Starting phenix.real_space_refine on Sat Feb 17 12:27:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az3_7025/02_2024/6az3_7025_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az3_7025/02_2024/6az3_7025.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az3_7025/02_2024/6az3_7025_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az3_7025/02_2024/6az3_7025_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az3_7025/02_2024/6az3_7025_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az3_7025/02_2024/6az3_7025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az3_7025/02_2024/6az3_7025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az3_7025/02_2024/6az3_7025_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az3_7025/02_2024/6az3_7025_neut_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3505 5.49 5 Mg 34 5.21 5 S 241 5.16 5 C 65310 2.51 5 N 23645 2.21 5 O 33826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 23": "NH1" <-> "NH2" Residue "A ARG 23": "NH1" <-> "NH2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 58": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B ARG 116": "NH1" <-> "NH2" Residue "B ARG 116": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B ARG 264": "NH1" <-> "NH2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "G ARG 115": "NH1" <-> "NH2" Residue "G ARG 129": "NH1" <-> "NH2" Residue "G ARG 133": "NH1" <-> "NH2" Residue "G ARG 136": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "G ARG 226": "NH1" <-> "NH2" Residue "G ARG 234": "NH1" <-> "NH2" Residue "G ARG 256": "NH1" <-> "NH2" Residue "G ARG 277": "NH1" <-> "NH2" Residue "G ARG 310": "NH1" <-> "NH2" Residue "G ARG 315": "NH1" <-> "NH2" Residue "G ARG 316": "NH1" <-> "NH2" Residue "G ARG 328": "NH1" <-> "NH2" Residue "G ARG 332": "NH1" <-> "NH2" Residue "G ARG 337": "NH1" <-> "NH2" Residue "H ARG 11": "NH1" <-> "NH2" Residue "H ARG 55": "NH1" <-> "NH2" Residue "H ARG 55": "NH1" <-> "NH2" Residue "H ARG 112": "NH1" <-> "NH2" Residue "I ARG 157": "NH1" <-> "NH2" Residue "I ARG 198": "NH1" <-> "NH2" Residue "I ARG 203": "NH1" <-> "NH2" Residue "I ARG 206": "NH1" <-> "NH2" Residue "I ARG 209": "NH1" <-> "NH2" Residue "K ARG 153": "NH1" <-> "NH2" Residue "K ARG 175": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 109": "NH1" <-> "NH2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 21": "NH1" <-> "NH2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N ARG 39": "NH1" <-> "NH2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 90": "NH1" <-> "NH2" Residue "N ARG 128": "NH1" <-> "NH2" Residue "N ARG 130": "NH1" <-> "NH2" Residue "N ARG 139": "NH1" <-> "NH2" Residue "N ARG 154": "NH1" <-> "NH2" Residue "N ARG 178": "NH1" <-> "NH2" Residue "N ARG 185": "NH1" <-> "NH2" Residue "N ARG 193": "NH1" <-> "NH2" Residue "O ARG 21": "NH1" <-> "NH2" Residue "O ARG 33": "NH1" <-> "NH2" Residue "O ARG 54": "NH1" <-> "NH2" Residue "O ARG 108": "NH1" <-> "NH2" Residue "O ARG 158": "NH1" <-> "NH2" Residue "O ARG 164": "NH1" <-> "NH2" Residue "O ARG 185": "NH1" <-> "NH2" Residue "O ARG 202": "NH1" <-> "NH2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 52": "NH1" <-> "NH2" Residue "Q ARG 60": "NH1" <-> "NH2" Residue "Q ARG 74": "NH1" <-> "NH2" Residue "Q ARG 81": "NH1" <-> "NH2" Residue "Q ARG 85": "NH1" <-> "NH2" Residue "Q ARG 88": "NH1" <-> "NH2" Residue "Q ARG 97": "NH1" <-> "NH2" Residue "Q ARG 98": "NH1" <-> "NH2" Residue "Q ARG 107": "NH1" <-> "NH2" Residue "Q ARG 110": "NH1" <-> "NH2" Residue "Q ARG 117": "NH1" <-> "NH2" Residue "Q ARG 121": "NH1" <-> "NH2" Residue "Q ARG 126": "NH1" <-> "NH2" Residue "Q ARG 136": "NH1" <-> "NH2" Residue "R ARG 7": "NH1" <-> "NH2" Residue "R ARG 42": "NH1" <-> "NH2" Residue "R ARG 86": "NH1" <-> "NH2" Residue "R ARG 119": "NH1" <-> "NH2" Residue "R PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 157": "NH1" <-> "NH2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "S ARG 149": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "V ARG 32": "NH1" <-> "NH2" Residue "V ARG 32": "