S 442 5.16 5 C 45480 2.51 5 N 12416 2.21 5 O 12356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 88": "NH1" <-> "NH2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "D ARG 125": "NH1" <-> "NH2" Residue "D ARG 212": "NH1" <-> "NH2" Residue "E ARG 5": "NH1" <-> "NH2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "I ARG 89": "NH1" <-> "NH2" Residue "J ARG 25": "NH1" <-> "NH2" Residue "J ARG 69": "NH1" <-> "NH2" Residue "J ARG 79": "NH1" <-> "NH2" Residue "K ARG 153": "NH1" <-> "NH2" Residue "L ARG 107": "NH1" <-> "NH2" Residue "L ARG 186": "NH1" <-> "NH2" Residue "M ARG 99": "NH1" <-> "NH2" Residue "M ARG 194": "NH1" <-> "NH2" Residue "N ARG 100": "NH1" <-> "NH2" Residue "O ARG 88": "NH1" <-> "NH2" Residue "P ARG 90": "NH1" <-> "NH2" Residue "R ARG 125": "NH1" <-> "NH2" Residue "R ARG 212": "NH1" <-> "NH2" Residue "S ARG 5": "NH1" <-> "NH2" Residue "S ARG 53": "NH1" <-> "NH2" Residue "T ARG 101": "NH1" <-> "NH2" Residue "W ARG 89": "NH1" <-> "NH2" Residue "X ARG 25": "NH1" <-> "NH2" Residue "X ARG 69": "NH1" <-> "NH2" Residue "X ARG 79": "NH1" <-> "NH2" Residue "Y ARG 153": "NH1" <-> "NH2" Residue "Z ARG 107": "NH1" <-> "NH2" Residue "Z ARG 186": "NH1" <-> "NH2" Residue "a ARG 99": "NH1" <-> "NH2" Residue "a ARG 194": "NH1" <-> "NH2" Residue "b ARG 100": "NH1" <-> "NH2" Residue "c ARG 285": "NH1" <-> "NH2" Residue "c ARG 359": "NH1" <-> "NH2" Residue "c ARG 685": "NH1" <-> "NH2" Residue "c ARG 807": "NH1" <-> "NH2" Residue "c ARG 861": "NH1" <-> "NH2" Residue "c ARG 865": "NH1" <-> "NH2" Residue "c ARG 943": "NH1" <-> "NH2" Residue "c ARG 1085": "NH1" <-> "NH2" Residue "c ARG 1299": "NH1" <-> "NH2" Residue "c ARG 1350": "NH1" <-> "NH2" Residue "c ARG 1478": "NH1" <-> "NH2" Residue "c ARG 1702": "NH1" <-> "NH2" Residue "d ARG 285": "NH1" <-> "NH2" Residue "d ARG 359": "NH1" <-> "NH2" Residue "d ARG 685": "NH1" <-> "NH2" Residue "d ARG 807": "NH1" <-> "NH2" Residue "d ARG 861": "NH1" <-> "NH2" Residue "d ARG 865": "NH1" <-> "NH2" Residue "d ARG 943": "NH1" <-> "NH2" Residue "d ARG 1085": "NH1" <-> "NH2" Residue "d ARG 1299": "NH1" <-> "NH2" Residue "d ARG 1350": "NH1" <-> "NH2" Residue "d ARG 1478": "NH1" <-> "NH2" Residue "d ARG 1702": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 70722 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1670 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 8, 'TRANS': 225} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 111 Chain: "B" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1580 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 9, 'TRANS': 204} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 14, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1424 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 3, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 6, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 16, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 126 Chain: "D" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1508 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "E" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1629 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 77 Chain: "F" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1745 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 9, 'TRANS': 226} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 10, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 94 Chain: "G" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1767 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 236} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'GLU:plan': 13, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 84 Chain: "H" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1441 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 191} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "I" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1591 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 9, 'TRANS': 211} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "J" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1531 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 48 Chain: "K" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1507 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "L" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1503 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 38 Chain: "M" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1573 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "N" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1549 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 7, 'TRANS': 198} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 40 Chain: "O" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1670 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 8, 'TRANS': 225} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 111 Chain: "P" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1580 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 9, 'TRANS': 204} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 14, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 76 Chain: "Q" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1424 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 3, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 6, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 16, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 126 Chain: "R" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1508 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "S" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1629 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 77 Chain: "T" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1745 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 9, 'TRANS': 226} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 10, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 94 Chain: "U" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1767 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 236} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'GLU:plan': 13, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 84 Chain: "V" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1441 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 191} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "W" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1591 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 9, 'TRANS': 211} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "X" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1531 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 48 Chain: "Y" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1507 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "Z" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1503 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 38 Chain: "a" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1573 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "b" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1549 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 7, 'TRANS': 198} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 40 Chain: "c" Number of atoms: 13263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1773, 13263 Classifications: {'peptide': 1773} Incomplete info: {'truncation_to_alanine': 346} Link IDs: {'PTRANS': 92, 'TRANS': 1680} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1097 Unresolved non-hydrogen angles: 1377 Unresolved non-hydrogen dihedrals: 845 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 4, 'ASN:plan1': 20, 'TRP:plan': 2, 'ASP:plan': 67, 'PHE:plan': 2, 'GLU:plan': 79, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 756 Chain: "d" Number of atoms: 13263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1773, 13263 Classifications: {'peptide': 1773} Incomplete info: {'truncation_to_alanine': 346} Link IDs: {'PTRANS': 92, 'TRANS': 1680} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1097 Unresolved non-hydrogen angles: 1377 Unresolved non-hydrogen dihedrals: 845 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 4, 'ASN:plan1': 20, 'TRP:plan': 2, 'ASP:plan': 67, 'PHE:plan': 2, 'GLU:plan': 79, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 756 Chain: "c" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'IHP': 1, 'K0W': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'IHP': 1, 'K0W': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 28.54, per 1000 atoms: 0.40 Number of scatterers: 70722 At special positions: 0 Unit cell: (133.65, 289.17, 140.13, 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 442 16.00 P 28 15.00 O 12356 8.00 N 12416 7.00 C 45480 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.75 Conformation dependent library (CDL) restraints added in 10.6 seconds 18956 Ramachandran restraints generated. 9478 Oldfield, 0 Emsley, 9478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17884 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 338 helices and 74 sheets defined 41.9% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 13.03 Creating SS restraints... Processing helix chain 'A' and resid 23 through 34 removed outlier: 3.598A pdb=" N LYS A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 105 removed outlier: 3.612A pdb=" N LYS A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.876A pdb=" N VAL A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 185 removed outlier: 3.533A pdb=" N PHE A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 182 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 206 removed outlier: 3.565A pdb=" N VAL A 195 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE A 199 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 200 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 202 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 204 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL A 205 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A 206 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 240 removed outlier: 3.594A pdb=" N ALA A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N HIS A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 29 removed outlier: 3.553A pdb=" N ALA B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 100 removed outlier: 3.630A pdb=" N ARG B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL B 99 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 122 removed outlier: 3.530A pdb=" N ARG B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 175 removed outlier: 3.567A pdb=" N LYS B 175 " --> pdb=" O THR B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 195 removed outlier: 3.781A pdb=" N HIS B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 228 removed outlier: 3.916A pdb=" N ASP B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 101 removed outlier: 3.616A pdb=" N ASN C 88 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 92 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 117 removed outlier: 3.599A pdb=" N LEU C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 177 removed outlier: 3.757A pdb=" N MET C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 196 removed outlier: 3.554A pdb=" N ILE C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 245 removed outlier: 3.659A pdb=" N LEU C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE C 237 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA C 245 " --> pdb=" O GLU C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 26 removed outlier: 3.642A pdb=" N GLU D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA D 25 " --> pdb=" O TYR D 21 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 20 through 26' Processing helix chain 'D' and resid 77 through 97 removed outlier: 3.621A pdb=" N ARG D 81 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL D 89 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN D 92 " --> pdb=" O ARG D 88 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG D 95 " --> pdb=" O CYS D 91 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 114 Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.680A pdb=" N LYS D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'D' and resid 183 through 189 removed outlier: 3.703A pdb=" N THR D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 195 Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.828A pdb=" N LYS D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL D 229 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 29 removed outlier: 4.608A pdb=" N ALA E 27 " --> pdb=" O GLN E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 63 No H-bonds generated for 'chain 'E' and resid 61 through 63' Processing helix chain 'E' and resid 86 through 103 removed outlier: 3.891A pdb=" N LYS E 91 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 119 removed outlier: 4.385A pdb=" N LEU E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 184 removed outlier: 6.191A pdb=" N SER E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 205 removed outlier: 3.771A pdb=" N LYS E 196 " --> pdb=" O LYS E 192 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE E 201 " --> pdb=" O SER E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 238 removed outlier: 3.583A pdb=" N GLU E 235 " --> pdb=" O LYS E 231 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL E 237 " --> pdb=" O GLU E 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 28 removed outlier: 3.521A pdb=" N GLU F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA F 28 " --> pdb=" O TYR F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 98 removed outlier: 3.688A pdb=" N LEU F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE F 87 " --> pdb=" O LEU F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 120 removed outlier: 3.527A pdb=" N VAL F 109 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Proline residue: F 119 - end of helix Processing helix chain 'F' and resid 166 through 174 removed outlier: 3.514A pdb=" N TYR F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 181 removed outlier: 4.299A pdb=" N MET F 180 " --> pdb=" O SER F 177 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU F 181 " --> pdb=" O GLU F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 198 removed outlier: 3.696A pdb=" N LYS F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU F 197 " --> pdb=" O ARG F 193 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR F 198 " --> pdb=" O ALA F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 233 No H-bonds generated for 'chain 'F' and resid 230 through 233' Processing helix chain 'G' and resid 21 through 29 removed outlier: 4.086A pdb=" N LYS G 28 " --> pdb=" O GLU G 24 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA G 29 " --> pdb=" O TYR G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 99 removed outlier: 3.574A pdb=" N SER G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG G 99 " --> pdb=" O ALA G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 114 removed outlier: 3.932A pdb=" N ASP G 113 " --> pdb=" O LYS G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 122 removed outlier: 3.560A pdb=" N ALA G 121 " --> pdb=" O MET G 117 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR G 122 " --> pdb=" O TYR G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 178 removed outlier: 3.563A pdb=" N THR G 174 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS G 178 " --> pdb=" O THR G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 200 removed outlier: 3.567A pdb=" N VAL G 190 " --> pdb=" O CYS G 186 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU G 192 " --> pdb=" O ASP G 188 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR G 198 " --> pdb=" O ALA G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 220 No H-bonds generated for 'chain 'G' and resid 218 through 220' Processing helix chain 'G' and resid 231 through 241 Processing helix chain 'H' and resid 51 through 70 removed outlier: 3.774A pdb=" N ALA H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 89 Processing helix chain 'H' and resid 132 through 141 removed outlier: 4.028A pdb=" N TYR H 136 " --> pdb=" O SER H 133 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLY H 137 " --> pdb=" O TYR H 134 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL H 139 " --> pdb=" O TYR H 136 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP H 140 " --> pdb=" O GLY H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 166 removed outlier: 3.625A pdb=" N ARG H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'I' and resid 49 through 70 removed outlier: 3.838A pdb=" N THR I 55 " --> pdb=" O ASP I 51 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU I 58 " --> pdb=" O MET I 54 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU I 64 " --> pdb=" O SER I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 87 Processing helix chain 'I' and resid 131 through 141 removed outlier: 3.594A pdb=" N ALA I 136 " --> pdb=" O LEU I 132 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL I 137 " --> pdb=" O ALA I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 163 Processing helix chain 'J' and resid 2 through 4 No H-bonds generated for 'chain 'J' and resid 2 through 4' Processing helix chain 'J' and resid 56 through 76 removed outlier: 3.568A pdb=" N ALA J 63 " --> pdb=" O VAL J 59 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU J 72 " --> pdb=" O PHE J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 96 removed outlier: 3.660A pdb=" N SER J 88 " --> pdb=" O TYR J 84 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR J 95 " --> pdb=" O ALA J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 152 removed outlier: 3.520A pdb=" N MET J 148 " --> pdb=" O GLN J 144 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER J 151 " --> pdb=" O GLY J 147 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU J 152 " --> pdb=" O MET J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 174 removed outlier: 3.762A pdb=" N GLU J 164 " --> pdb=" O ASP J 160 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN J 172 " --> pdb=" O GLN J 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 71 removed outlier: 3.859A pdb=" N GLU K 58 " --> pdb=" O VAL K 54 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR K 59 " --> pdb=" O GLN K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 90 Processing helix chain 'K' and resid 134 through 146 removed outlier: 4.643A pdb=" N LEU K 140 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER K 141 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE K 142 " --> pdb=" O THR K 139 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP K 144 " --> pdb=" O SER K 141 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR K 146 " --> pdb=" O LEU K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 170 removed outlier: 3.621A pdb=" N GLU K 158 " --> pdb=" O GLU K 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 53 Processing helix chain 'L' and resid 57 through 70 Processing helix chain 'L' and resid 76 through 90 removed outlier: 3.740A pdb=" N LYS L 81 " --> pdb=" O ALA L 77 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU L 83 " --> pdb=" O ALA L 79 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN L 89 " --> pdb=" O ASN L 85 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR L 90 " --> pdb=" O MET L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 142 removed outlier: 4.272A pdb=" N GLY L 137 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG L 141 " --> pdb=" O GLY L 137 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY L 142 " --> pdb=" O VAL L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 166 removed outlier: 3.617A pdb=" N ALA L 156 " --> pdb=" O ALA L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 192 through 199 removed outlier: 3.921A pdb=" N GLU L 197 " --> pdb=" O ALA L 193 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS L 198 " --> pdb=" O ASP L 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 79 removed outlier: 3.680A pdb=" N THR M 63 " --> pdb=" O GLY M 59 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR M 65 " --> pdb=" O CYS M 61 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS M 73 " --> pdb=" O GLU M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 98 removed outlier: 3.603A pdb=" N ALA M 90 " --> pdb=" O GLY M 86 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR M 94 " --> pdb=" O ALA M 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 152 Proline residue: M 147 - end of helix Processing helix chain 'M' and resid 168 through 184 removed outlier: 3.511A pdb=" N VAL M 178 " --> pdb=" O LEU M 174 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE M 180 " --> pdb=" O LYS M 176 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER M 181 " --> pdb=" O ASP M 177 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU M 184 " --> pdb=" O ILE M 180 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 77 removed outlier: 3.611A pdb=" N GLN N 65 " --> pdb=" O GLN N 61 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU N 77 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 101 Processing helix chain 'N' and resid 140 through 145 removed outlier: 3.573A pdb=" N LEU N 145 " --> pdb=" O GLY N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 156 removed outlier: 3.909A pdb=" N VAL N 153 " --> pdb=" O LEU N 149 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS N 156 " --> pdb=" O GLU N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 179 Processing helix chain 'O' and resid 23 through 34 removed outlier: 3.598A pdb=" N LYS O 30 " --> pdb=" O GLU O 26 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE O 32 " --> pdb=" O ALA O 28 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN O 33 " --> pdb=" O PHE O 29 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN O 34 " --> pdb=" O LYS O 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 105 removed outlier: 3.612A pdb=" N LYS O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 126 removed outlier: 3.875A pdb=" N VAL O 124 " --> pdb=" O ASP O 120 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR O 125 " --> pdb=" O ILE O 121 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR O 126 " --> pdb=" O SER O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 185 removed outlier: 3.533A pdb=" N PHE O 178 " --> pdb=" O GLU O 174 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS O 182 " --> pdb=" O PHE O 178 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS O 185 " --> pdb=" O LYS O 181 " (cutoff:3.500A) Processing helix chain 'O' and resid 192 through 206 removed outlier: 3.566A pdb=" N VAL O 195 " --> pdb=" O GLU O 192 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE O 199 " --> pdb=" O GLU O 196 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR O 200 " --> pdb=" O THR O 197 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU O 202 " --> pdb=" O ILE O 199 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR O 204 " --> pdb=" O CYS O 201 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL O 205 " --> pdb=" O LEU O 202 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU O 206 " --> pdb=" O SER O 203 " (cutoff:3.500A) Processing helix chain 'O' and resid 232 through 240 removed outlier: 3.594A pdb=" N ALA O 237 " --> pdb=" O ALA O 233 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N HIS O 238 " --> pdb=" O GLU O 234 " (cutoff:3.500A) Processing helix chain 'P' and resid 19 through 29 removed outlier: 3.552A pdb=" N ALA P 26 " --> pdb=" O GLU P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 100 removed outlier: 3.630A pdb=" N ARG P 83 " --> pdb=" O GLY P 79 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL P 84 " --> pdb=" O PRO P 80 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU P 85 " --> pdb=" O ASP P 81 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG P 90 " --> pdb=" O VAL P 86 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL P 99 " --> pdb=" O GLN P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 122 removed outlier: 3.530A pdb=" N ARG P 112 " --> pdb=" O GLN P 108 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR P 120 " --> pdb=" O VAL P 116 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR P 121 " --> pdb=" O MET P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 175 removed outlier: 3.568A pdb=" N LYS P 175 " --> pdb=" O THR P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 195 removed outlier: 3.780A pdb=" N HIS P 188 " --> pdb=" O GLU P 184 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR P 189 " --> pdb=" O ASP P 185 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR P 193 " --> pdb=" O THR P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 222 through 228 removed outlier: 3.917A pdb=" N ASP P 227 " --> pdb=" O THR P 223 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR P 228 " --> pdb=" O GLU P 224 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 101 removed outlier: 3.617A pdb=" N ASN Q 88 " --> pdb=" O ASN Q 84 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU Q 92 " --> pdb=" O ASN Q 88 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU Q 98 " --> pdb=" O ALA Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 109 through 117 removed outlier: 3.599A pdb=" N LEU Q 114 " --> pdb=" O LEU Q 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 177 removed outlier: 3.758A pdb=" N MET Q 174 " --> pdb=" O ALA Q 170 " (cutoff:3.500A) Processing helix chain 'Q' and resid 186 through 196 removed outlier: 3.553A pdb=" N ILE Q 194 " --> pdb=" O LEU Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 230 through 245 removed outlier: 3.659A pdb=" N LEU Q 236 " --> pdb=" O GLU Q 232 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE Q 237 " --> pdb=" O VAL Q 233 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU Q 243 " --> pdb=" O LYS Q 239 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA Q 245 " --> pdb=" O GLU Q 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 26 removed outlier: 3.642A pdb=" N GLU R 24 " --> pdb=" O GLU R 20 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA R 25 " --> pdb=" O TYR R 21 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL R 26 " --> pdb=" O ALA R 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 20 through 26' Processing helix chain 'R' and resid 77 through 97 removed outlier: 3.621A pdb=" N ARG R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN R 85 " --> pdb=" O ARG R 81 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN R 92 " --> pdb=" O ARG R 88 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG R 95 " --> pdb=" O CYS R 91 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR R 97 " --> pdb=" O SER R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 114 Processing helix chain 'R' and resid 165 through 174 removed outlier: 3.681A pdb=" N LYS R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 179 No H-bonds generated for 'chain 'R' and resid 177 through 179' Processing helix chain 'R' and resid 183 through 189 removed outlier: 3.702A pdb=" N THR R 187 " --> pdb=" O THR R 183 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS R 189 " --> pdb=" O ASP R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 195 Processing helix chain 'R' and resid 222 through 233 removed outlier: 3.828A pdb=" N LYS R 227 " --> pdb=" O GLU R 223 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR R 228 " --> pdb=" O GLU R 224 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL R 229 " --> pdb=" O ILE R 225 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU R 231 " --> pdb=" O LYS R 227 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 29 removed outlier: 4.608A pdb=" N ALA S 27 " --> pdb=" O GLN S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 63 No H-bonds generated for 'chain 'S' and resid 61 through 63' Processing helix chain 'S' and resid 86 through 103 removed outlier: 3.891A pdb=" N LYS S 91 " --> pdb=" O THR S 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 109 through 119 removed outlier: 4.384A pdb=" N LEU S 119 " --> pdb=" O ALA S 115 " (cutoff:3.500A) Processing helix chain 'S' and resid 174 through 184 removed outlier: 6.190A pdb=" N SER S 179 " --> pdb=" O GLU S 175 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER S 180 " --> pdb=" O GLY S 176 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU S 183 " --> pdb=" O SER S 179 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 205 removed outlier: 3.770A pdb=" N LYS S 196 " --> pdb=" O LYS S 192 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE S 201 " --> pdb=" O SER S 197 " (cutoff:3.500A) Processing helix chain 'S' and resid 231 through 238 removed outlier: 3.583A pdb=" N GLU S 235 " --> pdb=" O LYS S 231 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL S 237 " --> pdb=" O GLU S 233 " (cutoff:3.500A) Processing helix chain 'T' and resid 20 through 28 removed outlier: 3.521A pdb=" N GLU T 27 " --> pdb=" O GLU T 23 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA T 28 " --> pdb=" O TYR T 24 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 98 removed outlier: 3.686A pdb=" N LEU T 83 " --> pdb=" O ALA T 79 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE T 87 " --> pdb=" O LEU T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 120 removed outlier: 3.527A pdb=" N VAL T 109 " --> pdb=" O VAL T 105 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE T 118 " --> pdb=" O SER T 114 " (cutoff:3.500A) Proline residue: T 119 - end of helix Processing helix chain 'T' and resid 166 through 174 removed outlier: 3.513A pdb=" N TYR T 171 " --> pdb=" O SER T 167 " (cutoff:3.500A) Processing helix chain 'T' and resid 176 through 181 removed outlier: 4.299A pdb=" N MET T 180 " --> pdb=" O SER T 177 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU T 181 " --> pdb=" O GLU T 178 " (cutoff:3.500A) Processing helix chain 'T' and resid 184 through 198 removed outlier: 3.696A pdb=" N LYS T 189 " --> pdb=" O ASN T 185 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU T 197 " --> pdb=" O ARG T 193 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR T 198 " --> pdb=" O ALA T 194 " (cutoff:3.500A) Processing helix chain 'T' and resid 230 through 233 No H-bonds generated for 'chain 'T' and resid 230 through 233' Processing helix chain 'U' and resid 21 through 29 removed outlier: 4.085A pdb=" N LYS U 28 " --> pdb=" O GLU U 24 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA U 29 " --> pdb=" O TYR U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 99 removed outlier: 3.573A pdb=" N SER U 86 " --> pdb=" O ALA U 82 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG U 99 " --> pdb=" O ALA U 95 " (cutoff:3.500A) Processing helix chain 'U' and resid 108 through 114 removed outlier: 3.932A pdb=" N ASP U 113 " --> pdb=" O LYS U 109 " (cutoff:3.500A) Processing helix chain 'U' and resid 116 through 122 removed outlier: 3.560A pdb=" N ALA U 121 " --> pdb=" O MET U 117 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR U 122 " --> pdb=" O TYR U 118 " (cutoff:3.500A) Processing helix chain 'U' and resid 169 through 178 removed outlier: 3.563A pdb=" N THR U 174 " --> pdb=" O GLN U 170 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU U 175 " --> pdb=" O ALA U 171 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS U 178 " --> pdb=" O THR U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 186 through 200 removed outlier: 3.566A pdb=" N VAL U 190 " --> pdb=" O CYS U 186 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS U 191 " --> pdb=" O ARG U 187 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU U 192 " --> pdb=" O ASP U 188 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR U 198 " --> pdb=" O ALA U 194 " (cutoff:3.500A) Processing helix chain 'U' and resid 218 through 220 No H-bonds generated for 'chain 'U' and resid 218 through 220' Processing helix chain 'U' and resid 231 through 241 Processing helix chain 'V' and resid 51 through 70 removed outlier: 3.774A pdb=" N ALA V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 89 Processing helix chain 'V' and resid 132 through 141 removed outlier: 4.027A pdb=" N TYR V 136 " --> pdb=" O SER V 133 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLY V 137 " --> pdb=" O TYR V 134 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL V 139 " --> pdb=" O TYR V 136 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP V 140 " --> pdb=" O GLY V 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 149 through 166 removed outlier: 3.625A pdb=" N ARG V 166 " --> pdb=" O LEU V 162 " (cutoff:3.500A) Processing helix chain 'V' and resid 191 through 193 No H-bonds generated for 'chain 'V' and resid 191 through 193' Processing helix chain 'W' and resid 49 through 70 removed outlier: 3.837A pdb=" N THR W 55 " --> pdb=" O ASP W 51 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU W 58 " --> pdb=" O MET W 54 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU W 64 " --> pdb=" O SER W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 76 through 87 Processing helix chain 'W' and resid 131 through 141 removed outlier: 3.594A pdb=" N ALA W 136 " --> pdb=" O LEU W 132 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL W 137 " --> pdb=" O ALA W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 148 through 163 Processing helix chain 'X' and resid 2 through 4 No H-bonds generated for 'chain 'X' and resid 2 through 4' Processing helix chain 'X' and resid 56 through 76 removed outlier: 3.567A pdb=" N ALA X 63 " --> pdb=" O VAL X 59 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN X 64 " --> pdb=" O GLN X 60 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU X 72 " --> pdb=" O PHE X 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 96 removed outlier: 3.660A pdb=" N SER X 88 " --> pdb=" O TYR X 84 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR X 95 " --> pdb=" O ALA X 91 " (cutoff:3.500A) Processing helix chain 'X' and resid 142 through 152 removed outlier: 3.521A pdb=" N MET X 148 " --> pdb=" O GLN X 144 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER X 151 " --> pdb=" O GLY X 147 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU X 152 " --> pdb=" O MET X 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 159 through 174 removed outlier: 3.762A pdb=" N GLU X 164 " --> pdb=" O ASP X 160 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN X 172 " --> pdb=" O GLN X 168 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 71 removed outlier: 3.859A pdb=" N GLU Y 58 " --> pdb=" O VAL Y 54 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR Y 59 " --> pdb=" O GLN Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 90 Processing helix chain 'Y' and resid 134 through 146 removed outlier: 4.643A pdb=" N LEU Y 140 " --> pdb=" O PHE Y 137 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER Y 141 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE Y 142 " --> pdb=" O THR Y 139 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP Y 144 " --> pdb=" O SER Y 141 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR Y 146 " --> pdb=" O LEU Y 143 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 170 removed outlier: 3.621A pdb=" N GLU Y 158 " --> pdb=" O GLU Y 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 53 Processing helix chain 'Z' and resid 57 through 70 Processing helix chain 'Z' and resid 76 through 90 removed outlier: 3.740A pdb=" N LYS Z 81 " --> pdb=" O ALA Z 77 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU Z 83 " --> pdb=" O ALA Z 79 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN Z 89 " --> pdb=" O ASN Z 85 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR Z 90 " --> pdb=" O MET Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 142 removed outlier: 4.273A pdb=" N GLY Z 137 " --> pdb=" O VAL Z 133 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL Z 138 " --> pdb=" O TYR Z 134 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG Z 141 " --> pdb=" O GLY Z 137 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY Z 142 " --> pdb=" O VAL Z 138 " (cutoff:3.500A) Processing helix chain 'Z' and resid 149 through 166 removed outlier: 3.617A pdb=" N ALA Z 156 " --> pdb=" O ALA Z 152 " (cutoff:3.500A) Processing helix chain 'Z' and resid 192 through 199 removed outlier: 3.921A pdb=" N GLU Z 197 " --> pdb=" O ALA Z 193 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS Z 198 " --> pdb=" O ASP Z 194 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 79 removed outlier: 3.681A pdb=" N THR a 63 " --> pdb=" O GLY a 59 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR a 65 " --> pdb=" O CYS a 61 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS a 73 " --> pdb=" O GLU a 69 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 98 removed outlier: 3.603A pdb=" N ALA a 90 " --> pdb=" O GLY a 86 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR a 94 " --> pdb=" O ALA a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 142 through 152 Proline residue: a 147 - end of helix Processing helix chain 'a' and resid 168 through 184 removed outlier: 3.511A pdb=" N VAL a 178 " --> pdb=" O LEU a 174 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE a 180 " --> pdb=" O LYS a 176 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER a 181 " --> pdb=" O ASP a 177 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU a 184 " --> pdb=" O ILE a 180 " (cutoff:3.500A) Processing helix chain 'b' and resid 57 through 77 removed outlier: 3.611A pdb=" N GLN b 65 " --> pdb=" O GLN b 61 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU b 77 " --> pdb=" O ASP b 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 101 Processing helix chain 'b' and resid 140 through 145 removed outlier: 3.573A pdb=" N LEU b 145 " --> pdb=" O GLY b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 147 through 156 removed outlier: 3.909A pdb=" N VAL b 153 " --> pdb=" O LEU b 149 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS b 156 " --> pdb=" O GLU b 152 " (cutoff:3.500A) Processing helix chain 'b' and resid 162 through 179 Processing helix chain 'c' and resid 41 through 43 No H-bonds generated for 'chain 'c' and resid 41 through 43' Processing helix chain 'c' and resid 46 through 64 removed outlier: 3.533A pdb=" N LEU c 50 " --> pdb=" O ALA c 46 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN c 51 " --> pdb=" O GLU c 47 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY c 60 " --> pdb=" O LYS c 56 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 86 removed outlier: 3.576A pdb=" N TRP c 75 " --> pdb=" O GLY c 71 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR c 76 " --> pdb=" O GLY c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 92 through 106 removed outlier: 3.926A pdb=" N GLU c 104 " --> pdb=" O LYS c 100 " (cutoff:3.500A) Processing helix chain 'c' and resid 113 through 125 removed outlier: 4.047A pdb=" N LEU c 122 " --> pdb=" O GLY c 118 " (cutoff:3.500A) Processing helix chain 'c' and resid 130 through 132 No H-bonds generated for 'chain 'c' and resid 130 through 132' Processing helix chain 'c' and resid 143 through 153 Processing helix chain 'c' and resid 169 through 183 removed outlier: 3.568A pdb=" N LEU c 173 " --> pdb=" O VAL c 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS c 174 " --> pdb=" O GLU c 170 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER c 179 " --> pdb=" O THR c 175 " (cutoff:3.500A) Proline residue: c 182 - end of helix Processing helix chain 'c' and resid 197 through 199 No H-bonds generated for 'chain 'c' and resid 197 through 199' Processing helix chain 'c' and resid 206 through 217 removed outlier: 3.674A pdb=" N ALA c 210 " --> pdb=" O THR c 206 " (cutoff:3.500A) Processing helix chain 'c' and resid 224 through 226 No H-bonds generated for 'chain 'c' and resid 224 through 226' Processing helix chain 'c' and resid 231 through 233 No H-bonds generated for 'chain 'c' and resid 231 through 233' Processing helix chain 'c' and resid 235 through 244 removed outlier: 3.860A pdb=" N LEU c 241 " --> pdb=" O GLU c 237 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER c 244 " --> pdb=" O GLY c 240 " (cutoff:3.500A) Processing helix chain 'c' and resid 252 through 265 removed outlier: 3.726A pdb=" N ASN c 257 " --> pdb=" O GLY c 253 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG c 261 " --> pdb=" O ASN c 257 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP c 265 " --> pdb=" O ARG c 261 " (cutoff:3.500A) Processing helix chain 'c' and resid 272 through 274 No H-bonds generated for 'chain 'c' and resid 272 through 274' Processing helix chain 'c' and resid 276 through 287 removed outlier: 3.959A pdb=" N ARG c 282 " --> pdb=" O LYS c 278 " (cutoff:3.500A) Processing helix chain 'c' and resid 300 through 302 No H-bonds generated for 'chain 'c' and resid 300 through 302' Processing helix chain 'c' and resid 308 through 318 removed outlier: 3.740A pdb=" N ILE c 313 " --> pdb=" O GLY c 309 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA c 317 " --> pdb=" O ILE c 313 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N MET c 318 " --> pdb=" O TRP c 314 " (cutoff:3.500A) Processing helix chain 'c' and resid 325 through 334 removed outlier: 3.664A pdb=" N HIS c 329 " --> pdb=" O LEU c 325 " (cutoff:3.500A) Processing helix chain 'c' and resid 338 through 340 No H-bonds generated for 'chain 'c' and resid 338 through 340' Processing helix chain 'c' and resid 348 through 372 removed outlier: 3.877A pdb=" N ASN c 351 " --> pdb=" O ARG c 348 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N MET c 354 " --> pdb=" O ASN c 351 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS c 355 " --> pdb=" O LYS c 352 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU c 356 " --> pdb=" O LEU c 353 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG c 359 " --> pdb=" O LEU c 356 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU c 360 " --> pdb=" O LEU c 357 " (cutoff:3.500A) Proline residue: c 361 - end of helix removed outlier: 3.885A pdb=" N VAL c 364 " --> pdb=" O PRO c 361 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL c 365 " --> pdb=" O ASN c 362 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG c 372 " --> pdb=" O HIS c 369 " (cutoff:3.500A) Processing helix chain 'c' and resid 390 through 397 Processing helix chain 'c' and resid 401 through 409 removed outlier: 4.342A pdb=" N PHE c 409 " --> pdb=" O LEU c 405 " (cutoff:3.500A) Processing helix chain 'c' and resid 415 through 427 removed outlier: 3.719A pdb=" N ASN c 423 " --> pdb=" O GLN c 419 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET c 427 " --> pdb=" O ASN c 423 " (cutoff:3.500A) Processing helix chain 'c' and resid 429 through 432 No H-bonds generated for 'chain 'c' and resid 429 through 432' Processing helix chain 'c' and resid 434 through 437 No H-bonds generated for 'chain 'c' and resid 434 through 437' Processing helix chain 'c' and resid 441 through 444 No H-bonds generated for 'chain 'c' and resid 441 through 444' Processing helix chain 'c' and resid 450 through 468 removed outlier: 4.323A pdb=" N THR c 456 " --> pdb=" O LEU c 453 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU c 457 " --> pdb=" O THR c 454 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER c 458 " --> pdb=" O ALA c 455 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE c 461 " --> pdb=" O SER c 458 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY c 462 " --> pdb=" O CYS c 459 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG c 465 " --> pdb=" O GLY c 462 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL c 468 " --> pdb=" O ARG c 465 " (cutoff:3.500A) Processing helix chain 'c' and resid 478 through 487 removed outlier: 4.634A pdb=" N LEU c 482 " --> pdb=" O THR c 479 " (cutoff:3.500A) Proline residue: c 483 - end of helix removed outlier: 3.630A pdb=" N MET c 486 " --> pdb=" O PRO c 483 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG c 487 " --> pdb=" O LEU c 484 " (cutoff:3.500A) Processing helix chain 'c' and resid 489 through 491 No H-bonds generated for 'chain 'c' and resid 489 through 491' Processing helix chain 'c' and resid 498 through 510 Processing helix chain 'c' and resid 531 through 559 removed outlier: 3.594A pdb=" N GLU c 535 " --> pdb=" O GLU c 531 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA c 539 " --> pdb=" O GLU c 535 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA c 541 " --> pdb=" O CYS c 537 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLU c 542 " --> pdb=" O SER c 538 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE c 543 " --> pdb=" O ALA c 539 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLU c 544 " --> pdb=" O THR c 540 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP c 545 " --> pdb=" O ALA c 541 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN c 549 " --> pdb=" O ASP c 545 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY c 556 " --> pdb=" O ASP c 552 " (cutoff:3.500A) Processing helix chain 'c' and resid 577 through 595 removed outlier: 3.744A pdb=" N VAL c 582 " --> pdb=" O LEU c 578 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER c 591 " --> pdb=" O SER c 587 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE c 593 " --> pdb=" O THR c 589 " (cutoff:3.500A) Processing helix chain 'c' and resid 599 through 613 removed outlier: 3.673A pdb=" N VAL c 604 " --> pdb=" O GLU c 600 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN c 607 " --> pdb=" O MET c 603 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS c 608 " --> pdb=" O VAL c 604 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE c 612 " --> pdb=" O LYS c 608 " (cutoff:3.500A) Processing helix chain 'c' and resid 624 through 635 removed outlier: 3.639A pdb=" N MET c 630 " --> pdb=" O MET c 626 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA c 634 " --> pdb=" O MET c 630 " (cutoff:3.500A) Processing helix chain 'c' and resid 639 through 643 Processing helix chain 'c' and resid 647 through 657 removed outlier: 3.514A pdb=" N VAL c 653 " --> pdb=" O HIS c 649 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN c 656 " --> pdb=" O SER c 652 " (cutoff:3.500A) Processing helix chain 'c' and resid 673 through 681 removed outlier: 4.197A pdb=" N GLN c 678 " --> pdb=" O LEU c 674 " (cutoff:3.500A) Processing helix chain 'c' and resid 692 through 705 removed outlier: 3.950A pdb=" N ARG c 695 " --> pdb=" O LEU c 692 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLU c 696 " --> pdb=" O LEU c 693 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN c 697 " --> pdb=" O TYR c 694 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU c 698 " --> pdb=" O ARG c 695 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL c 699 " --> pdb=" O GLU c 696 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE c 701 " --> pdb=" O LEU c 698 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN c 703 " --> pdb=" O LYS c 700 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR c 705 " --> pdb=" O LEU c 702 " (cutoff:3.500A) Processing helix chain 'c' and resid 713 through 727 Processing helix chain 'c' and resid 752 through 754 No H-bonds generated for 'chain 'c' and resid 752 through 754' Processing helix chain 'c' and resid 774 through 782 Processing helix chain 'c' and resid 789 through 799 removed outlier: 3.718A pdb=" N LYS c 794 " --> pdb=" O PRO c 790 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU c 795 " --> pdb=" O GLU c 791 " (cutoff:3.500A) Processing helix chain 'c' and resid 807 through 821 removed outlier: 3.683A pdb=" N LEU c 811 " --> pdb=" O ARG c 807 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR c 815 " --> pdb=" O LEU c 811 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE c 816 " --> pdb=" O GLN c 812 " (cutoff:3.500A) Processing helix chain 'c' and resid 825 through 827 No H-bonds generated for 'chain 'c' and resid 825 through 827' Processing helix chain 'c' and resid 864 through 882 removed outlier: 3.582A pdb=" N ARG c 873 " --> pdb=" O ALA c 869 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN c 877 " --> pdb=" O ARG c 873 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP c 881 " --> pdb=" O ASN c 877 " (cutoff:3.500A) Processing helix chain 'c' and resid 887 through 900 removed outlier: 3.755A pdb=" N LEU c 892 " --> pdb=" O LYS c 888 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP c 899 " --> pdb=" O LYS c 895 " (cutoff:3.500A) Processing helix chain 'c' and resid 910 through 922 Processing helix chain 'c' and resid 932 through 934 No H-bonds generated for 'chain 'c' and resid 932 through 934' Processing helix chain 'c' and resid 937 through 951 removed outlier: 3.768A pdb=" N ASP c 942 " --> pdb=" O ALA c 938 " (cutoff:3.500A) Processing helix chain 'c' and resid 962 through 974 removed outlier: 3.631A pdb=" N ILE c 968 " --> pdb=" O HIS c 964 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG c 969 " --> pdb=" O GLN c 965 " (cutoff:3.500A) Processing helix chain 'c' and resid 980 through 994 removed outlier: 3.541A pdb=" N LYS c 985 " --> pdb=" O GLN c 981 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN c 988 " --> pdb=" O ASN c 984 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR c 989 " --> pdb=" O LYS c 985 " (cutoff:3.500A) Processing helix chain 'c' and resid 1001 through 1011 Proline residue: c1006 - end of helix removed outlier: 4.191A pdb=" N GLU c1010 " --> pdb=" O PRO c1006 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N PHE c1011 " --> pdb=" O LEU c1007 " (cutoff:3.500A) Processing helix chain 'c' and resid 1021 through 1031 removed outlier: 3.572A pdb=" N ALA c1027 " --> pdb=" O GLN c1023 " (cutoff:3.500A) Processing helix chain 'c' and resid 1046 through 1061 removed outlier: 4.698A pdb=" N GLN c1051 " --> pdb=" O ASP c1047 " (cutoff:3.500A) Proline residue: c1054 - end of helix removed outlier: 3.565A pdb=" N VAL c1057 " --> pdb=" O TRP c1053 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLY c1060 " --> pdb=" O ILE c1056 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU c1061 " --> pdb=" O VAL c1057 " (cutoff:3.500A) Processing helix chain 'c' and resid 1070 through 1086 removed outlier: 3.557A pdb=" N GLU c1081 " --> pdb=" O ASP c1077 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE c1083 " --> pdb=" O LEU c1079 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG c1085 " --> pdb=" O GLU c1081 " (cutoff:3.500A) Processing helix chain 'c' and resid 1101 through 1107 Processing helix chain 'c' and resid 1124 through 1154 Processing helix chain 'c' and resid 1161 through 1163 No H-bonds generated for 'chain 'c' and resid 1161 through 1163' Processing helix chain 'c' and resid 1165 through 1171 Processing helix chain 'c' and resid 1183 through 1191 Processing helix chain 'c' and resid 1198 through 1214 removed outlier: 3.547A pdb=" N SER c1206 " --> pdb=" O LYS c1202 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY c1210 " --> pdb=" O SER c1206 " (cutoff:3.500A) Processing helix chain 'c' and resid 1247 through 1252 removed outlier: 3.896A pdb=" N HIS c1250 " --> pdb=" O HIS c1247 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR c1251 " --> pdb=" O TRP c1248 " (cutoff:3.500A) Processing helix chain 'c' and resid 1309 through 1313 Processing helix chain 'c' and resid 1316 through 1326 Processing helix chain 'c' and resid 1339 through 1352 removed outlier: 3.696A pdb=" N CYS c1343 " --> pdb=" O PRO c1339 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU c1344 " --> pdb=" O ARG c1340 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN c1351 " --> pdb=" O GLY c1347 " (cutoff:3.500A) Processing helix chain 'c' and resid 1357 through 1368 removed outlier: 3.824A pdb=" N LYS c1361 " --> pdb=" O PRO c1358 " (cutoff:3.500A) Proline residue: c1362 - end of helix removed outlier: 4.857A pdb=" N HIS c1366 " --> pdb=" O HIS c1363 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU c1367 " --> pdb=" O LEU c1364 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL c1368 " --> pdb=" O GLU c1365 " (cutoff:3.500A) Processing helix chain 'c' and resid 1373 through 1389 removed outlier: 3.693A pdb=" N GLU c1381 " --> pdb=" O ARG c1377 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE c1382 " --> pdb=" O CYS c1378 " (cutoff:3.500A) Processing helix chain 'c' and resid 1395 through 1414 removed outlier: 4.347A pdb=" N LEU c1404 " --> pdb=" O LYS c1400 " (cutoff:3.500A) Proline residue: c1407 - end of helix removed outlier: 3.591A pdb=" N ARG c1410 " --> pdb=" O CYS c1406 " (cutoff:3.500A) Processing helix chain 'c' and resid 1421 through 1425 Processing helix chain 'c' and resid 1442 through 1446 Processing helix chain 'c' and resid 1459 through 1474 removed outlier: 3.676A pdb=" N LEU c1468 " --> pdb=" O ARG c1464 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY c1470 " --> pdb=" O TYR c1466 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY c1471 " --> pdb=" O VAL c1467 " (cutoff:3.500A) Processing helix chain 'c' and resid 1481 through 1495 Proline residue: c1492 - end of helix removed outlier: 5.650A pdb=" N THR c1495 " --> pdb=" O GLU c1491 " (cutoff:3.500A) Processing helix chain 'c' and resid 1499 through 1512 removed outlier: 3.722A pdb=" N ARG c1504 " --> pdb=" O ASN c1500 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER c1507 " --> pdb=" O GLU c1503 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR c1510 " --> pdb=" O GLY c1506 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR c1511 " --> pdb=" O SER c1507 " (cutoff:3.500A) Processing helix chain 'c' and resid 1530 through 1540 removed outlier: 3.575A pdb=" N ALA c1535 " --> pdb=" O PRO c1531 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG c1536 " --> pdb=" O GLU c1532 " (cutoff:3.500A) Processing helix chain 'c' and resid 1571 through 1581 removed outlier: 3.710A pdb=" N LYS c1575 " --> pdb=" O ILE c1571 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR c1576 " --> pdb=" O LYS c1572 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS c1579 " --> pdb=" O LYS c1575 " (cutoff:3.500A) Processing helix chain 'c' and resid 1597 through 1604 Proline residue: c1601 - end of helix removed outlier: 3.874A pdb=" N PHE c1604 " --> pdb=" O PRO c1601 " (cutoff:3.500A) Processing helix chain 'c' and resid 1617 through 1630 removed outlier: 3.643A pdb=" N LEU c1624 " --> pdb=" O ARG c1620 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU c1628 " --> pdb=" O LEU c1624 " (cutoff:3.500A) Processing helix chain 'c' and resid 1639 through 1649 removed outlier: 3.841A pdb=" N LEU c1643 " --> pdb=" O VAL c1639 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL c1645 " --> pdb=" O LEU c1641 " (cutoff:3.500A) Processing helix chain 'c' and resid 1655 through 1667 removed outlier: 3.786A pdb=" N LEU c1662 " --> pdb=" O ARG c1658 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR c1667 " --> pdb=" O THR c1663 " (cutoff:3.500A) Processing helix chain 'c' and resid 1673 through 1676 No H-bonds generated for 'chain 'c' and resid 1673 through 1676' Processing helix chain 'c' and resid 1680 through 1692 removed outlier: 3.890A pdb=" N LYS c1684 " --> pdb=" O GLU c1680 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP c1685 " --> pdb=" O ASP c1681 " (cutoff:3.500A) Processing helix chain 'c' and resid 1699 through 1714 removed outlier: 3.710A pdb=" N MET c1704 " --> pdb=" O GLU c1700 " (cutoff:3.500A) Processing helix chain 'c' and resid 1722 through 1732 removed outlier: 3.993A pdb=" N LEU c1731 " --> pdb=" O HIS c1727 " (cutoff:3.500A) Processing helix chain 'c' and resid 1755 through 1770 removed outlier: 4.019A pdb=" N GLY c1762 " --> pdb=" O LYS c1758 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL c1763 " --> pdb=" O ARG c1759 " (cutoff:3.500A) Processing helix chain 'c' and resid 1783 through 1791 removed outlier: 3.570A pdb=" N ASN c1787 " --> pdb=" O GLN c1783 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU c1788 " --> pdb=" O LEU c1784 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N HIS c1791 " --> pdb=" O ASN c1787 " (cutoff:3.500A) Processing helix chain 'c' and resid 1796 through 1814 removed outlier: 3.822A pdb=" N THR c1801 " --> pdb=" O PRO c1797 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N HIS c1814 " --> pdb=" O ARG c1810 " (cutoff:3.500A) Processing helix chain 'c' and resid 1817 through 1823 removed outlier: 4.363A pdb=" N GLN c1822 " --> pdb=" O GLN c1818 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN c1823 " --> pdb=" O GLU c1819 " (cutoff:3.500A) Processing helix chain 'c' and resid 1826 through 1833 removed outlier: 3.814A pdb=" N LEU c1830 " --> pdb=" O ASP c1826 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL c1831 " --> pdb=" O ASP c1827 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 43 No H-bonds generated for 'chain 'd' and resid 41 through 43' Processing helix chain 'd' and resid 46 through 64 removed outlier: 3.534A pdb=" N LEU d 50 " --> pdb=" O ALA d 46 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN d 51 " --> pdb=" O GLU d 47 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY d 60 " --> pdb=" O LYS d 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 71 through 86 removed outlier: 3.576A pdb=" N TRP d 75 " --> pdb=" O GLY d 71 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR d 76 " --> pdb=" O GLY d 72 " (cutoff:3.500A) Processing helix chain 'd' and resid 92 through 106 removed outlier: 3.927A pdb=" N GLU d 104 " --> pdb=" O LYS d 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 113 through 125 removed outlier: 4.047A pdb=" N LEU d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 132 No H-bonds generated for 'chain 'd' and resid 130 through 132' Processing helix chain 'd' and resid 143 through 153 Processing helix chain 'd' and resid 169 through 183 removed outlier: 3.567A pdb=" N LEU d 173 " --> pdb=" O VAL d 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS d 174 " --> pdb=" O GLU d 170 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER d 179 " --> pdb=" O THR d 175 " (cutoff:3.500A) Proline residue: d 182 - end of helix Processing helix chain 'd' and resid 197 through 199 No H-bonds generated for 'chain 'd' and resid 197 through 199' Processing helix chain 'd' and resid 206 through 217 removed outlier: 3.674A pdb=" N ALA d 210 " --> pdb=" O THR d 206 " (cutoff:3.500A) Processing helix chain 'd' and resid 224 through 226 No H-bonds generated for 'chain 'd' and resid 224 through 226' Processing helix chain 'd' and resid 231 through 233 No H-bonds generated for 'chain 'd' and resid 231 through 233' Processing helix chain 'd' and resid 235 through 244 removed outlier: 3.861A pdb=" N LEU d 241 " --> pdb=" O GLU d 237 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER d 244 " --> pdb=" O GLY d 240 " (cutoff:3.500A) Processing helix chain 'd' and resid 252 through 265 removed outlier: 3.727A pdb=" N ASN d 257 " --> pdb=" O GLY d 253 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG d 261 " --> pdb=" O ASN d 257 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP d 265 " --> pdb=" O ARG d 261 " (cutoff:3.500A) Processing helix chain 'd' and resid 272 through 274 No H-bonds generated for 'chain 'd' and resid 272 through 274' Processing helix chain 'd' and resid 276 through 287 removed outlier: 3.959A pdb=" N ARG d 282 " --> pdb=" O LYS d 278 " (cutoff:3.500A) Processing helix chain 'd' and resid 300 through 302 No H-bonds generated for 'chain 'd' and resid 300 through 302' Processing helix chain 'd' and resid 308 through 318 removed outlier: 3.739A pdb=" N ILE d 313 " --> pdb=" O GLY d 309 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA d 317 " --> pdb=" O ILE d 313 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N MET d 318 " --> pdb=" O TRP d 314 " (cutoff:3.500A) Processing helix chain 'd' and resid 325 through 334 removed outlier: 3.665A pdb=" N HIS d 329 " --> pdb=" O LEU d 325 " (cutoff:3.500A) Processing helix chain 'd' and resid 338 through 340 No H-bonds generated for 'chain 'd' and resid 338 through 340' Processing helix chain 'd' and resid 348 through 372 removed outlier: 3.877A pdb=" N ASN d 351 " --> pdb=" O ARG d 348 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N MET d 354 " --> pdb=" O ASN d 351 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS d 355 " --> pdb=" O LYS d 352 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU d 356 " --> pdb=" O LEU d 353 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG d 359 " --> pdb=" O LEU d 356 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU d 360 " --> pdb=" O LEU d 357 " (cutoff:3.500A) Proline residue: d 361 - end of helix removed outlier: 3.885A pdb=" N VAL d 364 " --> pdb=" O PRO d 361 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL d 365 " --> pdb=" O ASN d 362 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG d 372 " --> pdb=" O HIS d 369 " (cutoff:3.500A) Processing helix chain 'd' and resid 390 through 397 Processing helix chain 'd' and resid 401 through 409 removed outlier: 4.342A pdb=" N PHE d 409 " --> pdb=" O LEU d 405 " (cutoff:3.500A) Processing helix chain 'd' and resid 415 through 427 removed outlier: 3.718A pdb=" N ASN d 423 " --> pdb=" O GLN d 419 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET d 427 " --> pdb=" O ASN d 423 " (cutoff:3.500A) Processing helix chain 'd' and resid 429 through 432 No H-bonds generated for 'chain 'd' and resid 429 through 432' Processing helix chain 'd' and resid 434 through 437 No H-bonds generated for 'chain 'd' and resid 434 through 437' Processing helix chain 'd' and resid 441 through 444 No H-bonds generated for 'chain 'd' and resid 441 through 444' Processing helix chain 'd' and resid 450 through 468 removed outlier: 4.324A pdb=" N THR d 456 " --> pdb=" O LEU d 453 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU d 457 " --> pdb=" O THR d 454 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER d 458 " --> pdb=" O ALA d 455 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE d 461 " --> pdb=" O SER d 458 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY d 462 " --> pdb=" O CYS d 459 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG d 465 " --> pdb=" O GLY d 462 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL d 468 " --> pdb=" O ARG d 465 " (cutoff:3.500A) Processing helix chain 'd' and resid 478 through 487 removed outlier: 4.634A pdb=" N LEU d 482 " --> pdb=" O THR d 479 " (cutoff:3.500A) Proline residue: d 483 - end of helix removed outlier: 3.631A pdb=" N MET d 486 " --> pdb=" O PRO d 483 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG d 487 " --> pdb=" O LEU d 484 " (cutoff:3.500A) Processing helix chain 'd' and resid 489 through 491 No H-bonds generated for 'chain 'd' and resid 489 through 491' Processing helix chain 'd' and resid 498 through 510 Processing helix chain 'd' and resid 531 through 559 removed outlier: 3.595A pdb=" N GLU d 535 " --> pdb=" O GLU d 531 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA d 539 " --> pdb=" O GLU d 535 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA d 541 " --> pdb=" O CYS d 537 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLU d 542 " --> pdb=" O SER d 538 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N PHE d 543 " --> pdb=" O ALA d 539 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLU d 544 " --> pdb=" O THR d 540 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP d 545 " --> pdb=" O ALA d 541 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN d 549 " --> pdb=" O ASP d 545 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY d 556 " --> pdb=" O ASP d 552 " (cutoff:3.500A) Processing helix chain 'd' and resid 577 through 595 removed outlier: 3.745A pdb=" N VAL d 582 " --> pdb=" O LEU d 578 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER d 591 " --> pdb=" O SER d 587 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE d 593 " --> pdb=" O THR d 589 " (cutoff:3.500A) Processing helix chain 'd' and resid 599 through 613 removed outlier: 3.674A pdb=" N VAL d 604 " --> pdb=" O GLU d 600 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN d 607 " --> pdb=" O MET d 603 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS d 608 " --> pdb=" O VAL d 604 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE d 612 " --> pdb=" O LYS d 608 " (cutoff:3.500A) Processing helix chain 'd' and resid 624 through 635 removed outlier: 3.639A pdb=" N MET d 630 " --> pdb=" O MET d 626 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA d 634 " --> pdb=" O MET d 630 " (cutoff:3.500A) Processing helix chain 'd' and resid 639 through 643 Processing helix chain 'd' and resid 647 through 657 removed outlier: 3.514A pdb=" N VAL d 653 " --> pdb=" O HIS d 649 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN d 656 " --> pdb=" O SER d 652 " (cutoff:3.500A) Processing helix chain 'd' and resid 673 through 681 removed outlier: 4.196A pdb=" N GLN d 678 " --> pdb=" O LEU d 674 " (cutoff:3.500A) Processing helix chain 'd' and resid 692 through 705 removed outlier: 3.950A pdb=" N ARG d 695 " --> pdb=" O LEU d 692 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLU d 696 " --> pdb=" O LEU d 693 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN d 697 " --> pdb=" O TYR d 694 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU d 698 " --> pdb=" O ARG d 695 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL d 699 " --> pdb=" O GLU d 696 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE d 701 " --> pdb=" O LEU d 698 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN d 703 " --> pdb=" O LYS d 700 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR d 705 " --> pdb=" O LEU d 702 " (cutoff:3.500A) Processing helix chain 'd' and resid 713 through 727 Processing helix chain 'd' and resid 752 through 754 No H-bonds generated for 'chain 'd' and resid 752 through 754' Processing helix chain 'd' and resid 774 through 782 Processing helix chain 'd' and resid 789 through 799 removed outlier: 3.718A pdb=" N LYS d 794 " --> pdb=" O PRO d 790 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU d 795 " --> pdb=" O GLU d 791 " (cutoff:3.500A) Processing helix chain 'd' and resid 807 through 821 removed outlier: 3.683A pdb=" N LEU d 811 " --> pdb=" O ARG d 807 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR d 815 " --> pdb=" O LEU d 811 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE d 816 " --> pdb=" O GLN d 812 " (cutoff:3.500A) Processing helix chain 'd' and resid 825 through 827 No H-bonds generated for 'chain 'd' and resid 825 through 827' Processing helix chain 'd' and resid 864 through 882 removed outlier: 3.583A pdb=" N ARG d 873 " --> pdb=" O ALA d 869 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN d 877 " --> pdb=" O ARG d 873 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP d 881 " --> pdb=" O ASN d 877 " (cutoff:3.500A) Processing helix chain 'd' and resid 887 through 900 removed outlier: 3.755A pdb=" N LEU d 892 " --> pdb=" O LYS d 888 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP d 899 " --> pdb=" O LYS d 895 " (cutoff:3.500A) Processing helix chain 'd' and resid 910 through 922 Processing helix chain 'd' and resid 932 through 934 No H-bonds generated for 'chain 'd' and resid 932 through 934' Processing helix chain 'd' and resid 937 through 951 removed outlier: 3.768A pdb=" N ASP d 942 " --> pdb=" O ALA d 938 " (cutoff:3.500A) Processing helix chain 'd' and resid 962 through 974 removed outlier: 3.631A pdb=" N ILE d 968 " --> pdb=" O HIS d 964 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG d 969 " --> pdb=" O GLN d 965 " (cutoff:3.500A) Processing helix chain 'd' and resid 980 through 994 removed outlier: 3.542A pdb=" N LYS d 985 " --> pdb=" O GLN d 981 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN d 988 " --> pdb=" O ASN d 984 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR d 989 " --> pdb=" O LYS d 985 " (cutoff:3.500A) Processing helix chain 'd' and resid 1001 through 1011 Proline residue: d1006 - end of helix removed outlier: 4.191A pdb=" N GLU d1010 " --> pdb=" O PRO d1006 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N PHE d1011 " --> pdb=" O LEU d1007 " (cutoff:3.500A) Processing helix chain 'd' and resid 1021 through 1031 removed outlier: 3.573A pdb=" N ALA d1027 " --> pdb=" O GLN d1023 " (cutoff:3.500A) Processing helix chain 'd' and resid 1046 through 1061 removed outlier: 4.697A pdb=" N GLN d1051 " --> pdb=" O ASP d1047 " (cutoff:3.500A) Proline residue: d1054 - end of helix removed outlier: 3.565A pdb=" N VAL d1057 " --> pdb=" O TRP d1053 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLY d1060 " --> pdb=" O ILE d1056 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU d1061 " --> pdb=" O VAL d1057 " (cutoff:3.500A) Processing helix chain 'd' and resid 1070 through 1086 removed outlier: 3.558A pdb=" N GLU d1081 " --> pdb=" O ASP d1077 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE d1083 " --> pdb=" O LEU d1079 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG d1085 " --> pdb=" O GLU d1081 " (cutoff:3.500A) Processing helix chain 'd' and resid 1101 through 1107 Processing helix chain 'd' and resid 1124 through 1154 Processing helix chain 'd' and resid 1161 through 1163 No H-bonds generated for 'chain 'd' and resid 1161 through 1163' Processing helix chain 'd' and resid 1165 through 1171 Processing helix chain 'd' and resid 1183 through 1191 Processing helix chain 'd' and resid 1198 through 1214 removed outlier: 3.547A pdb=" N SER d1206 " --> pdb=" O LYS d1202 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY d1210 " --> pdb=" O SER d1206 " (cutoff:3.500A) Processing helix chain 'd' and resid 1247 through 1252 removed outlier: 3.897A pdb=" N HIS d1250 " --> pdb=" O HIS d1247 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR d1251 " --> pdb=" O TRP d1248 " (cutoff:3.500A) Processing helix chain 'd' and resid 1309 through 1313 Processing helix chain 'd' and resid 1316 through 1326 Processing helix chain 'd' and resid 1339 through 1352 removed outlier: 3.696A pdb=" N CYS d1343 " --> pdb=" O PRO d1339 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU d1344 " --> pdb=" O ARG d1340 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN d1351 " --> pdb=" O GLY d1347 " (cutoff:3.500A) Processing helix chain 'd' and resid 1357 through 1368 removed outlier: 3.824A pdb=" N LYS d1361 " --> pdb=" O PRO d1358 " (cutoff:3.500A) Proline residue: d1362 - end of helix removed outlier: 4.857A pdb=" N HIS d1366 " --> pdb=" O HIS d1363 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU d1367 " --> pdb=" O LEU d1364 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL d1368 " --> pdb=" O GLU d1365 " (cutoff:3.500A) Processing helix chain 'd' and resid 1373 through 1389 removed outlier: 3.693A pdb=" N GLU d1381 " --> pdb=" O ARG d1377 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE d1382 " --> pdb=" O CYS d1378 " (cutoff:3.500A) Processing helix chain 'd' and resid 1395 through 1414 removed outlier: 4.347A pdb=" N LEU d1404 " --> pdb=" O LYS d1400 " (cutoff:3.500A) Proline residue: d1407 - end of helix removed outlier: 3.591A pdb=" N ARG d1410 " --> pdb=" O CYS d1406 " (cutoff:3.500A) Processing helix chain 'd' and resid 1421 through 1425 Processing helix chain 'd' and resid 1442 through 1446 Processing helix chain 'd' and resid 1459 through 1474 removed outlier: 3.676A pdb=" N LEU d1468 " --> pdb=" O ARG d1464 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY d1470 " --> pdb=" O TYR d1466 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY d1471 " --> pdb=" O VAL d1467 " (cutoff:3.500A) Processing helix chain 'd' and resid 1481 through 1495 Proline residue: d1492 - end of helix removed outlier: 5.651A pdb=" N THR d1495 " --> pdb=" O GLU d1491 " (cutoff:3.500A) Processing helix chain 'd' and resid 1499 through 1512 removed outlier: 3.722A pdb=" N ARG d1504 " --> pdb=" O ASN d1500 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER d1507 " --> pdb=" O GLU d1503 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR d1510 " --> pdb=" O GLY d1506 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR d1511 " --> pdb=" O SER d1507 " (cutoff:3.500A) Processing helix chain 'd' and resid 1530 through 1540 removed outlier: 3.575A pdb=" N ALA d1535 " --> pdb=" O PRO d1531 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG d1536 " --> pdb=" O GLU d1532 " (cutoff:3.500A) Processing helix chain 'd' and resid 1571 through 1581 removed outlier: 3.710A pdb=" N LYS d1575 " --> pdb=" O ILE d1571 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR d1576 " --> pdb=" O LYS d1572 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS d1579 " --> pdb=" O LYS d1575 " (cutoff:3.500A) Processing helix chain 'd' and resid 1597 through 1604 Proline residue: d1601 - end of helix removed outlier: 3.873A pdb=" N PHE d1604 " --> pdb=" O PRO d1601 " (cutoff:3.500A) Processing helix chain 'd' and resid 1617 through 1630 removed outlier: 3.642A pdb=" N LEU d1624 " --> pdb=" O ARG d1620 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU d1628 " --> pdb=" O LEU d1624 " (cutoff:3.500A) Processing helix chain 'd' and resid 1639 through 1649 removed outlier: 3.841A pdb=" N LEU d1643 " --> pdb=" O VAL d1639 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL d1645 " --> pdb=" O LEU d1641 " (cutoff:3.500A) Processing helix chain 'd' and resid 1655 through 1667 removed outlier: 3.787A pdb=" N LEU d1662 " --> pdb=" O ARG d1658 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR d1667 " --> pdb=" O THR d1663 " (cutoff:3.500A) Processing helix chain 'd' and resid 1673 through 1676 No H-bonds generated for 'chain 'd' and resid 1673 through 1676' Processing helix chain 'd' and resid 1680 through 1692 removed outlier: 3.889A pdb=" N LYS d1684 " --> pdb=" O GLU d1680 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP d1685 " --> pdb=" O ASP d1681 " (cutoff:3.500A) Processing helix chain 'd' and resid 1699 through 1714 removed outlier: 3.712A pdb=" N MET d1704 " --> pdb=" O GLU d1700 " (cutoff:3.500A) Processing helix chain 'd' and resid 1722 through 1732 removed outlier: 3.993A pdb=" N LEU d1731 " --> pdb=" O HIS d1727 " (cutoff:3.500A) Processing helix chain 'd' and resid 1755 through 1770 removed outlier: 4.019A pdb=" N GLY d1762 " --> pdb=" O LYS d1758 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL d1763 " --> pdb=" O ARG d1759 " (cutoff:3.500A) Processing helix chain 'd' and resid 1783 through 1791 removed outlier: 3.570A pdb=" N ASN d1787 " --> pdb=" O GLN d1783 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU d1788 " --> pdb=" O LEU d1784 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N HIS d1791 " --> pdb=" O ASN d1787 " (cutoff:3.500A) Processing helix chain 'd' and resid 1796 through 1814 removed outlier: 3.821A pdb=" N THR d1801 " --> pdb=" O PRO d1797 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS d1814 " --> pdb=" O ARG d1810 " (cutoff:3.500A) Processing helix chain 'd' and resid 1817 through 1823 removed outlier: 4.363A pdb=" N GLN d1822 " --> pdb=" O GLN d1818 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN d1823 " --> pdb=" O GLU d1819 " (cutoff:3.500A) Processing helix chain 'd' and resid 1826 through 1833 removed outlier: 3.814A pdb=" N LEU d1830 " --> pdb=" O ASP d1826 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL d1831 " --> pdb=" O ASP d1827 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 165 through 169 removed outlier: 5.746A pdb=" N THR A 38 " --> pdb=" O GLN A 53 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 69 through 71 Processing sheet with id= C, first strand: chain 'B' and resid 159 through 162 Processing sheet with id= D, first strand: chain 'B' and resid 73 through 77 Processing sheet with id= E, first strand: chain 'C' and resid 161 through 165 removed outlier: 3.616A pdb=" N CYS C 34 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR C 33 " --> pdb=" O GLU C 48 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU C 48 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY C 42 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA C 47 " --> pdb=" O GLU C 212 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS C 222 " --> pdb=" O GLU C 219 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 144 through 150 removed outlier: 6.373A pdb=" N CYS C 74 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LYS C 67 " --> pdb=" O CYS C 74 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 158 through 161 Processing sheet with id= H, first strand: chain 'D' and resid 142 through 144 removed outlier: 3.599A pdb=" N VAL D 69 " --> pdb=" O ASP D 66 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N MET D 71 " --> pdb=" O ALA D 64 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ALA D 64 " --> pdb=" O MET D 71 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE D 73 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE D 62 " --> pdb=" O PHE D 73 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.678A pdb=" N HIS D 154 " --> pdb=" O GLN D 146 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 167 through 170 removed outlier: 3.642A pdb=" N GLY E 45 " --> pdb=" O THR E 42 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 161 through 164 removed outlier: 3.597A pdb=" N THR E 161 " --> pdb=" O ASP E 157 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU E 141 " --> pdb=" O MET E 156 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N CYS E 76 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLU E 69 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N MET E 78 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE E 67 " --> pdb=" O MET E 78 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 158 through 161 removed outlier: 3.823A pdb=" N ILE F 212 " --> pdb=" O TYR F 224 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 63 through 65 Processing sheet with id= N, first strand: chain 'G' and resid 162 through 165 removed outlier: 4.768A pdb=" N ALA G 208 " --> pdb=" O VAL G 53 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 66 through 68 removed outlier: 3.507A pdb=" N TYR G 158 " --> pdb=" O MET G 150 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 125 through 128 removed outlier: 3.525A pdb=" N GLY H 11 " --> pdb=" O PHE H 8 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 34 through 36 Processing sheet with id= R, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.555A pdb=" N THR H 22 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE H 26 " --> pdb=" O THR H 22 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 124 through 127 Processing sheet with id= T, first strand: chain 'I' and resid 107 through 110 removed outlier: 3.511A pdb=" N ALA I 97 " --> pdb=" O ALA I 46 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS I 44 " --> pdb=" O VAL I 99 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N CYS I 43 " --> pdb=" O PHE I 36 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N PHE I 36 " --> pdb=" O CYS I 43 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLY I 45 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE I 34 " --> pdb=" O GLY I 45 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 111 through 113 Processing sheet with id= V, first strand: chain 'J' and resid 135 through 139 removed outlier: 6.467A pdb=" N ALA J 9 " --> pdb=" O ASP J 24 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N CYS J 18 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL J 184 " --> pdb=" O LEU J 199 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 41 through 43 Processing sheet with id= X, first strand: chain 'J' and resid 27 through 29 removed outlier: 6.199A pdb=" N ILE J 29 " --> pdb=" O MET J 33 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N MET J 33 " --> pdb=" O ILE J 29 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 129 through 132 removed outlier: 3.797A pdb=" N LEU K 4 " --> pdb=" O HIS K 132 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 35 through 37 removed outlier: 3.753A pdb=" N ALA K 105 " --> pdb=" O LEU K 43 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 125 through 129 removed outlier: 3.732A pdb=" N SER L 188 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HIS L 178 " --> pdb=" O ARG L 186 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ARG L 186 " --> pdb=" O HIS L 178 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG L 180 " --> pdb=" O TRP L 184 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N TRP L 184 " --> pdb=" O ARG L 180 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'L' and resid 99 through 105 Processing sheet with id= AC, first strand: chain 'L' and resid 20 through 22 removed outlier: 3.556A pdb=" N SER L 28 " --> pdb=" O ALA L 20 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA L 22 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE L 26 " --> pdb=" O ALA L 22 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.734A pdb=" N LEU L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'M' and resid 11 through 15 Processing sheet with id= AF, first strand: chain 'M' and resid 20 through 26 removed outlier: 3.537A pdb=" N GLY M 202 " --> pdb=" O THR M 199 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'M' and resid 130 through 133 removed outlier: 3.747A pdb=" N VAL M 121 " --> pdb=" O ASP M 133 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASN M 108 " --> pdb=" O PHE M 124 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR M 50 " --> pdb=" O THR M 47 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR M 47 " --> pdb=" O THR M 50 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE M 52 " --> pdb=" O LYS M 45 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LYS M 45 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N CYS M 54 " --> pdb=" O CYS M 43 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N CYS M 43 " --> pdb=" O CYS M 54 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'M' and resid 29 through 31 removed outlier: 6.236A pdb=" N GLU M 31 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILE M 35 " --> pdb=" O GLU M 31 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'N' and resid 14 through 16 removed outlier: 3.508A pdb=" N GLY N 19 " --> pdb=" O PHE N 16 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'N' and resid 131 through 133 removed outlier: 3.541A pdb=" N THR N 49 " --> pdb=" O ASN N 46 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU N 51 " --> pdb=" O ARG N 44 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ARG N 44 " --> pdb=" O LEU N 51 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ALA N 53 " --> pdb=" O ILE N 42 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE N 42 " --> pdb=" O ALA N 53 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'O' and resid 165 through 169 removed outlier: 5.747A pdb=" N THR O 38 " --> pdb=" O GLN O 53 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'O' and resid 69 through 71 Processing sheet with id= AM, first strand: chain 'P' and resid 159 through 162 Processing sheet with id= AN, first strand: chain 'P' and resid 73 through 77 Processing sheet with id= AO, first strand: chain 'Q' and resid 161 through 165 removed outlier: 3.615A pdb=" N CYS Q 34 " --> pdb=" O ILE Q 164 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR Q 33 " --> pdb=" O GLU Q 48 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU Q 48 " --> pdb=" O THR Q 33 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY Q 42 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA Q 47 " --> pdb=" O GLU Q 212 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS Q 222 " --> pdb=" O GLU Q 219 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'Q' and resid 144 through 150 removed outlier: 6.373A pdb=" N CYS Q 74 " --> pdb=" O LYS Q 67 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYS Q 67 " --> pdb=" O CYS Q 74 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'R' and resid 158 through 161 Processing sheet with id= AR, first strand: chain 'R' and resid 142 through 144 removed outlier: 3.598A pdb=" N VAL R 69 " --> pdb=" O ASP R 66 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N MET R 71 " --> pdb=" O ALA R 64 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ALA R 64 " --> pdb=" O MET R 71 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE R 73 " --> pdb=" O ILE R 62 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE R 62 " --> pdb=" O PHE R 73 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'R' and resid 145 through 147 removed outlier: 3.679A pdb=" N HIS R 154 " --> pdb=" O GLN R 146 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'S' and resid 167 through 170 removed outlier: 3.642A pdb=" N GLY S 45 " --> pdb=" O THR S 42 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'S' and resid 161 through 164 removed outlier: 3.597A pdb=" N THR S 161 " --> pdb=" O ASP S 157 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU S 141 " --> pdb=" O MET S 156 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N CYS S 76 " --> pdb=" O GLU S 69 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLU S 69 " --> pdb=" O CYS S 76 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N MET S 78 " --> pdb=" O ILE S 67 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE S 67 " --> pdb=" O MET S 78 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'T' and resid 158 through 161 removed outlier: 3.823A pdb=" N ILE T 212 " --> pdb=" O TYR T 224 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'T' and resid 63 through 65 Processing sheet with id= AX, first strand: chain 'U' and resid 162 through 165 removed outlier: 4.767A pdb=" N ALA U 208 " --> pdb=" O VAL U 53 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'U' and resid 66 through 68 removed outlier: 3.507A pdb=" N TYR U 158 " --> pdb=" O MET U 150 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'V' and resid 125 through 128 removed outlier: 3.525A pdb=" N GLY V 11 " --> pdb=" O PHE V 8 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'V' and resid 34 through 36 Processing sheet with id= BB, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.556A pdb=" N THR V 22 " --> pdb=" O ILE V 26 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE V 26 " --> pdb=" O THR V 22 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'W' and resid 124 through 127 Processing sheet with id= BD, first strand: chain 'W' and resid 107 through 110 removed outlier: 3.511A pdb=" N ALA W 97 " --> pdb=" O ALA W 46 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS W 44 " --> pdb=" O VAL W 99 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N CYS W 43 " --> pdb=" O PHE W 36 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N PHE W 36 " --> pdb=" O CYS W 43 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLY W 45 " --> pdb=" O ILE W 34 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE W 34 " --> pdb=" O GLY W 45 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'W' and resid 111 through 113 Processing sheet with id= BF, first strand: chain 'X' and resid 135 through 139 removed outlier: 6.466A pdb=" N ALA X 9 " --> pdb=" O ASP X 24 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N CYS X 18 " --> pdb=" O GLY X 15 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL X 184 " --> pdb=" O LEU X 199 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'X' and resid 41 through 43 Processing sheet with id= BH, first strand: chain 'X' and resid 27 through 29 removed outlier: 6.199A pdb=" N ILE X 29 " --> pdb=" O MET X 33 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N MET X 33 " --> pdb=" O ILE X 29 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'Y' and resid 129 through 132 removed outlier: 3.797A pdb=" N LEU Y 4 " --> pdb=" O HIS Y 132 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'Y' and resid 35 through 37 removed outlier: 3.753A pdb=" N ALA Y 105 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'Z' and resid 125 through 129 removed outlier: 3.732A pdb=" N SER Z 188 " --> pdb=" O LEU Z 176 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HIS Z 178 " --> pdb=" O ARG Z 186 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ARG Z 186 " --> pdb=" O HIS Z 178 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG Z 180 " --> pdb=" O TRP Z 184 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP Z 184 " --> pdb=" O ARG Z 180 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'Z' and resid 99 through 105 Processing sheet with id= BM, first strand: chain 'Z' and resid 20 through 22 removed outlier: 3.556A pdb=" N SER Z 28 " --> pdb=" O ALA Z 20 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA Z 22 " --> pdb=" O ILE Z 26 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE Z 26 " --> pdb=" O ALA Z 22 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.734A pdb=" N LEU Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'a' and resid 11 through 15 Processing sheet with id= BP, first strand: chain 'a' and resid 20 through 26 removed outlier: 3.536A pdb=" N GLY a 202 " --> pdb=" O THR a 199 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'a' and resid 130 through 133 removed outlier: 3.747A pdb=" N VAL a 121 " --> pdb=" O ASP a 133 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN a 108 " --> pdb=" O PHE a 124 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR a 50 " --> pdb=" O THR a 47 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR a 47 " --> pdb=" O THR a 50 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE a 52 " --> pdb=" O LYS a 45 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LYS a 45 " --> pdb=" O ILE a 52 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N CYS a 54 " --> pdb=" O CYS a 43 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N CYS a 43 " --> pdb=" O CYS a 54 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'a' and resid 29 through 31 removed outlier: 6.237A pdb=" N GLU a 31 " --> pdb=" O ILE a 35 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILE a 35 " --> pdb=" O GLU a 31 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'b' and resid 14 through 16 removed outlier: 3.507A pdb=" N GLY b 19 " --> pdb=" O PHE b 16 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'b' and resid 131 through 133 removed outlier: 3.540A pdb=" N THR b 49 " --> pdb=" O ASN b 46 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU b 51 " --> pdb=" O ARG b 44 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ARG b 44 " --> pdb=" O LEU b 51 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ALA b 53 " --> pdb=" O ILE b 42 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE b 42 " --> pdb=" O ALA b 53 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'c' and resid 1221 through 1224 removed outlier: 4.201A pdb=" N MET c1283 " --> pdb=" O ILE c1224 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'd' and resid 1221 through 1224 removed outlier: 4.201A pdb=" N MET d1283 " --> pdb=" O ILE d1224 " (cutoff:3.500A) 2938 hydrogen bonds defined for protein. 8328 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: 34.51 Time building geometry restraints manager: 22.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 11157 1.32 - 1.44: 19038 1.44 - 1.57: 41204 1.57 - 1.69: 59 1.69 - 1.81: 702 Bond restraints: 72160 Sorted by residual: bond pdb=" CD GLN d1796 " pdb=" OE1 GLN d1796 " ideal model delta sigma weight residual 1.231 1.326 -0.095 1.90e-02 2.77e+03 2.51e+01 bond pdb=" CD GLN d1796 " pdb=" NE2 GLN d1796 " ideal model delta sigma weight residual 1.328 1.226 0.102 2.10e-02 2.27e+03 2.37e+01 bond pdb=" C TRP J 153 " pdb=" N GLU J 154 " ideal model delta sigma weight residual 1.333 1.205 0.128 2.74e-02 1.33e+03 2.17e+01 bond pdb=" C TRP X 153 " pdb=" N GLU X 154 " ideal model delta sigma weight residual 1.333 1.205 0.127 2.74e-02 1.33e+03 2.16e+01 bond pdb=" O22 IHP c1901 " pdb=" P2 IHP c1901 " ideal model delta sigma weight residual 1.526 1.611 -0.085 2.00e-02 2.50e+03 1.80e+01 ... (remaining 72155 not shown) Histogram of bond angle deviations from ideal: 95.31 - 103.24: 736 103.24 - 111.18: 29119 111.18 - 119.11: 29594 119.11 - 127.05: 37955 127.05 - 134.98: 804 Bond angle restraints: 98208 Sorted by residual: angle pdb=" C TYR c 34 " pdb=" CA TYR c 34 " pdb=" CB TYR c 34 " ideal model delta sigma weight residual 110.56 99.68 10.88 1.69e+00 3.50e-01 4.14e+01 angle pdb=" C TYR d 34 " pdb=" CA TYR d 34 " pdb=" CB TYR d 34 " ideal model delta sigma weight residual 110.56 99.76 10.80 1.69e+00 3.50e-01 4.08e+01 angle pdb=" N THR O 190 " pdb=" CA THR O 190 " pdb=" C THR O 190 " ideal model delta sigma weight residual 110.80 99.07 11.73 2.13e+00 2.20e-01 3.03e+01 angle pdb=" N THR A 190 " pdb=" CA THR A 190 " pdb=" C THR A 190 " ideal model delta sigma weight residual 110.80 99.08 11.72 2.13e+00 2.20e-01 3.03e+01 angle pdb=" C GLY W 170 " pdb=" N SER W 171 " pdb=" CA SER W 171 " ideal model delta sigma weight residual 121.54 130.93 -9.39 1.91e+00 2.74e-01 2.42e+01 ... (remaining 98203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.81: 42223 24.81 - 49.63: 757 49.63 - 74.44: 50 74.44 - 99.26: 4 99.26 - 124.07: 12 Dihedral angle restraints: 43046 sinusoidal: 15268 harmonic: 27778 Sorted by residual: dihedral pdb=" CA ASN Y 24 " pdb=" C ASN Y 24 " pdb=" N ILE Y 25 " pdb=" CA ILE Y 25 " ideal model delta harmonic sigma weight residual -180.00 -140.17 -39.83 0 5.00e+00 4.00e-02 6.34e+01 dihedral pdb=" CA ASN K 24 " pdb=" C ASN K 24 " pdb=" N ILE K 25 " pdb=" CA ILE K 25 " ideal model delta harmonic sigma weight residual -180.00 -140.19 -39.81 0 5.00e+00 4.00e-02 6.34e+01 dihedral pdb=" CA VAL d 296 " pdb=" C VAL d 296 " pdb=" N LEU d 297 " pdb=" CA LEU d 297 " ideal model delta harmonic sigma weight residual 180.00 142.47 37.53 0 5.00e+00 4.00e-02 5.63e+01 ... (remaining 43043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.019: 11588 1.019 - 2.038: 0 2.038 - 3.057: 0 3.057 - 4.076: 0 4.076 - 5.095: 4 Chirality restraints: 11592 Sorted by residual: chirality pdb=" C2 IHP c1901 " pdb=" C1 IHP c1901 " pdb=" C3 IHP c1901 " pdb=" O12 IHP c1901 " both_signs ideal model delta sigma weight residual False -2.52 2.58 -5.09 2.00e-01 2.50e+01 6.49e+02 chirality pdb=" C2 IHP d1901 " pdb=" C1 IHP d1901 " pdb=" C3 IHP d1901 " pdb=" O12 IHP d1901 " both_signs ideal model delta sigma weight residual False -2.52 2.58 -5.09 2.00e-01 2.50e+01 6.49e+02 chirality pdb=" C1 IHP c1901 " pdb=" C2 IHP c1901 " pdb=" C6 IHP c1901 " pdb=" O11 IHP c1901 " both_signs ideal model delta sigma weight residual False 2.32 -2.58 4.89 2.00e-01 2.50e+01 5.99e+02 ... (remaining 11589 not shown) Planarity restraints: 12350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 K0W d1902 " 0.134 2.00e-02 2.50e+03 5.64e-01 9.53e+03 pdb=" C2 K0W d1902 " -0.218 2.00e-02 2.50e+03 pdb=" C3 K0W d1902 " 0.116 2.00e-02 2.50e+03 pdb=" C4 K0W d1902 " -0.333 2.00e-02 2.50e+03 pdb=" C5 K0W d1902 " -0.793 2.00e-02 2.50e+03 pdb=" C6 K0W d1902 " -0.097 2.00e-02 2.50e+03 pdb=" O11 K0W d1902 " 1.166 2.00e-02 2.50e+03 pdb=" O12 K0W d1902 " 0.606 2.00e-02 2.50e+03 pdb=" O13 K0W d1902 " -0.335 2.00e-02 2.50e+03 pdb=" O14 K0W d1902 " 0.779 2.00e-02 2.50e+03 pdb=" O15 K0W d1902 " -0.430 2.00e-02 2.50e+03 pdb=" O16 K0W d1902 " -0.595 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 K0W c1902 " -0.134 2.00e-02 2.50e+03 5.64e-01 9.53e+03 pdb=" C2 K0W c1902 " 0.218 2.00e-02 2.50e+03 pdb=" C3 K0W c1902 " -0.116 2.00e-02 2.50e+03 pdb=" C4 K0W c1902 " 0.333 2.00e-02 2.50e+03 pdb=" C5 K0W c1902 " 0.792 2.00e-02 2.50e+03 pdb=" C6 K0W c1902 " 0.097 2.00e-02 2.50e+03 pdb=" O11 K0W c1902 " -1.166 2.00e-02 2.50e+03 pdb=" O12 K0W c1902 " -0.606 2.00e-02 2.50e+03 pdb=" O13 K0W c1902 " 0.336 2.00e-02 2.50e+03 pdb=" O14 K0W c1902 " -0.779 2.00e-02 2.50e+03 pdb=" O15 K0W c1902 " 0.430 2.00e-02 2.50e+03 pdb=" O16 K0W c1902 " 0.594 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL W 99 " 0.020 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C VAL W 99 " -0.071 2.00e-02 2.50e+03 pdb=" O VAL W 99 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU W 100 " 0.024 2.00e-02 2.50e+03 ... (remaining 12347 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 12159 2.76 - 3.29: 63381 3.29 - 3.83: 118089 3.83 - 4.36: 144217 4.36 - 4.90: 245676 Nonbonded interactions: 583522 Sorted by model distance: nonbonded pdb=" OH TYR d 34 " pdb=" O26 K0W d1902 " model vdw 2.221 2.440 nonbonded pdb=" OH TYR c 34 " pdb=" O26 K0W c1902 " model vdw 2.228 2.440 nonbonded pdb=" OE2 GLU d 252 " pdb=" OH TYR d 306 " model vdw 2.232 2.440 nonbonded pdb=" OE2 GLU c 252 " pdb=" OH TYR c 306 " model vdw 2.232 2.440 nonbonded pdb=" OD1 ASP Y 52 " pdb=" OH TYR Z 88 " model vdw 2.298 2.440 ... (remaining 583517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } ncs_group { reference = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 39.720 Check model and map are aligned: 0.770 Set scattering table: 0.480 Process input model: 154.540 Find NCS groups from input model: 5.160 Set up NCS constraints: 0.560 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: 0.020 Load rotamer database and sin/cos tables:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 221.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 : 0.009 0.128 72160 Z= 0.582 Angle : 1.030 12.983 98208 Z= 0.538 Chirality : 0.110 5.095 11592 Planarity : 0.011 0.564 12350 Dihedral : 10.397 124.072 25162 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.90 % Favored : 92.99 % Rotamer: Outliers : 0.71 % Allowed : 2.82 % Favored : 96.47 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -4.99 (0.06), residues: 9478 helix: -4.23 (0.04), residues: 4218 sheet: -1.85 (0.12), residues: 1504 loop : -2.51 (0.09), residues: 3756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.004 TRP c 314 HIS 0.017 0.003 HIS d 964 PHE 0.041 0.004 PHE O 29 TYR 0.050 0.004 TYR M 130 ARG 0.015 0.001 ARG M 194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18956 Ramachandran restraints generated. 9478 Oldfield, 0 Emsley, 9478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18956 Ramachandran restraints generated. 9478 Oldfield, 0 Emsley, 9478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2260 residues out of total 8238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 2212 time to evaluate : 6.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 LYS cc_start: 0.8109 (mttm) cc_final: 0.7905 (mtmp) REVERT: D 171 PHE cc_start: 0.9141 (t80) cc_final: 0.8892 (t80) REVERT: F 6 TYR cc_start: 0.8796 (m-80) cc_final: 0.8576 (m-80) REVERT: G 175 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8406 (mp0) REVERT: H 151 GLU cc_start: 0.7680 (tt0) cc_final: 0.7399 (tt0) REVERT: J 33 MET cc_start: 0.8042 (tmm) cc_final: 0.7542 (tmm) REVERT: L 30 THR cc_start: 0.9071 (p) cc_final: 0.8855 (p) REVERT: L 119 ASN cc_start: 0.8439 (m-40) cc_final: 0.8202 (m-40) REVERT: M 118 LYS cc_start: 0.8942 (mttt) cc_final: 0.8613 (mttm) REVERT: P 158 LYS cc_start: 0.8080 (mttm) cc_final: 0.7766 (mtmt) REVERT: R 171 PHE cc_start: 0.9091 (t80) cc_final: 0.8863 (t80) REVERT: U 175 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8434 (mp0) REVERT: V 151 GLU cc_start: 0.7648 (tt0) cc_final: 0.7365 (tt0) REVERT: Z 30 THR cc_start: 0.9078 (p) cc_final: 0.8861 (p) REVERT: Z 119 ASN cc_start: 0.8434 (m-40) cc_final: 0.8208 (m-40) REVERT: a 118 LYS cc_start: 0.8945 (mttt) cc_final: 0.8612 (mttm) REVERT: c 146 TYR cc_start: 0.8085 (t80) cc_final: 0.7698 (t80) REVERT: c 415 LEU cc_start: 0.9030 (tt) cc_final: 0.8742 (tp) REVERT: c 975 SER cc_start: 0.9164 (m) cc_final: 0.8959 (m) REVERT: c 1044 HIS cc_start: 0.7726 (t70) cc_final: 0.7462 (t70) REVERT: c 1195 HIS cc_start: 0.7883 (t-170) cc_final: 0.7662 (t-170) REVERT: c 1286 TYR cc_start: 0.7879 (m-80) cc_final: 0.7642 (m-80) REVERT: c 1516 ASP cc_start: 0.8037 (t0) cc_final: 0.7621 (t0) REVERT: c 1602 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8730 (tp) REVERT: c 1703 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8120 (mt-10) REVERT: d 146 TYR cc_start: 0.7951 (t80) cc_final: 0.7555 (t80) REVERT: d 415 LEU cc_start: 0.9028 (tt) cc_final: 0.8760 (tp) REVERT: d 981 GLN cc_start: 0.8509 (mm110) cc_final: 0.8238 (mm110) REVERT: d 1044 HIS cc_start: 0.7728 (t70) cc_final: 0.7503 (t70) REVERT: d 1195 HIS cc_start: 0.7864 (t-170) cc_final: 0.7646 (t-170) REVERT: d 1286 TYR cc_start: 0.7952 (m-80) cc_final: 0.7694 (m-80) REVERT: d 1602 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8669 (tp) REVERT: d 1699 LEU cc_start: 0.9025 (tp) cc_final: 0.8822 (tm) REVERT: d 1703 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8124 (mt-10) outliers start: 48 outliers final: 10 residues processed: 2244 average time/residue: 1.4280 time to fit residues: 4248.1729 Evaluate side-chains 1350 residues out of total 8238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1338 time to evaluate : 6.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain c residue 32 ILE Chi-restraints excluded: chain c residue 578 LEU Chi-restraints excluded: chain c residue 1440 LEU Chi-restraints excluded: chain c residue 1602 LEU Chi-restraints excluded: chain d residue 32 ILE Chi-restraints excluded: chain d residue 578 LEU Chi-restraints excluded: chain d residue 1440 LEU Chi-restraints excluded: chain d residue 1602 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 944 random chunks: chunk 797 optimal weight: 0.6980 chunk 715 optimal weight: 6.9990 chunk 397 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 482 optimal weight: 0.9990 chunk 382 optimal weight: 0.7980 chunk 739 optimal weight: 5.9990 chunk 286 optimal weight: 1.9990 chunk 449 optimal weight: 0.9990 chunk 550 optimal weight: 1.9990 chunk 857 optimal weight: 0.2980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 224 ASN B 95 GLN B 111 GLN B 206 ASN C 102 GLN ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN D 159 ASN E 99 HIS F 20 HIS F 68 ASN G 97 ASN H 106 GLN I 57 GLN J 80 GLN J 172 ASN K 8 GLN K 189 HIS M 8 ASN M 80 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 GLN M 157 ASN ** N 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 GLN O 128 ASN O 224 ASN P 95 GLN P 111 GLN P 201 GLN P 206 ASN Q 102 GLN ** Q 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN R 159 ASN S 99 HIS T 20 HIS T 68 ASN V 106 GLN W 57 GLN X 172 ASN Y 8 GLN Y 189 HIS a 8 ASN a 80 ASN ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 131 GLN a 157 ASN ** b 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 117 GLN c 246 GLN c 327 GLN c 335 ASN c 369 HIS c 398 GLN c 616 HIS c 712 GLN c 864 HIS c 907 HIS c 935 HIS c 948 HIS c1086 GLN c1165 HIS c1273 HIS c1392 HIS ** c1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c1521 ASN ** c1672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 117 GLN d 246 GLN d 327 GLN d 369 HIS d 398 GLN d 423 ASN d 616 HIS d 712 GLN d 864 HIS d 907 HIS d 935 HIS d 948 HIS d1086 GLN d1165 HIS d1273 HIS d1392 HIS d1521 ASN ** d1672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 78 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 72160 Z= 0.193 Angle : 0.700 16.580 98208 Z= 0.343 Chirality : 0.045 0.535 11592 Planarity : 0.005 0.057 12350 Dihedral : 6.640 52.209 10546 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.14 % Favored : 94.80 % Rotamer: Outliers : 4.42 % Allowed : 15.34 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.10 (0.08), residues: 9478 helix: -2.17 (0.06), residues: 4250 sheet: -1.24 (0.13), residues: 1428 loop : -2.04 (0.09), residues: 3800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP U 215 HIS 0.006 0.001 HIS d 964 PHE 0.019 0.001 PHE c 119 TYR 0.035 0.001 TYR c 857 ARG 0.007 0.001 ARG P 176 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18956 Ramachandran restraints generated. 9478 Oldfield, 0 Emsley, 9478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18956 Ramachandran restraints generated. 9478 Oldfield, 0 Emsley, 9478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1966 residues out of total 8238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1668 time to evaluate : 6.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 TYR cc_start: 0.8668 (m-10) cc_final: 0.8467 (m-80) REVERT: B 158 LYS cc_start: 0.8106 (mttm) cc_final: 0.7856 (mtmt) REVERT: D 60 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6631 (ptm-80) REVERT: D 127 PHE cc_start: 0.6493 (m-10) cc_final: 0.6155 (m-80) REVERT: E 187 LYS cc_start: 0.8551 (mtmt) cc_final: 0.8330 (mtpm) REVERT: G 225 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7511 (mt-10) REVERT: H 149 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7689 (tmmm) REVERT: I 143 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7895 (ptm-80) REVERT: I 217 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8713 (p) REVERT: K 31 ASP cc_start: 0.8571 (p0) cc_final: 0.8235 (p0) REVERT: K 37 LYS cc_start: 0.8703 (tttt) cc_final: 0.8435 (tttp) REVERT: K 68 LYS cc_start: 0.9073 (tmmm) cc_final: 0.8823 (tppt) REVERT: O 23 TYR cc_start: 0.8668 (m-10) cc_final: 0.8457 (m-80) REVERT: P 158 LYS cc_start: 0.8052 (mttm) cc_final: 0.7758 (mtmp) REVERT: R 38 ARG cc_start: 0.7149 (mtp180) cc_final: 0.6557 (mtp180) REVERT: R 60 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6596 (ptm-80) REVERT: R 97 THR cc_start: 0.8969 (p) cc_final: 0.8767 (p) REVERT: S 187 LYS cc_start: 0.8982 (mtpm) cc_final: 0.8760 (mtmt) REVERT: S 216 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7077 (mm-30) REVERT: V 149 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7693 (tmmm) REVERT: W 143 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7884 (ptm-80) REVERT: W 217 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8700 (p) REVERT: Y 31 ASP cc_start: 0.8601 (p0) cc_final: 0.8260 (p0) REVERT: Y 37 LYS cc_start: 0.8683 (tttt) cc_final: 0.8426 (tttp) REVERT: Y 68 LYS cc_start: 0.9088 (tmmm) cc_final: 0.8823 (tppt) REVERT: c 423 ASN cc_start: 0.8971 (m-40) cc_final: 0.8676 (m-40) REVERT: c 501 MET cc_start: 0.8400 (mmm) cc_final: 0.8092 (mmt) REVERT: c 967 MET cc_start: 0.8796 (mmp) cc_final: 0.8565 (mmp) REVERT: c 975 SER cc_start: 0.9073 (m) cc_final: 0.8771 (m) REVERT: c 1132 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: c 1134 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: c 1195 HIS cc_start: 0.7891 (t-170) cc_final: 0.7674 (t-170) REVERT: c 1602 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8712 (tt) REVERT: d 423 ASN cc_start: 0.8842 (m110) cc_final: 0.8631 (m-40) REVERT: d 967 MET cc_start: 0.8774 (mmp) cc_final: 0.8547 (mmp) REVERT: d 1132 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: d 1195 HIS cc_start: 0.7855 (t-170) cc_final: 0.7629 (t-170) REVERT: d 1602 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8760 (tt) outliers start: 298 outliers final: 87 residues processed: 1823 average time/residue: 1.2845 time to fit residues: 3208.2824 Evaluate side-chains 1427 residues out of total 8238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1327 time to evaluate : 6.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 133 CYS Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain J residue 180 SER Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain P residue 34 SER Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 104 ILE Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 151 SER Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain R residue 60 ARG Chi-restraints excluded: chain R residue 154 HIS Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 142 VAL Chi-restraints excluded: chain U residue 226 ILE Chi-restraints excluded: chain V residue 149 LYS Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 143 ARG Chi-restraints excluded: chain W residue 217 THR Chi-restraints excluded: chain X residue 180 SER Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain c residue 32 ILE Chi-restraints excluded: chain c residue 169 VAL Chi-restraints excluded: chain c residue 193 LEU Chi-restraints excluded: chain c residue 511 SER Chi-restraints excluded: chain c residue 576 THR Chi-restraints excluded: chain c residue 578 LEU Chi-restraints excluded: chain c residue 588 SER Chi-restraints excluded: chain c residue 594 LEU Chi-restraints excluded: chain c residue 710 CYS Chi-restraints excluded: chain c residue 872 ILE Chi-restraints excluded: chain c residue 1132 GLN Chi-restraints excluded: chain c residue 1134 GLU Chi-restraints excluded: chain c residue 1348 ILE Chi-restraints excluded: chain c residue 1440 LEU Chi-restraints excluded: chain c residue 1590 SER Chi-restraints excluded: chain c residue 1602 LEU Chi-restraints excluded: chain c residue 1736 LEU Chi-restraints excluded: chain d residue 32 ILE Chi-restraints excluded: chain d residue 44 LEU Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 458 SER Chi-restraints excluded: chain d residue 511 SER Chi-restraints excluded: chain d residue 576 THR Chi-restraints excluded: chain d residue 578 LEU Chi-restraints excluded: chain d residue 588 SER Chi-restraints excluded: chain d residue 594 LEU Chi-restraints excluded: chain d residue 710 CYS Chi-restraints excluded: chain d residue 1132 GLN Chi-restraints excluded: chain d residue 1272 THR Chi-restraints excluded: chain d residue 1348 ILE Chi-restraints excluded: chain d residue 1440 LEU Chi-restraints excluded: chain d residue 1510 THR Chi-restraints excluded: chain d residue 1590 SER Chi-restraints excluded: chain d residue 1602 LEU Chi-restraints excluded: chain d residue 1736 LEU Chi-restraints excluded: chain d residue 1792 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 944 random chunks: chunk 476 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 chunk 713 optimal weight: 10.0000 chunk 583 optimal weight: 0.0040 chunk 236 optimal weight: 5.9990 chunk 858 optimal weight: 3.9990 chunk 927 optimal weight: 0.9990 chunk 764 optimal weight: 8.9990 chunk 851 optimal weight: 0.9990 chunk 292 optimal weight: 3.9990 chunk 688 optimal weight: 0.2980 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN D 85 ASN H 106 GLN I 57 GLN K 8 GLN K 87 ASN M 8 ASN M 80 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 224 ASN ** P 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 95 GLN ** P 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 ASN R 85 ASN V 106 GLN W 57 GLN Y 8 GLN Y 87 ASN a 8 ASN a 80 ASN ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 35 ASN ** c 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 335 ASN ** d 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d1672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d1796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 72160 Z= 0.223 Angle : 0.649 16.340 98208 Z= 0.315 Chirality : 0.044 0.393 11592 Planarity : 0.004 0.062 12350 Dihedral : 6.211 58.107 10542 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.17 % Favored : 94.79 % Rotamer: Outliers : 4.76 % Allowed : 18.10 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.08), residues: 9478 helix: -0.86 (0.08), residues: 4272 sheet: -1.04 (0.13), residues: 1492 loop : -1.73 (0.10), residues: 3714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP d 314 HIS 0.006 0.001 HIS P 70 PHE 0.024 0.001 PHE R 171 TYR 0.031 0.001 TYR c 857 ARG 0.012 0.000 ARG c 285 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18956 Ramachandran restraints generated. 9478 Oldfield, 0 Emsley, 9478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18956 Ramachandran restraints generated. 9478 Oldfield, 0 Emsley, 9478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1742 residues out of total 8238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 1421 time to evaluate : 6.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 60 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6759 (ptm-80) REVERT: E 216 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7157 (mm-30) REVERT: G 80 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8221 (tp) REVERT: H 91 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7787 (ptt180) REVERT: I 53 ASP cc_start: 0.7918 (m-30) cc_final: 0.7650 (m-30) REVERT: I 217 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8736 (p) REVERT: K 31 ASP cc_start: 0.8649 (p0) cc_final: 0.8303 (p0) REVERT: K 37 LYS cc_start: 0.8698 (tttt) cc_final: 0.8396 (tttp) REVERT: N 191 THR cc_start: 0.8959 (p) cc_final: 0.8755 (p) REVERT: O 23 TYR cc_start: 0.8697 (m-10) cc_final: 0.8434 (m-80) REVERT: P 175 LYS cc_start: 0.8609 (mtpp) cc_final: 0.8352 (tptp) REVERT: R 60 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6709 (ptm-80) REVERT: S 187 LYS cc_start: 0.8991 (mtpm) cc_final: 0.8782 (mtmt) REVERT: U 80 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8226 (tp) REVERT: V 91 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7845 (ptt180) REVERT: W 53 ASP cc_start: 0.7895 (m-30) cc_final: 0.7622 (m-30) REVERT: W 217 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8752 (p) REVERT: X 112 ASP cc_start: 0.8006 (t0) cc_final: 0.7791 (t0) REVERT: Y 31 ASP cc_start: 0.8684 (p0) cc_final: 0.8318 (p0) REVERT: Y 37 LYS cc_start: 0.8689 (tttt) cc_final: 0.8412 (tttp) REVERT: a 60 ASP cc_start: 0.8492 (m-30) cc_final: 0.8292 (m-30) REVERT: c 362 ASN cc_start: 0.8733 (t0) cc_final: 0.8529 (t0) REVERT: c 415 LEU cc_start: 0.8894 (tt) cc_final: 0.8423 (tp) REVERT: c 419 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: c 423 ASN cc_start: 0.8917 (m-40) cc_final: 0.8450 (m110) REVERT: c 656 GLN cc_start: 0.8477 (tt0) cc_final: 0.8253 (tt0) REVERT: c 967 MET cc_start: 0.8903 (mmp) cc_final: 0.8654 (mmp) REVERT: c 975 SER cc_start: 0.9105 (m) cc_final: 0.8820 (m) REVERT: c 1132 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7193 (tm-30) REVERT: c 1195 HIS cc_start: 0.7865 (t-170) cc_final: 0.7646 (t-170) REVERT: c 1602 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8782 (tt) REVERT: d 415 LEU cc_start: 0.8905 (tt) cc_final: 0.8482 (tp) REVERT: d 419 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: d 423 ASN cc_start: 0.8836 (m110) cc_final: 0.8415 (m110) REVERT: d 925 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7841 (ptt) REVERT: d 967 MET cc_start: 0.8856 (mmp) cc_final: 0.8628 (mmp) REVERT: d 1132 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7185 (tm-30) REVERT: d 1195 HIS cc_start: 0.7859 (t-170) cc_final: 0.7608 (t-170) REVERT: d 1602 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8717 (tt) REVERT: d 1629 MET cc_start: 0.8758 (mtp) cc_final: 0.8504 (mtp) outliers start: 321 outliers final: 134 residues processed: 1601 average time/residue: 1.2845 time to fit residues: 2844.5410 Evaluate side-chains 1414 residues out of total 8238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1265 time to evaluate : 6.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain F residue 43 HIS Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 169 ARG Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain J residue 180 SER Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 180 VAL Chi-restraints excluded: chain K residue 182 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain P residue 34 SER Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 104 ILE Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 211 VAL Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 60 ARG Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 154 HIS Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 221 ASN Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain T residue 43 HIS Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 220 THR Chi-restraints excluded: chain V residue 43 CYS Chi-restraints excluded: chain V residue 91 ARG Chi-restraints excluded: chain V residue 187 GLN Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 217 THR Chi-restraints excluded: chain X residue 180 SER Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Y residue 182 ILE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain c residue 44 LEU Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 419 GLN Chi-restraints excluded: chain c residue 569 GLU Chi-restraints excluded: chain c residue 576 THR Chi-restraints excluded: chain c residue 578 LEU Chi-restraints excluded: chain c residue 594 LEU Chi-restraints excluded: chain c residue 651 CYS Chi-restraints excluded: chain c residue 655 THR Chi-restraints excluded: chain c residue 855 LEU Chi-restraints excluded: chain c residue 1132 GLN Chi-restraints excluded: chain c residue 1250 HIS Chi-restraints excluded: chain c residue 1272 THR Chi-restraints excluded: chain c residue 1309 ILE Chi-restraints excluded: chain c residue 1440 LEU Chi-restraints excluded: chain c residue 1525 THR Chi-restraints excluded: chain c residue 1590 SER Chi-restraints excluded: chain c residue 1602 LEU Chi-restraints excluded: chain c residue 1624 LEU Chi-restraints excluded: chain c residue 1660 THR Chi-restraints excluded: chain c residue 1736 LEU Chi-restraints excluded: chain c residue 1764 LEU Chi-restraints excluded: chain d residue 44 LEU Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain d residue 345 ASN Chi-restraints excluded: chain d residue 380 THR Chi-restraints excluded: chain d residue 419 GLN Chi-restraints excluded: chain d residue 458 SER Chi-restraints excluded: chain d residue 569 GLU Chi-restraints excluded: chain d residue 576 THR Chi-restraints excluded: chain d residue 578 LEU Chi-restraints excluded: chain d residue 594 LEU Chi-restraints excluded: chain d residue 651 CYS Chi-restraints excluded: chain d residue 655 THR Chi-restraints excluded: chain d residue 855 LEU Chi-restraints excluded: chain d residue 880 LEU Chi-restraints excluded: chain d residue 925 MET Chi-restraints excluded: chain d residue 1132 GLN Chi-restraints excluded: chain d residue 1250 HIS Chi-restraints excluded: chain d residue 1272 THR Chi-restraints excluded: chain d residue 1309 ILE Chi-restraints excluded: chain d residue 1348 ILE Chi-restraints excluded: chain d residue 1404 LEU Chi-restraints excluded: chain d residue 1405 LEU Chi-restraints excluded: chain d residue 1440 LEU Chi-restraints excluded: chain d residue 1510 THR Chi-restraints excluded: chain d residue 1590 SER Chi-restraints excluded: chain d residue 1602 LEU Chi-restraints excluded: chain d residue 1624 LEU Chi-restraints excluded: chain d residue 1660 THR Chi-restraints excluded: chain d residue 1736 LEU Chi-restraints excluded: chain d residue 1764 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 944 random chunks: chunk 848 optimal weight: 20.0000 chunk 645 optimal weight: 6.9990 chunk 445 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 409 optimal weight: 6.9990 chunk 576 optimal weight: 1.9990 chunk 861 optimal weight: 1.9990 chunk 912 optimal weight: 0.5980 chunk 450 optimal weight: 2.9990 chunk 816 optimal weight: 10.0000 chunk 245 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN B 111 GLN B 206 ASN C 142 HIS C 235 GLN D 54 GLN H 106 GLN I 57 GLN K 87 ASN M 8 ASN M 108 ASN ** N 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN O 224 ASN ** P 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 ASN Q 142 HIS Q 235 GLN R 54 GLN V 106 GLN W 57 GLN ** Y 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 87 ASN a 8 ASN a 108 ASN b 188 GLN c1042 ASN ** c1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d1042 ASN ** d1672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d1796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 72160 Z= 0.326 Angle : 0.671 15.987 98208 Z= 0.326 Chirality : 0.045 0.328 11592 Planarity : 0.004 0.057 12350 Dihedral : 6.072 59.803 10538 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.51 % Favored : 94.45 % Rotamer: Outliers : 5.28 % Allowed : 18.77 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.34 (0.08), residues: 9478 helix: -0.22 (0.08), residues: 4308 sheet: -0.83 (0.13), residues: 1474 loop : -1.60 (0.10), residues: 3696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 215 HIS 0.008 0.001 HIS P 70 PHE 0.017 0.002 PHE X 116 TYR 0.037 0.002 TYR d 857 ARG 0.010 0.000 ARG d 285 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18956 Ramachandran restraints generated. 9478 Oldfield, 0 Emsley, 9478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18956 Ramachandran restraints generated. 9478 Oldfield, 0 Emsley, 9478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1666 residues out of total 8238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 356 poor density : 1310 time to evaluate : 6.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 60 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6773 (ptm-80) REVERT: E 210 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8747 (mt) REVERT: E 216 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7226 (mm-30) REVERT: G 80 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8326 (tp) REVERT: H 91 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7857 (ptt180) REVERT: I 143 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7690 (ptm-80) REVERT: I 217 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8755 (p) REVERT: J 150 GLU cc_start: 0.7824 (tp30) cc_final: 0.7620 (tp30) REVERT: K 31 ASP cc_start: 0.8706 (p0) cc_final: 0.8379 (p0) REVERT: K 37 LYS cc_start: 0.8706 (tttt) cc_final: 0.8435 (tttp) REVERT: M 60 ASP cc_start: 0.8573 (m-30) cc_final: 0.8338 (m-30) REVERT: O 23 TYR cc_start: 0.8723 (m-80) cc_final: 0.8463 (m-80) REVERT: R 60 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6791 (ptm-80) REVERT: S 184 VAL cc_start: 0.9443 (m) cc_final: 0.9198 (p) REVERT: S 210 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8769 (mt) REVERT: T 159 MET cc_start: 0.8412 (tpp) cc_final: 0.8067 (tpt) REVERT: U 80 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8354 (tp) REVERT: U 225 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7433 (mt-10) REVERT: V 91 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7886 (ptt180) REVERT: W 53 ASP cc_start: 0.7924 (m-30) cc_final: 0.7605 (m-30) REVERT: W 143 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7686 (ptm-80) REVERT: W 217 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8760 (p) REVERT: Y 31 ASP cc_start: 0.8692 (p0) cc_final: 0.8345 (p0) REVERT: Y 37 LYS cc_start: 0.8724 (tttt) cc_final: 0.8470 (tttp) REVERT: c 67 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: c 362 ASN cc_start: 0.8840 (t0) cc_final: 0.8639 (t0) REVERT: c 419 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: c 423 ASN cc_start: 0.8915 (m-40) cc_final: 0.8450 (m110) REVERT: c 656 GLN cc_start: 0.8488 (tt0) cc_final: 0.8260 (tt0) REVERT: c 975 SER cc_start: 0.9152 (m) cc_final: 0.8887 (m) REVERT: c 1132 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: c 1195 HIS cc_start: 0.7897 (t-170) cc_final: 0.7696 (t-170) REVERT: c 1602 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8805 (tt) REVERT: c 1629 MET cc_start: 0.8738 (mtp) cc_final: 0.8529 (mtp) REVERT: c 1703 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8200 (mt-10) REVERT: c 1720 MET cc_start: 0.8697 (tpt) cc_final: 0.7718 (tpt) REVERT: d 67 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6733 (tm-30) REVERT: d 419 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7414 (tm-30) REVERT: d 423 ASN cc_start: 0.8826 (m110) cc_final: 0.8508 (m-40) REVERT: d 501 MET cc_start: 0.8356 (mmm) cc_final: 0.8053 (mmt) REVERT: d 803 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8024 (tt) REVERT: d 925 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7947 (ptt) REVERT: d 967 MET cc_start: 0.8873 (mmp) cc_final: 0.8643 (mmp) REVERT: d 1132 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7195 (tm-30) REVERT: d 1195 HIS cc_start: 0.7912 (t-170) cc_final: 0.7683 (t-170) REVERT: d 1602 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8753 (tt) REVERT: d 1629 MET cc_start: 0.8731 (mtp) cc_final: 0.8510 (mtp) REVERT: d 1703 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8188 (mt-10) REVERT: d 1720 MET cc_start: 0.8809 (tpt) cc_final: 0.8521 (tpt) outliers start: 356 outliers final: 178 residues processed: 1526 average time/residue: 1.2800 time to fit residues: 2687.6951 Evaluate side-chains 1406 residues out of total 8238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1206 time to evaluate : 6.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 43 HIS Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 169 ARG Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain J residue 180 SER Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 180 VAL Chi-restraints excluded: chain K residue 182 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 115 CYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain O residue 194 THR Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 104 ILE Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 211 VAL Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 60 ARG Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 154 HIS Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 221 ASN Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain S residue 210 LEU Chi-restraints excluded: chain T residue 43 HIS Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 142 VAL Chi-restraints excluded: chain U residue 169 ARG Chi-restraints excluded: chain U residue 220 THR Chi-restraints excluded: chain V residue 43 CYS Chi-restraints excluded: chain V residue 91 ARG Chi-restraints excluded: chain V residue 187 GLN Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 69 SER Chi-restraints excluded: chain W residue 143 ARG Chi-restraints excluded: chain W residue 184 ASP Chi-restraints excluded: chain W residue 217 THR Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain X residue 180 SER Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Y residue 182 ILE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 66 LYS Chi-restraints excluded: chain c residue 32 ILE Chi-restraints excluded: chain c residue 44 LEU Chi-restraints excluded: chain c residue 67 GLU Chi-restraints excluded: chain c residue 125 ASN Chi-restraints excluded: chain c residue 169 VAL Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 419 GLN Chi-restraints excluded: chain c residue 458 SER Chi-restraints excluded: chain c residue 482 LEU Chi-restraints excluded: chain c residue 569 GLU Chi-restraints excluded: chain c residue 576 THR Chi-restraints excluded: chain c residue 578 LEU Chi-restraints excluded: chain c residue 593 ILE Chi-restraints excluded: chain c residue 594 LEU Chi-restraints excluded: chain c residue 613 SER Chi-restraints excluded: chain c residue 651 CYS Chi-restraints excluded: chain c residue 692 LEU Chi-restraints excluded: chain c residue 710 CYS Chi-restraints excluded: chain c residue 855 LEU Chi-restraints excluded: chain c residue 880 LEU Chi-restraints excluded: chain c residue 913 SER Chi-restraints excluded: chain c residue 1132 GLN Chi-restraints excluded: chain c residue 1159 LEU Chi-restraints excluded: chain c residue 1250 HIS Chi-restraints excluded: chain c residue 1259 THR Chi-restraints excluded: chain c residue 1272 THR Chi-restraints excluded: chain c residue 1309 ILE Chi-restraints excluded: chain c residue 1404 LEU Chi-restraints excluded: chain c residue 1405 LEU Chi-restraints excluded: chain c residue 1440 LEU Chi-restraints excluded: chain c residue 1590 SER Chi-restraints excluded: chain c residue 1602 LEU Chi-restraints excluded: chain c residue 1624 LEU Chi-restraints excluded: chain c residue 1660 THR Chi-restraints excluded: chain c residue 1663 THR Chi-restraints excluded: chain c residue 1736 LEU Chi-restraints excluded: chain c residue 1764 LEU Chi-restraints excluded: chain d residue 32 ILE Chi-restraints excluded: chain d residue 44 LEU Chi-restraints excluded: chain d residue 67 GLU Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 345 ASN Chi-restraints excluded: chain d residue 380 THR Chi-restraints excluded: chain d residue 419 GLN Chi-restraints excluded: chain d residue 458 SER Chi-restraints excluded: chain d residue 482 LEU Chi-restraints excluded: chain d residue 511 SER Chi-restraints excluded: chain d residue 569 GLU Chi-restraints excluded: chain d residue 576 THR Chi-restraints excluded: chain d residue 578 LEU Chi-restraints excluded: chain d residue 593 ILE Chi-restraints excluded: chain d residue 594 LEU Chi-restraints excluded: chain d residue 651 CYS Chi-restraints excluded: chain d residue 655 THR Chi-restraints excluded: chain d residue 803 LEU Chi-restraints excluded: chain d residue 855 LEU Chi-restraints excluded: chain d residue 872 ILE Chi-restraints excluded: chain d residue 880 LEU Chi-restraints excluded: chain d residue 913 SER Chi-restraints excluded: chain d residue 925 MET Chi-restraints excluded: chain d residue 975 SER Chi-restraints excluded: chain d residue 1132 GLN Chi-restraints excluded: chain d residue 1140 LEU Chi-restraints excluded: chain d residue 1159 LEU Chi-restraints excluded: chain d residue 1250 HIS Chi-restraints excluded: chain d residue 1259 THR Chi-restraints excluded: chain d residue 1272 THR Chi-restraints excluded: chain d residue 1309 ILE Chi-restraints excluded: chain d residue 1348 ILE Chi-restraints excluded: chain d residue 1404 LEU Chi-restraints excluded: chain d residue 1405 LEU Chi-restraints excluded: chain d residue 1440 LEU Chi-restraints excluded: chain d residue 1510 THR Chi-restraints excluded: chain d residue 1590 SER Chi-restraints excluded: chain d residue 1602 LEU Chi-restraints excluded: chain d residue 1624 LEU Chi-restraints excluded: chain d residue 1660 THR Chi-restraints excluded: chain d residue 1663 THR Chi-restraints excluded: chain d residue 1736 LEU Chi-restraints excluded: chain d residue 1764 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 944 random chunks: chunk 759 optimal weight: 6.9990 chunk 517 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 679 optimal weight: 8.9990 chunk 376 optimal weight: 1.9990 chunk 778 optimal weight: 1.9990 chunk 630 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 465 optimal weight: 0.9990 chunk 819 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN C 235 GLN H 106 GLN I 57 GLN O 224 ASN ** P 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 ASN Q 235 GLN V 106 GLN W 57 GLN Y 8 GLN ** c1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 246 GLN ** d1796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 72160 Z= 0.247 Angle : 0.635 14.822 98208 Z= 0.307 Chirality : 0.044 0.276 11592 Planarity : 0.004 0.043 12350 Dihedral : 5.922 59.262 10538 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.16 % Favored : 94.81 % Rotamer: Outliers : 5.08 % Allowed : 19.67 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.92 (0.09), residues: 9478 helix: 0.23 (0.08), residues: 4320 sheet: -0.77 (0.13), residues: 1498 loop : -1.46 (0.10), residues: 3660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP d 75 HIS 0.007 0.001 HIS P 70 PHE 0.025 0.001 PHE R 171 TYR 0.033 0.001 TYR d 857 ARG 0.011 0.000 ARG d 285 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18956 Ramachandran restraints generated. 9478 Oldfield, 0 Emsley, 9478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18956 Ramachandran restraints generated. 9478 Oldfield, 0 Emsley, 9478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1689 residues out of total 8238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 343 poor density : 1346 time to evaluate : 6.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 60 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6831 (ptm-80) REVERT: E 184 VAL cc_start: 0.9442 (m) cc_final: 0.9203 (p) REVERT: E 216 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7272 (mm-30) REVERT: G 80 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8257 (tp) REVERT: G 212 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7615 (mt-10) REVERT: H 91 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8083 (ptt180) REVERT: I 53 ASP cc_start: 0.7923 (m-30) cc_final: 0.7599 (m-30) REVERT: I 217 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8784 (p) REVERT: J 177 ASP cc_start: 0.8391 (t0) cc_final: 0.8163 (t0) REVERT: K 31 ASP cc_start: 0.8623 (p0) cc_final: 0.8334 (p0) REVERT: K 37 LYS cc_start: 0.8729 (tttt) cc_final: 0.8454 (tttp) REVERT: R 60 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6806 (ptm-80) REVERT: S 184 VAL cc_start: 0.9437 (m) cc_final: 0.9201 (p) REVERT: T 53 GLN cc_start: 0.8197 (tt0) cc_final: 0.7893 (tt0) REVERT: U 225 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7417 (mt-10) REVERT: W 53 ASP cc_start: 0.7918 (m-30) cc_final: 0.7602 (m-30) REVERT: W 217 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8767 (p) REVERT: Y 31 ASP cc_start: 0.8612 (p0) cc_final: 0.8320 (p0) REVERT: Y 37 LYS cc_start: 0.8733 (tttt) cc_final: 0.8448 (tttp) REVERT: c 67 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6550 (tm-30) REVERT: c 156 LYS cc_start: 0.8633 (mptp) cc_final: 0.8403 (mmmt) REVERT: c 415 LEU cc_start: 0.8870 (tt) cc_final: 0.8508 (tp) REVERT: c 419 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7335 (tm-30) REVERT: c 423 ASN cc_start: 0.8872 (m-40) cc_final: 0.8380 (m110) REVERT: c 501 MET cc_start: 0.8173 (mmm) cc_final: 0.7946 (mmt) REVERT: c 656 GLN cc_start: 0.8447 (tt0) cc_final: 0.8187 (tt0) REVERT: c 803 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7954 (tt) REVERT: c 975 SER cc_start: 0.9159 (m) cc_final: 0.8899 (m) REVERT: c 1195 HIS cc_start: 0.7877 (t-170) cc_final: 0.7648 (t-170) REVERT: c 1602 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8808 (tt) REVERT: d 67 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6569 (tm-30) REVERT: d 156 LYS cc_start: 0.8645 (mptp) cc_final: 0.8409 (mmmt) REVERT: d 419 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: d 423 ASN cc_start: 0.8797 (m110) cc_final: 0.8375 (m110) REVERT: d 501 MET cc_start: 0.8320 (mmm) cc_final: 0.8032 (mmt) REVERT: d 803 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7956 (tt) REVERT: d 925 MET cc_start: 0.8194 (ptm) cc_final: 0.7968 (ptt) REVERT: d 967 MET cc_start: 0.8876 (mmp) cc_final: 0.8661 (mmp) REVERT: d 1195 HIS cc_start: 0.7867 (t-170) cc_final: 0.7647 (t-170) REVERT: d 1602 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8770 (tt) REVERT: d 1629 MET cc_start: 0.8723 (mtp) cc_final: 0.8504 (mtp) REVERT: d 1720 MET cc_start: 0.8887 (tpt) cc_final: 0.8093 (tpt) outliers start: 343 outliers final: 162 residues processed: 1551 average time/residue: 1.2504 time to fit residues: 2679.7346 Evaluate side-chains 1390 residues out of total 8238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1214 time to evaluate : 6.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 43 HIS Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 169 ARG Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 180 VAL Chi-restraints excluded: chain K residue 182 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 172 MET Chi-restraints excluded: chain N residue 173 MET Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 115 CYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain P residue 34 SER Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 104 ILE Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 211 VAL Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 60 ARG Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 154 HIS Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 221 ASN Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain T residue 43 HIS Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 142 VAL Chi-restraints excluded: chain U residue 169 ARG Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain U residue 220 THR Chi-restraints excluded: chain V residue 24 SER Chi-restraints excluded: chain V residue 43 CYS Chi-restraints excluded: chain V residue 187 GLN Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 122 LEU Chi-restraints excluded: chain W residue 217 THR Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Y residue 182 ILE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 66 LYS Chi-restraints excluded: chain a residue 172 MET Chi-restraints excluded: chain b residue 173 MET Chi-restraints excluded: chain c residue 67 GLU Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 419 GLN Chi-restraints excluded: chain c residue 458 SER Chi-restraints excluded: chain c residue 482 LEU Chi-restraints excluded: chain c residue 569 GLU Chi-restraints excluded: chain c residue 576 THR Chi-restraints excluded: chain c residue 578 LEU Chi-restraints excluded: chain c residue 588 SER Chi-restraints excluded: chain c residue 593 ILE Chi-restraints excluded: chain c residue 594 LEU Chi-restraints excluded: chain c residue 613 SER Chi-restraints excluded: chain c residue 622 VAL Chi-restraints excluded: chain c residue 626 MET Chi-restraints excluded: chain c residue 651 CYS Chi-restraints excluded: chain c residue 710 CYS Chi-restraints excluded: chain c residue 803 LEU Chi-restraints excluded: chain c residue 855 LEU Chi-restraints excluded: chain c residue 880 LEU Chi-restraints excluded: chain c residue 1140 LEU Chi-restraints excluded: chain c residue 1159 LEU Chi-restraints excluded: chain c residue 1223 THR Chi-restraints excluded: chain c residue 1250 HIS Chi-restraints excluded: chain c residue 1259 THR Chi-restraints excluded: chain c residue 1272 THR Chi-restraints excluded: chain c residue 1309 ILE Chi-restraints excluded: chain c residue 1440 LEU Chi-restraints excluded: chain c residue 1590 SER Chi-restraints excluded: chain c residue 1602 LEU Chi-restraints excluded: chain c residue 1624 LEU Chi-restraints excluded: chain c residue 1660 THR Chi-restraints excluded: chain c residue 1736 LEU Chi-restraints excluded: chain c residue 1764 LEU Chi-restraints excluded: chain d residue 67 GLU Chi-restraints excluded: chain d residue 248 LEU Chi-restraints excluded: chain d residue 345 ASN Chi-restraints excluded: chain d residue 380 THR Chi-restraints excluded: chain d residue 419 GLN Chi-restraints excluded: chain d residue 458 SER Chi-restraints excluded: chain d residue 482 LEU Chi-restraints excluded: chain d residue 569 GLU Chi-restraints excluded: chain d residue 576 THR Chi-restraints excluded: chain d residue 578 LEU Chi-restraints excluded: chain d residue 593 ILE Chi-restraints excluded: chain d residue 594 LEU Chi-restraints excluded: chain d residue 613 SER Chi-restraints excluded: chain d residue 626 MET Chi-restraints excluded: chain d residue 651 CYS Chi-restraints excluded: chain d residue 710 CYS Chi-restraints excluded: chain d residue 803 LEU Chi-restraints excluded: chain d residue 855 LEU Chi-restraints excluded: chain d residue 880 LEU Chi-restraints excluded: chain d residue 1140 LEU Chi-restraints excluded: chain d residue 1159 LEU Chi-restraints excluded: chain d residue 1223 THR Chi-restraints excluded: chain d residue 1250 HIS Chi-restraints excluded: chain d residue 1259 THR Chi-restraints excluded: chain d residue 1272 THR Chi-restraints excluded: chain d residue 1309 ILE Chi-restraints excluded: chain d residue 1404 LEU Chi-restraints excluded: chain d residue 1440 LEU Chi-restraints excluded: chain d residue 1590 SER Chi-restraints excluded: chain d residue 1602 LEU Chi-restraints excluded: chain d residue 1624 LEU Chi-restraints excluded: chain d residue 1660 THR Chi-restraints excluded: chain d residue 1724 MET Chi-restraints excluded: chain d residue 1736 LEU Chi-restraints excluded: chain d residue 1764 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 944 random chunks: chunk 306 optimal weight: 4.9990 chunk 821 optimal weight: 0.0970 chunk 180 optimal weight: 0.4980 chunk 535 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 913 optimal weight: 0.0010 chunk 758 optimal weight: 7.9990 chunk 422 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 302 optimal weight: 3.9990 chunk 479 optimal weight: 1.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 51 GLN B 95 GLN B 206 ASN C 235 GLN H 106 GLN I 57 GLN K 87 ASN N 188 GLN O 224 ASN ** P 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 ASN Q 235 GLN V 106 GLN W 57 GLN Y 87 ASN c 246 GLN ** c1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 246 GLN d 422 GLN ** d1672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d1796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 72160 Z= 0.203 Angle : 0.624 14.200 98208 Z= 0.299 Chirality : 0.043 0.246 11592 Planarity : 0.004 0.068 12350 Dihedral : 5.735 54.642 10534 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.28 % Favored : 94.70 % Rotamer: Outliers : 4.65 % Allowed : 20.80 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.60 (0.09), residues: 9478 helix: 0.53 (0.08), residues: 4318 sheet: -0.64 (0.13), residues: 1496 loop : -1.34 (0.10), residues: 3664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP d 75 HIS 0.006 0.001 HIS B 70 PHE 0.018 0.001 PHE R 73 TYR 0.036 0.001 TYR I 8 ARG 0.009 0.000 ARG c 285 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18956 Ramachandran restraints generated. 9478 Oldfield, 0 Emsley, 9478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18956 Ramachandran restraints generated. 9478 Oldfield, 0 Emsley, 9478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1672 residues out of total 8238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 1358 time to evaluate : 6.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 108 GLU cc_start: 0.8171 (tt0) cc_final: 0.7864 (tp30) REVERT: D 60 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.6807 (ptm-80) REVERT: E 184 VAL cc_start: 0.9445 (m) cc_final: 0.9212 (p) REVERT: E 216 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7268 (mm-30) REVERT: G 59 GLU cc_start: 0.8439 (tp30) cc_final: 0.8122 (tp30) REVERT: G 216 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8869 (p) REVERT: I 53 ASP cc_start: 0.7902 (m-30) cc_final: 0.7605 (m-30) REVERT: I 217 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8783 (p) REVERT: K 31 ASP cc_start: 0.8573 (p0) cc_final: 0.8346 (p0) REVERT: K 37 LYS cc_start: 0.8673 (tttt) cc_final: 0.8428 (tttp) REVERT: K 118 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7607 (ttp) REVERT: P 82 TYR cc_start: 0.8824 (t80) cc_final: 0.8591 (t80) REVERT: Q 108 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7812 (tp30) REVERT: R 60 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6826 (ptm-80) REVERT: S 184 VAL cc_start: 0.9438 (m) cc_final: 0.9207 (p) REVERT: U 175 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8290 (mt-10) REVERT: W 53 ASP cc_start: 0.7898 (m-30) cc_final: 0.7608 (m-30) REVERT: W 217 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8781 (p) REVERT: X 64 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7601 (mt0) REVERT: X 112 ASP cc_start: 0.8034 (t0) cc_final: 0.7830 (t0) REVERT: Y 31 ASP cc_start: 0.8592 (p0) cc_final: 0.8350 (p0) REVERT: Y 37 LYS cc_start: 0.8653 (tttt) cc_final: 0.8409 (tttp) REVERT: Y 118 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7609 (ttp) REVERT: c 156 LYS cc_start: 0.8637 (mptp) cc_final: 0.8410 (mmmt) REVERT: c 419 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7338 (tm-30) REVERT: c 423 ASN cc_start: 0.8858 (m-40) cc_final: 0.8336 (m110) REVERT: c 803 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7942 (tt) REVERT: c 975 SER cc_start: 0.9157 (m) cc_final: 0.8905 (m) REVERT: c 1195 HIS cc_start: 0.7817 (t-170) cc_final: 0.7598 (t-170) REVERT: c 1720 MET cc_start: 0.8733 (tpt) cc_final: 0.8367 (tpt) REVERT: d 156 LYS cc_start: 0.8625 (mptp) cc_final: 0.8411 (mmmt) REVERT: d 415 LEU cc_start: 0.8905 (tt) cc_final: 0.8525 (mm) REVERT: d 419 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7367 (tm-30) REVERT: d 423 ASN cc_start: 0.8748 (m110) cc_final: 0.8328 (m110) REVERT: d 1195 HIS cc_start: 0.7818 (t-170) cc_final: 0.7600 (t-170) REVERT: d 1629 MET cc_start: 0.8701 (mtp) cc_final: 0.8481 (mtp) outliers start: 314 outliers final: 173 residues processed: 1554 average time/residue: 1.2902 time to fit residues: 2793.3750 Evaluate side-chains 1431 residues out of total 8238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1246 time to evaluate : 6.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 169 ARG Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 118 MET Chi-restraints excluded: chain K residue 180 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 18 GLU Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain N residue 173 MET Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain P residue 34 SER Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 104 ILE Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 108 GLU Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 211 VAL Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 60 ARG Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 154 HIS Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 221 ASN Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain T residue 211 SER Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 142 VAL Chi-restraints excluded: chain U residue 169 ARG Chi-restraints excluded: chain U residue 220 THR Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 43 CYS Chi-restraints excluded: chain V residue 86 MET Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 119 MET Chi-restraints excluded: chain V residue 187 GLN Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 122 LEU Chi-restraints excluded: chain W residue 175 LEU Chi-restraints excluded: chain W residue 217 THR Chi-restraints excluded: chain X residue 64 GLN Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 118 MET Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 18 GLU Chi-restraints excluded: chain a residue 66 LYS Chi-restraints excluded: chain a residue 172 MET Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 173 MET Chi-restraints excluded: chain c residue 169 VAL Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 419 GLN Chi-restraints excluded: chain c residue 458 SER Chi-restraints excluded: chain c residue 482 LEU Chi-restraints excluded: chain c residue 569 GLU Chi-restraints excluded: chain c residue 576 THR Chi-restraints excluded: chain c residue 578 LEU Chi-restraints excluded: chain c residue 588 SER Chi-restraints excluded: chain c residue 594 LEU Chi-restraints excluded: chain c residue 613 SER Chi-restraints excluded: chain c residue 622 VAL Chi-restraints excluded: chain c residue 626 MET Chi-restraints excluded: chain c residue 651 CYS Chi-restraints excluded: chain c residue 803 LEU Chi-restraints excluded: chain c residue 855 LEU Chi-restraints excluded: chain c residue 880 LEU Chi-restraints excluded: chain c residue 1159 LEU Chi-restraints excluded: chain c residue 1223 THR Chi-restraints excluded: chain c residue 1250 HIS Chi-restraints excluded: chain c residue 1259 THR Chi-restraints excluded: chain c residue 1272 THR Chi-restraints excluded: chain c residue 1309 ILE Chi-restraints excluded: chain c residue 1405 LEU Chi-restraints excluded: chain c residue 1440 LEU Chi-restraints excluded: chain c residue 1590 SER Chi-restraints excluded: chain c residue 1624 LEU Chi-restraints excluded: chain c residue 1660 THR Chi-restraints excluded: chain c residue 1663 THR Chi-restraints excluded: chain c residue 1724 MET Chi-restraints excluded: chain c residue 1736 LEU Chi-restraints excluded: chain d residue 248 LEU Chi-restraints excluded: chain d residue 345 ASN Chi-restraints excluded: chain d residue 380 THR Chi-restraints excluded: chain d residue 419 GLN Chi-restraints excluded: chain d residue 426 LEU Chi-restraints excluded: chain d residue 458 SER Chi-restraints excluded: chain d residue 482 LEU Chi-restraints excluded: chain d residue 569 GLU Chi-restraints excluded: chain d residue 576 THR Chi-restraints excluded: chain d residue 578 LEU Chi-restraints excluded: chain d residue 588 SER Chi-restraints excluded: chain d residue 593 ILE Chi-restraints excluded: chain d residue 594 LEU Chi-restraints excluded: chain d residue 613 SER Chi-restraints excluded: chain d residue 626 MET Chi-restraints excluded: chain d residue 651 CYS Chi-restraints excluded: chain d residue 710 CYS Chi-restraints excluded: chain d residue 877 ASN Chi-restraints excluded: chain d residue 880 LEU Chi-restraints excluded: chain d residue 1140 LEU Chi-restraints excluded: chain d residue 1159 LEU Chi-restraints excluded: chain d residue 1223 THR Chi-restraints excluded: chain d residue 1259 THR Chi-restraints excluded: chain d residue 1272 THR Chi-restraints excluded: chain d residue 1348 ILE Chi-restraints excluded: chain d residue 1405 LEU Chi-restraints excluded: chain d residue 1440 LEU Chi-restraints excluded: chain d residue 1590 SER Chi-restraints excluded: chain d residue 1624 LEU Chi-restraints excluded: chain d residue 1634 LEU Chi-restraints excluded: chain d residue 1660 THR Chi-restraints excluded: chain d residue 1724 MET Chi-restraints excluded: chain d residue 1736 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 944 random chunks: chunk 880 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 520 optimal weight: 0.8980 chunk 666 optimal weight: 0.0670 chunk 516 optimal weight: 0.9990 chunk 768 optimal weight: 0.5980 chunk 510 optimal weight: 1.9990 chunk 909 optimal weight: 9.9990 chunk 569 optimal weight: 1.9990 chunk 554 optimal weight: 5.9990 chunk 420 optimal weight: 3.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 51 GLN B 95 GLN B 111 GLN B 206 ASN C 235 GLN H 106 GLN H 158 ASN I 57 GLN ** J 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 GLN M 8 ASN M 131 GLN N 188 GLN O 224 ASN ** P 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 95 GLN P 111 GLN P 206 ASN Q 235 GLN ** R 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 106 GLN W 57 GLN ** X 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 62 GLN a 131 GLN c 246 GLN d 246 GLN d 422 GLN ** d1672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d1796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 72160 Z= 0.182 Angle : 0.619 13.163 98208 Z= 0.297 Chirality : 0.043 0.228 11592 Planarity : 0.004 0.056 12350 Dihedral : 5.568 58.485 10530 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.92 % Favored : 95.06 % Rotamer: Outliers : 4.27 % Allowed : 21.78 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.36 (0.09), residues: 9478 helix: 0.77 (0.08), residues: 4298 sheet: -0.48 (0.13), residues: 1480 loop : -1.27 (0.10), residues: 3700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP d 75 HIS 0.006 0.001 HIS B 70 PHE 0.028 0.001 PHE D 171 TYR 0.041 0.001 TYR I 8 ARG 0.010 0.000 ARG c 285 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18956 Ramachandran restraints generated. 9478 Oldfield, 0 Emsley, 9478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18956 Ramachandran restraints generated. 9478 Oldfield, 0 Emsley, 9478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1649 residues out of total 8238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1361 time to evaluate : 6.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 108 GLU cc_start: 0.8175 (tt0) cc_final: 0.7835 (tp30) REVERT: D 60 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6807 (ptm-80) REVERT: E 184 VAL cc_start: 0.9450 (m) cc_final: 0.9220 (p) REVERT: G 80 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8062 (tp) REVERT: G 175 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8274 (mt-10) REVERT: G 216 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8832 (p) REVERT: I 53 ASP cc_start: 0.7882 (m-30) cc_final: 0.7614 (m-30) REVERT: I 217 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8790 (p) REVERT: K 31 ASP cc_start: 0.8569 (p0) cc_final: 0.8359 (p0) REVERT: K 37 LYS cc_start: 0.8674 (tttt) cc_final: 0.8444 (tttp) REVERT: K 118 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7601 (ttp) REVERT: Q 108 GLU cc_start: 0.8147 (tt0) cc_final: 0.7801 (tp30) REVERT: R 60 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6818 (ptm-80) REVERT: S 184 VAL cc_start: 0.9441 (m) cc_final: 0.9213 (p) REVERT: T 53 GLN cc_start: 0.8065 (tt0) cc_final: 0.7640 (tt0) REVERT: U 175 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8286 (mt-10) REVERT: U 225 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7399 (mt-10) REVERT: W 53 ASP cc_start: 0.7870 (m-30) cc_final: 0.7606 (m-30) REVERT: W 217 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8785 (p) REVERT: Y 31 ASP cc_start: 0.8585 (p0) cc_final: 0.8379 (p0) REVERT: Y 37 LYS cc_start: 0.8654 (tttt) cc_final: 0.8446 (tttp) REVERT: Y 118 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7609 (ttp) REVERT: a 91 MET cc_start: 0.8672 (tmm) cc_final: 0.8443 (ttt) REVERT: c 156 LYS cc_start: 0.8623 (mptp) cc_final: 0.8388 (mmmt) REVERT: c 419 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: c 423 ASN cc_start: 0.8818 (m-40) cc_final: 0.8274 (m110) REVERT: c 975 SER cc_start: 0.9156 (m) cc_final: 0.8911 (m) REVERT: c 1195 HIS cc_start: 0.7786 (t-170) cc_final: 0.7574 (t-170) REVERT: c 1440 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9101 (pp) REVERT: c 1720 MET cc_start: 0.8699 (tpt) cc_final: 0.8285 (tpt) REVERT: d 415 LEU cc_start: 0.8888 (tt) cc_final: 0.8492 (mm) REVERT: d 419 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: d 423 ASN cc_start: 0.8699 (m110) cc_final: 0.8268 (m110) REVERT: d 626 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8594 (mtt) REVERT: d 1132 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: d 1195 HIS cc_start: 0.7791 (t-170) cc_final: 0.7580 (t-170) REVERT: d 1629 MET cc_start: 0.8682 (mtp) cc_final: 0.8480 (mtp) REVERT: d 1720 MET cc_start: 0.8683 (tpt) cc_final: 0.8083 (tpt) outliers start: 288 outliers final: 151 residues processed: 1538 average time/residue: 1.2690 time to fit residues: 2693.8290 Evaluate side-chains 1410 residues out of total 8238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1246 time to evaluate : 6.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 154 HIS Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 169 ARG Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 118 MET Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 180 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 18 GLU Chi-restraints excluded: chain N residue 173 MET Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 115 CYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain P residue 34 SER Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 104 ILE Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 211 VAL Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 60 ARG Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 154 HIS Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 221 ASN Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 169 ARG Chi-restraints excluded: chain U residue 186 CYS Chi-restraints excluded: chain U residue 220 THR Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 24 SER Chi-restraints excluded: chain V residue 43 CYS Chi-restraints excluded: chain V residue 86 MET Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 119 MET Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 175 LEU Chi-restraints excluded: chain W residue 217 THR Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 118 MET Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 100 MET Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 18 GLU Chi-restraints excluded: chain a residue 172 MET Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain c residue 26 PHE Chi-restraints excluded: chain c residue 110 LYS Chi-restraints excluded: chain c residue 169 VAL Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 419 GLN Chi-restraints excluded: chain c residue 458 SER Chi-restraints excluded: chain c residue 482 LEU Chi-restraints excluded: chain c residue 569 GLU Chi-restraints excluded: chain c residue 576 THR Chi-restraints excluded: chain c residue 578 LEU Chi-restraints excluded: chain c residue 594 LEU Chi-restraints excluded: chain c residue 613 SER Chi-restraints excluded: chain c residue 622 VAL Chi-restraints excluded: chain c residue 651 CYS Chi-restraints excluded: chain c residue 710 CYS Chi-restraints excluded: chain c residue 855 LEU Chi-restraints excluded: chain c residue 880 LEU Chi-restraints excluded: chain c residue 1223 THR Chi-restraints excluded: chain c residue 1259 THR Chi-restraints excluded: chain c residue 1272 THR Chi-restraints excluded: chain c residue 1309 ILE Chi-restraints excluded: chain c residue 1405 LEU Chi-restraints excluded: chain c residue 1440 LEU Chi-restraints excluded: chain c residue 1590 SER Chi-restraints excluded: chain c residue 1624 LEU Chi-restraints excluded: chain c residue 1660 THR Chi-restraints excluded: chain c residue 1724 MET Chi-restraints excluded: chain c residue 1736 LEU Chi-restraints excluded: chain d residue 110 LYS Chi-restraints excluded: chain d residue 248 LEU Chi-restraints excluded: chain d residue 345 ASN Chi-restraints excluded: chain d residue 380 THR Chi-restraints excluded: chain d residue 419 GLN Chi-restraints excluded: chain d residue 426 LEU Chi-restraints excluded: chain d residue 458 SER Chi-restraints excluded: chain d residue 482 LEU Chi-restraints excluded: chain d residue 569 GLU Chi-restraints excluded: chain d residue 576 THR Chi-restraints excluded: chain d residue 578 LEU Chi-restraints excluded: chain d residue 594 LEU Chi-restraints excluded: chain d residue 613 SER Chi-restraints excluded: chain d residue 626 MET Chi-restraints excluded: chain d residue 651 CYS Chi-restraints excluded: chain d residue 710 CYS Chi-restraints excluded: chain d residue 877 ASN Chi-restraints excluded: chain d residue 880 LEU Chi-restraints excluded: chain d residue 1132 GLN Chi-restraints excluded: chain d residue 1159 LEU Chi-restraints excluded: chain d residue 1223 THR Chi-restraints excluded: chain d residue 1250 HIS Chi-restraints excluded: chain d residue 1259 THR Chi-restraints excluded: chain d residue 1272 THR Chi-restraints excluded: chain d residue 1309 ILE Chi-restraints excluded: chain d residue 1348 ILE Chi-restraints excluded: chain d residue 1405 LEU Chi-restraints excluded: chain d residue 1440 LEU Chi-restraints excluded: chain d residue 1590 SER Chi-restraints excluded: chain d residue 1624 LEU Chi-restraints excluded: chain d residue 1634 LEU Chi-restraints excluded: chain d residue 1660 THR Chi-restraints excluded: chain d residue 1736 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 944 random chunks: chunk 562 optimal weight: 6.9990 chunk 363 optimal weight: 6.9990 chunk 543 optimal weight: 9.9990 chunk 274 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 578 optimal weight: 3.9990 chunk 619 optimal weight: 10.0000 chunk 449 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 715 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 95 GLN B 147 GLN B 206 ASN C 235 GLN G 120 HIS H 106 GLN I 57 GLN K 87 ASN K 101 ASN L 62 GLN M 8 ASN M 131 GLN O 224 ASN ** P 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 95 GLN P 111 GLN ** Q 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 235 GLN U 120 HIS V 106 GLN V 158 ASN W 57 GLN Y 101 ASN Z 38 ASN Z 62 GLN ** c 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c1484 HIS ** d1672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 72160 Z= 0.377 Angle : 0.690 12.549 98208 Z= 0.336 Chirality : 0.046 0.290 11592 Planarity : 0.004 0.053 12350 Dihedral : 5.746 59.749 10530 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.63 % Favored : 94.34 % Rotamer: Outliers : 4.45 % Allowed : 22.25 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.33 (0.09), residues: 9478 helix: 0.81 (0.08), residues: 4290 sheet: -0.49 (0.13), residues: 1490 loop : -1.26 (0.10), residues: 3698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP U 215 HIS 0.008 0.001 HIS X 161 PHE 0.030 0.002 PHE R 73 TYR 0.053 0.002 TYR I 8 ARG 0.015 0.000 ARG P 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18956 Ramachandran restraints generated. 9478 Oldfield, 0 Emsley, 9478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18956 Ramachandran restraints generated. 9478 Oldfield, 0 Emsley, 9478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1531 residues out of total 8238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 1231 time to evaluate : 6.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 108 GLU cc_start: 0.8306 (tt0) cc_final: 0.7948 (tp30) REVERT: C 199 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7380 (mmpt) REVERT: D 60 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6863 (ptm-80) REVERT: E 184 VAL cc_start: 0.9452 (m) cc_final: 0.9231 (p) REVERT: G 50 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7905 (pt0) REVERT: G 175 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8281 (mt-10) REVERT: I 217 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8799 (p) REVERT: K 31 ASP cc_start: 0.8636 (p0) cc_final: 0.8374 (p0) REVERT: K 37 LYS cc_start: 0.8731 (tttt) cc_final: 0.8477 (tttp) REVERT: K 118 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7788 (ttp) REVERT: M 60 ASP cc_start: 0.8578 (m-30) cc_final: 0.8373 (m-30) REVERT: P 162 MET cc_start: 0.8454 (mtm) cc_final: 0.8246 (ptp) REVERT: Q 108 GLU cc_start: 0.8296 (tt0) cc_final: 0.7921 (tp30) REVERT: Q 199 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7380 (mmpt) REVERT: R 60 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.6838 (ptm-80) REVERT: R 173 GLU cc_start: 0.8533 (mp0) cc_final: 0.8288 (mp0) REVERT: S 184 VAL cc_start: 0.9439 (m) cc_final: 0.9210 (p) REVERT: T 53 GLN cc_start: 0.8121 (tt0) cc_final: 0.7676 (tt0) REVERT: U 50 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7860 (pt0) REVERT: U 175 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8322 (mt-10) REVERT: U 225 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7388 (mt-10) REVERT: W 217 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8786 (p) REVERT: Y 31 ASP cc_start: 0.8702 (p0) cc_final: 0.8434 (p0) REVERT: Y 37 LYS cc_start: 0.8729 (tttt) cc_final: 0.8467 (tttp) REVERT: Y 118 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7795 (ttp) REVERT: b 110 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7693 (mtp) REVERT: c 32 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7525 (mt) REVERT: c 156 LYS cc_start: 0.8631 (mptp) cc_final: 0.8379 (mmmt) REVERT: c 419 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7324 (tm-30) REVERT: c 423 ASN cc_start: 0.8861 (m-40) cc_final: 0.8368 (m110) REVERT: c 501 MET cc_start: 0.8269 (mmm) cc_final: 0.7997 (mmt) REVERT: c 967 MET cc_start: 0.8925 (mmp) cc_final: 0.8685 (mmp) REVERT: c 1132 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: c 1195 HIS cc_start: 0.7931 (t-170) cc_final: 0.7723 (t-170) REVERT: c 1525 THR cc_start: 0.9147 (p) cc_final: 0.8927 (t) REVERT: c 1720 MET cc_start: 0.8891 (tpt) cc_final: 0.8474 (tpt) REVERT: d 415 LEU cc_start: 0.8934 (tt) cc_final: 0.8547 (mm) REVERT: d 419 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7349 (tm-30) REVERT: d 423 ASN cc_start: 0.8700 (m110) cc_final: 0.8245 (m110) REVERT: d 501 MET cc_start: 0.8318 (mmm) cc_final: 0.8043 (mmt) REVERT: d 603 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7308 (mpp) REVERT: d 1132 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7302 (tm-30) REVERT: d 1195 HIS cc_start: 0.7923 (t-170) cc_final: 0.7713 (t-170) REVERT: d 1525 THR cc_start: 0.9138 (p) cc_final: 0.8922 (t) REVERT: d 1629 MET cc_start: 0.8731 (mtp) cc_final: 0.8507 (mtp) REVERT: d 1720 MET cc_start: 0.8866 (tpt) cc_final: 0.8493 (tpt) outliers start: 300 outliers final: 192 residues processed: 1428 average time/residue: 1.2843 time to fit residues: 2524.5427 Evaluate side-chains 1365 residues out of total 8238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1156 time to evaluate : 6.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 154 HIS Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain F residue 43 HIS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 169 ARG Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 61 TYR Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 118 MET Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 180 VAL Chi-restraints excluded: chain K residue 182 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 18 GLU Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 172 MET Chi-restraints excluded: chain N residue 173 MET Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 115 CYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain P residue 34 SER Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 104 ILE Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 199 LYS Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 211 VAL Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 60 ARG Chi-restraints excluded: chain R residue 154 HIS Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 221 ASN Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain T residue 43 HIS Chi-restraints excluded: chain T residue 211 SER Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 50 GLU Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 142 VAL Chi-restraints excluded: chain U residue 169 ARG Chi-restraints excluded: chain U residue 186 CYS Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 24 SER Chi-restraints excluded: chain V residue 43 CYS Chi-restraints excluded: chain V residue 61 TYR Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 187 GLN Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 69 SER Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 122 LEU Chi-restraints excluded: chain W residue 175 LEU Chi-restraints excluded: chain W residue 217 THR Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 118 MET Chi-restraints excluded: chain Y residue 150 THR Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Y residue 182 ILE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 18 GLU Chi-restraints excluded: chain a residue 25 SER Chi-restraints excluded: chain a residue 148 LEU Chi-restraints excluded: chain a residue 172 MET Chi-restraints excluded: chain b residue 110 MET Chi-restraints excluded: chain c residue 32 ILE Chi-restraints excluded: chain c residue 110 LYS Chi-restraints excluded: chain c residue 169 VAL Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 419 GLN Chi-restraints excluded: chain c residue 421 LEU Chi-restraints excluded: chain c residue 458 SER Chi-restraints excluded: chain c residue 482 LEU Chi-restraints excluded: chain c residue 569 GLU Chi-restraints excluded: chain c residue 576 THR Chi-restraints excluded: chain c residue 578 LEU Chi-restraints excluded: chain c residue 593 ILE Chi-restraints excluded: chain c residue 594 LEU Chi-restraints excluded: chain c residue 609 VAL Chi-restraints excluded: chain c residue 613 SER Chi-restraints excluded: chain c residue 622 VAL Chi-restraints excluded: chain c residue 651 CYS Chi-restraints excluded: chain c residue 855 LEU Chi-restraints excluded: chain c residue 877 ASN Chi-restraints excluded: chain c residue 880 LEU Chi-restraints excluded: chain c residue 1132 GLN Chi-restraints excluded: chain c residue 1140 LEU Chi-restraints excluded: chain c residue 1223 THR Chi-restraints excluded: chain c residue 1250 HIS Chi-restraints excluded: chain c residue 1259 THR Chi-restraints excluded: chain c residue 1272 THR Chi-restraints excluded: chain c residue 1309 ILE Chi-restraints excluded: chain c residue 1404 LEU Chi-restraints excluded: chain c residue 1405 LEU Chi-restraints excluded: chain c residue 1440 LEU Chi-restraints excluded: chain c residue 1590 SER Chi-restraints excluded: chain c residue 1624 LEU Chi-restraints excluded: chain c residue 1660 THR Chi-restraints excluded: chain c residue 1663 THR Chi-restraints excluded: chain c residue 1724 MET Chi-restraints excluded: chain c residue 1736 LEU Chi-restraints excluded: chain c residue 1764 LEU Chi-restraints excluded: chain d residue 110 LYS Chi-restraints excluded: chain d residue 248 LEU Chi-restraints excluded: chain d residue 345 ASN Chi-restraints excluded: chain d residue 380 THR Chi-restraints excluded: chain d residue 419 GLN Chi-restraints excluded: chain d residue 421 LEU Chi-restraints excluded: chain d residue 426 LEU Chi-restraints excluded: chain d residue 458 SER Chi-restraints excluded: chain d residue 482 LEU Chi-restraints excluded: chain d residue 569 GLU Chi-restraints excluded: chain d residue 576 THR Chi-restraints excluded: chain d residue 578 LEU Chi-restraints excluded: chain d residue 588 SER Chi-restraints excluded: chain d residue 593 ILE Chi-restraints excluded: chain d residue 594 LEU Chi-restraints excluded: chain d residue 603 MET Chi-restraints excluded: chain d residue 613 SER Chi-restraints excluded: chain d residue 626 MET Chi-restraints excluded: chain d residue 651 CYS Chi-restraints excluded: chain d residue 710 CYS Chi-restraints excluded: chain d residue 855 LEU Chi-restraints excluded: chain d residue 877 ASN Chi-restraints excluded: chain d residue 880 LEU Chi-restraints excluded: chain d residue 887 THR Chi-restraints excluded: chain d residue 1132 GLN Chi-restraints excluded: chain d residue 1140 LEU Chi-restraints excluded: chain d residue 1159 LEU Chi-restraints excluded: chain d residue 1223 THR Chi-restraints excluded: chain d residue 1250 HIS Chi-restraints excluded: chain d residue 1259 THR Chi-restraints excluded: chain d residue 1272 THR Chi-restraints excluded: chain d residue 1309 ILE Chi-restraints excluded: chain d residue 1348 ILE Chi-restraints excluded: chain d residue 1404 LEU Chi-restraints excluded: chain d residue 1405 LEU Chi-restraints excluded: chain d residue 1440 LEU Chi-restraints excluded: chain d residue 1590 SER Chi-restraints excluded: chain d residue 1624 LEU Chi-restraints excluded: chain d residue 1634 LEU Chi-restraints excluded: chain d residue 1660 THR Chi-restraints excluded: chain d residue 1663 THR Chi-restraints excluded: chain d residue 1736 LEU Chi-restraints excluded: chain d residue 1764 LEU Chi-restraints excluded: chain d residue 1800 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 944 random chunks: chunk 827 optimal weight: 0.9980 chunk 871 optimal weight: 0.8980 chunk 795 optimal weight: 0.9990 chunk 847 optimal weight: 4.9990 chunk 510 optimal weight: 0.7980 chunk 369 optimal weight: 0.6980 chunk 665 optimal weight: 6.9990 chunk 260 optimal weight: 0.8980 chunk 766 optimal weight: 5.9990 chunk 801 optimal weight: 6.9990 chunk 844 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 206 ASN C 146 GLN H 106 GLN I 57 GLN L 62 GLN M 8 ASN M 131 GLN M 146 GLN N 188 GLN O 224 ASN ** P 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 146 GLN ** R 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 106 GLN W 57 GLN ** X 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 87 ASN Y 168 GLN Z 62 GLN a 131 GLN a 146 GLN b 188 GLN c 246 GLN ** d 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d1672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 72160 Z= 0.185 Angle : 0.639 11.786 98208 Z= 0.306 Chirality : 0.043 0.234 11592 Planarity : 0.004 0.062 12350 Dihedral : 5.535 57.928 10530 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.90 % Favored : 95.08 % Rotamer: Outliers : 3.60 % Allowed : 23.53 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.11 (0.09), residues: 9478 helix: 1.01 (0.08), residues: 4282 sheet: -0.41 (0.13), residues: 1488 loop : -1.16 (0.11), residues: 3708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP d 75 HIS 0.005 0.001 HIS B 70 PHE 0.037 0.001 PHE d 743 TYR 0.052 0.001 TYR W 8 ARG 0.016 0.000 ARG P 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18956 Ramachandran restraints generated. 9478 Oldfield, 0 Emsley, 9478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18956 Ramachandran restraints generated. 9478 Oldfield, 0 Emsley, 9478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1540 residues out of total 8238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1297 time to evaluate : 6.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 108 GLU cc_start: 0.8257 (tt0) cc_final: 0.7905 (tp30) REVERT: D 60 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6897 (ptm-80) REVERT: E 25 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7991 (mm-30) REVERT: E 184 VAL cc_start: 0.9435 (m) cc_final: 0.9219 (p) REVERT: G 175 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8302 (mt-10) REVERT: G 216 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8794 (p) REVERT: I 53 ASP cc_start: 0.7913 (m-30) cc_final: 0.7611 (m-30) REVERT: J 84 TYR cc_start: 0.7737 (t80) cc_final: 0.7426 (t80) REVERT: K 37 LYS cc_start: 0.8671 (tttt) cc_final: 0.8463 (tttp) REVERT: Q 108 GLU cc_start: 0.8248 (tt0) cc_final: 0.7874 (tp30) REVERT: Q 229 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8085 (mttp) REVERT: R 60 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6792 (ptm-80) REVERT: S 184 VAL cc_start: 0.9403 (m) cc_final: 0.9188 (p) REVERT: T 53 GLN cc_start: 0.8059 (tt0) cc_final: 0.7621 (tt0) REVERT: U 50 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7748 (pt0) REVERT: U 175 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8324 (mt-10) REVERT: W 53 ASP cc_start: 0.7878 (m-30) cc_final: 0.7567 (m-30) REVERT: X 84 TYR cc_start: 0.7726 (t80) cc_final: 0.7448 (t80) REVERT: Y 27 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7960 (pt0) REVERT: Y 37 LYS cc_start: 0.8664 (tttt) cc_final: 0.8454 (tttp) REVERT: a 91 MET cc_start: 0.8714 (tmm) cc_final: 0.8453 (ttt) REVERT: b 110 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7672 (mtp) REVERT: c 32 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7384 (mt) REVERT: c 419 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7279 (tm-30) REVERT: c 423 ASN cc_start: 0.8792 (m-40) cc_final: 0.8275 (m110) REVERT: c 501 MET cc_start: 0.8234 (mmm) cc_final: 0.7971 (mmt) REVERT: c 967 MET cc_start: 0.8933 (mmp) cc_final: 0.8672 (mmp) REVERT: c 1132 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: c 1440 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9085 (pp) REVERT: c 1525 THR cc_start: 0.9108 (p) cc_final: 0.8875 (t) REVERT: c 1635 TYR cc_start: 0.7918 (m-80) cc_final: 0.7650 (m-10) REVERT: c 1720 MET cc_start: 0.8773 (tpt) cc_final: 0.8469 (tpt) REVERT: d 415 LEU cc_start: 0.8880 (tt) cc_final: 0.8496 (mm) REVERT: d 419 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7357 (tm-30) REVERT: d 423 ASN cc_start: 0.8688 (m110) cc_final: 0.8247 (m110) REVERT: d 501 MET cc_start: 0.8267 (mmm) cc_final: 0.8009 (mmt) REVERT: d 603 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7232 (mmt) REVERT: d 626 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8569 (mtt) REVERT: d 1132 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: d 1440 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9090 (pp) REVERT: d 1525 THR cc_start: 0.9128 (p) cc_final: 0.8927 (t) REVERT: d 1629 MET cc_start: 0.8688 (mtp) cc_final: 0.8482 (mtp) REVERT: d 1720 MET cc_start: 0.8744 (tpt) cc_final: 0.8526 (tpt) outliers start: 243 outliers final: 154 residues processed: 1450 average time/residue: 1.3186 time to fit residues: 2664.0493 Evaluate side-chains 1389 residues out of total 8238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1219 time to evaluate : 6.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 169 ARG Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 61 TYR Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 180 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 18 GLU Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 172 MET Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 115 CYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 104 ILE Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain Q residue 229 LYS Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 60 ARG Chi-restraints excluded: chain R residue 154 HIS Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 221 ASN Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 211 SER Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 50 GLU Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 142 VAL Chi-restraints excluded: chain U residue 169 ARG Chi-restraints excluded: chain U residue 186 CYS Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 24 SER Chi-restraints excluded: chain V residue 43 CYS Chi-restraints excluded: chain V residue 61 TYR Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 187 GLN Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 175 LEU Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 27 GLN Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 18 GLU Chi-restraints excluded: chain a residue 66 LYS Chi-restraints excluded: chain a residue 148 LEU Chi-restraints excluded: chain b residue 50 MET Chi-restraints excluded: chain b residue 110 MET Chi-restraints excluded: chain c residue 32 ILE Chi-restraints excluded: chain c residue 110 LYS Chi-restraints excluded: chain c residue 169 VAL Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 419 GLN Chi-restraints excluded: chain c residue 458 SER Chi-restraints excluded: chain c residue 482 LEU Chi-restraints excluded: chain c residue 569 GLU Chi-restraints excluded: chain c residue 576 THR Chi-restraints excluded: chain c residue 578 LEU Chi-restraints excluded: chain c residue 593 ILE Chi-restraints excluded: chain c residue 594 LEU Chi-restraints excluded: chain c residue 613 SER Chi-restraints excluded: chain c residue 622 VAL Chi-restraints excluded: chain c residue 651 CYS Chi-restraints excluded: chain c residue 855 LEU Chi-restraints excluded: chain c residue 880 LEU Chi-restraints excluded: chain c residue 1132 GLN Chi-restraints excluded: chain c residue 1223 THR Chi-restraints excluded: chain c residue 1250 HIS Chi-restraints excluded: chain c residue 1259 THR Chi-restraints excluded: chain c residue 1272 THR Chi-restraints excluded: chain c residue 1309 ILE Chi-restraints excluded: chain c residue 1405 LEU Chi-restraints excluded: chain c residue 1440 LEU Chi-restraints excluded: chain c residue 1590 SER Chi-restraints excluded: chain c residue 1624 LEU Chi-restraints excluded: chain c residue 1736 LEU Chi-restraints excluded: chain d residue 110 LYS Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 248 LEU Chi-restraints excluded: chain d residue 345 ASN Chi-restraints excluded: chain d residue 380 THR Chi-restraints excluded: chain d residue 419 GLN Chi-restraints excluded: chain d residue 426 LEU Chi-restraints excluded: chain d residue 458 SER Chi-restraints excluded: chain d residue 482 LEU Chi-restraints excluded: chain d residue 569 GLU Chi-restraints excluded: chain d residue 576 THR Chi-restraints excluded: chain d residue 578 LEU Chi-restraints excluded: chain d residue 594 LEU Chi-restraints excluded: chain d residue 603 MET Chi-restraints excluded: chain d residue 613 SER Chi-restraints excluded: chain d residue 626 MET Chi-restraints excluded: chain d residue 651 CYS Chi-restraints excluded: chain d residue 710 CYS Chi-restraints excluded: chain d residue 880 LEU Chi-restraints excluded: chain d residue 1132 GLN Chi-restraints excluded: chain d residue 1159 LEU Chi-restraints excluded: chain d residue 1223 THR Chi-restraints excluded: chain d residue 1250 HIS Chi-restraints excluded: chain d residue 1259 THR Chi-restraints excluded: chain d residue 1272 THR Chi-restraints excluded: chain d residue 1309 ILE Chi-restraints excluded: chain d residue 1348 ILE Chi-restraints excluded: chain d residue 1440 LEU Chi-restraints excluded: chain d residue 1590 SER Chi-restraints excluded: chain d residue 1624 LEU Chi-restraints excluded: chain d residue 1634 LEU Chi-restraints excluded: chain d residue 1724 MET Chi-restraints excluded: chain d residue 1736 LEU Chi-restraints excluded: chain d residue 1764 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 944 random chunks: chunk 556 optimal weight: 0.6980 chunk 896 optimal weight: 5.9990 chunk 547 optimal weight: 0.9990 chunk 425 optimal weight: 6.9990 chunk 623 optimal weight: 1.9990 chunk 940 optimal weight: 5.9990 chunk 865 optimal weight: 0.0050 chunk 748 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 578 optimal weight: 3.9990 chunk 459 optimal weight: 0.9980 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 95 GLN B 206 ASN C 146 GLN G 63 ASN H 106 GLN I 57 GLN K 87 ASN L 62 GLN M 131 GLN M 146 GLN N 188 GLN O 224 ASN P 95 GLN ** R 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 106 GLN W 57 GLN Z 62 GLN ** a 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 146 GLN b 188 GLN ** d 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d1637 HIS ** d1672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 72160 Z= 0.193 Angle : 0.645 11.735 98208 Z= 0.307 Chirality : 0.043 0.245 11592 Planarity : 0.004 0.057 12350 Dihedral : 5.415 58.215 10530 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.04 % Favored : 94.94 % Rotamer: Outliers : 2.89 % Allowed : 24.47 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.01 (0.09), residues: 9478 helix: 1.11 (0.08), residues: 4296 sheet: -0.38 (0.13), residues: 1492 loop : -1.12 (0.11), residues: 3690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP d 75 HIS 0.007 0.001 HIS d1195 PHE 0.029 0.001 PHE d 743 TYR 0.047 0.001 TYR W 8 ARG 0.014 0.000 ARG P 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18956 Ramachandran restraints generated. 9478 Oldfield, 0 Emsley, 9478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18956 Ramachandran restraints generated. 9478 Oldfield, 0 Emsley, 9478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1504 residues out of total 8238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1309 time to evaluate : 7.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 108 GLU cc_start: 0.8238 (tt0) cc_final: 0.7934 (tp30) REVERT: D 60 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6884 (ptm-80) REVERT: E 25 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8031 (mm-30) REVERT: E 184 VAL cc_start: 0.9424 (m) cc_final: 0.9200 (p) REVERT: F 88 MET cc_start: 0.7964 (mtm) cc_final: 0.7168 (mtm) REVERT: G 175 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8306 (mt-10) REVERT: G 216 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8826 (p) REVERT: I 53 ASP cc_start: 0.7905 (m-30) cc_final: 0.7624 (m-30) REVERT: J 2 ILE cc_start: 0.8610 (tp) cc_final: 0.8360 (mp) REVERT: J 84 TYR cc_start: 0.7741 (t80) cc_final: 0.7492 (t80) REVERT: K 37 LYS cc_start: 0.8659 (tttt) cc_final: 0.8447 (tttp) REVERT: P 154 TYR cc_start: 0.8846 (p90) cc_final: 0.8593 (p90) REVERT: Q 108 GLU cc_start: 0.8215 (tt0) cc_final: 0.7873 (tp30) REVERT: Q 229 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8047 (mttp) REVERT: R 60 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6824 (ptm-80) REVERT: S 184 VAL cc_start: 0.9424 (m) cc_final: 0.9206 (p) REVERT: T 53 GLN cc_start: 0.8068 (tt0) cc_final: 0.7508 (tt0) REVERT: W 53 ASP cc_start: 0.7856 (m-30) cc_final: 0.7582 (m-30) REVERT: Y 37 LYS cc_start: 0.8664 (tttt) cc_final: 0.8445 (tttp) REVERT: b 110 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7671 (mtp) REVERT: c 32 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7348 (mt) REVERT: c 419 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: c 423 ASN cc_start: 0.8776 (m-40) cc_final: 0.8251 (m110) REVERT: c 501 MET cc_start: 0.8228 (mmm) cc_final: 0.7969 (mmt) REVERT: c 603 MET cc_start: 0.7569 (tpp) cc_final: 0.7232 (mmt) REVERT: c 967 MET cc_start: 0.8919 (mmp) cc_final: 0.8668 (mmp) REVERT: c 1132 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7356 (tm-30) REVERT: c 1720 MET cc_start: 0.8740 (tpt) cc_final: 0.8449 (tpt) REVERT: d 415 LEU cc_start: 0.8882 (tt) cc_final: 0.8484 (mm) REVERT: d 419 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7333 (tm-30) REVERT: d 423 ASN cc_start: 0.8660 (m110) cc_final: 0.8212 (m110) REVERT: d 501 MET cc_start: 0.8247 (mmm) cc_final: 0.7992 (mmt) REVERT: d 603 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7225 (mmt) REVERT: d 1132 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7326 (tm-30) REVERT: d 1440 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9051 (pp) REVERT: d 1525 THR cc_start: 0.9117 (p) cc_final: 0.8897 (t) REVERT: d 1720 MET cc_start: 0.8704 (tpt) cc_final: 0.8482 (tpt) outliers start: 195 outliers final: 150 residues processed: 1431 average time/residue: 1.2678 time to fit residues: 2503.5605 Evaluate side-chains 1385 residues out of total 8238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1223 time to evaluate : 6.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 169 ARG Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 61 TYR Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 180 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 18 GLU Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 172 MET Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain N residue 173 MET Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 115 CYS Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 104 ILE Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain Q residue 229 LYS Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 60 ARG Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 154 HIS Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 221 ASN Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain T residue 211 SER Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 142 VAL Chi-restraints excluded: chain U residue 169 ARG Chi-restraints excluded: chain U residue 186 CYS Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 43 CYS Chi-restraints excluded: chain V residue 61 TYR Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 175 LEU Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 18 GLU Chi-restraints excluded: chain a residue 66 LYS Chi-restraints excluded: chain b residue 50 MET Chi-restraints excluded: chain b residue 110 MET Chi-restraints excluded: chain c residue 32 ILE Chi-restraints excluded: chain c residue 110 LYS Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 419 GLN Chi-restraints excluded: chain c residue 426 LEU Chi-restraints excluded: chain c residue 458 SER Chi-restraints excluded: chain c residue 482 LEU Chi-restraints excluded: chain c residue 569 GLU Chi-restraints excluded: chain c residue 576 THR Chi-restraints excluded: chain c residue 578 LEU Chi-restraints excluded: chain c residue 593 ILE Chi-restraints excluded: chain c residue 594 LEU Chi-restraints excluded: chain c residue 609 VAL Chi-restraints excluded: chain c residue 613 SER Chi-restraints excluded: chain c residue 622 VAL Chi-restraints excluded: chain c residue 651 CYS Chi-restraints excluded: chain c residue 710 CYS Chi-restraints excluded: chain c residue 855 LEU Chi-restraints excluded: chain c residue 880 LEU Chi-restraints excluded: chain c residue 1132 GLN Chi-restraints excluded: chain c residue 1140 LEU Chi-restraints excluded: chain c residue 1223 THR Chi-restraints excluded: chain c residue 1259 THR Chi-restraints excluded: chain c residue 1272 THR Chi-restraints excluded: chain c residue 1309 ILE Chi-restraints excluded: chain c residue 1405 LEU Chi-restraints excluded: chain c residue 1590 SER Chi-restraints excluded: chain c residue 1624 LEU Chi-restraints excluded: chain c residue 1736 LEU Chi-restraints excluded: chain d residue 110 LYS Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 248 LEU Chi-restraints excluded: chain d residue 380 THR Chi-restraints excluded: chain d residue 419 GLN Chi-restraints excluded: chain d residue 426 LEU Chi-restraints excluded: chain d residue 458 SER Chi-restraints excluded: chain d residue 482 LEU Chi-restraints excluded: chain d residue 569 GLU Chi-restraints excluded: chain d residue 578 LEU Chi-restraints excluded: chain d residue 594 LEU Chi-restraints excluded: chain d residue 603 MET Chi-restraints excluded: chain d residue 609 VAL Chi-restraints excluded: chain d residue 613 SER Chi-restraints excluded: chain d residue 651 CYS Chi-restraints excluded: chain d residue 710 CYS Chi-restraints excluded: chain d residue 855 LEU Chi-restraints excluded: chain d residue 880 LEU Chi-restraints excluded: chain d residue 1132 GLN Chi-restraints excluded: chain d residue 1140 LEU Chi-restraints excluded: chain d residue 1159 LEU Chi-restraints excluded: chain d residue 1223 THR Chi-restraints excluded: chain d residue 1259 THR Chi-restraints excluded: chain d residue 1272 THR Chi-restraints excluded: chain d residue 1309 ILE Chi-restraints excluded: chain d residue 1348 ILE Chi-restraints excluded: chain d residue 1440 LEU Chi-restraints excluded: chain d residue 1590 SER Chi-restraints excluded: chain d residue 1624 LEU Chi-restraints excluded: chain d residue 1634 LEU Chi-restraints excluded: chain d residue 1660 THR Chi-restraints excluded: chain d residue 1724 MET Chi-restraints excluded: chain d residue 1736 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 944 random chunks: chunk 594 optimal weight: 2.9990 chunk 797 optimal weight: 8.9990 chunk 229 optimal weight: 0.0060 chunk 690 optimal weight: 6.9990 chunk 110 optimal weight: 0.5980 chunk 208 optimal weight: 1.9990 chunk 750 optimal weight: 1.9990 chunk 313 optimal weight: 0.0980 chunk 770 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 95 GLN B 206 ASN H 106 GLN I 57 GLN K 168 GLN L 62 GLN M 146 GLN N 188 GLN O 224 ASN P 95 GLN ** R 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 201 HIS V 106 GLN W 57 GLN X 161 HIS Y 87 ASN Z 62 GLN ** a 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 146 GLN b 188 GLN c1246 ASN c1637 HIS ** d 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 422 GLN ** d1672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.116083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.092683 restraints weight = 118761.667| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.44 r_work: 0.3023 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 72160 Z= 0.160 Angle : 0.639 11.882 98208 Z= 0.303 Chirality : 0.043 0.318 11592 Planarity : 0.004 0.054 12350 Dihedral : 5.265 58.932 10528 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.76 % Favored : 95.22 % Rotamer: Outliers : 2.67 % Allowed : 25.23 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.12 (0.09), residues: 9478 helix: 1.23 (0.08), residues: 4292 sheet: -0.35 (0.13), residues: 1500 loop : -1.07 (0.11), residues: 3686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 75 HIS 0.006 0.001 HIS c1195 PHE 0.029 0.001 PHE D 171 TYR 0.047 0.001 TYR I 8 ARG 0.014 0.000 ARG P 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35960.85 seconds wall clock time: 621 minutes 19.98 seconds (37279.98 seconds total)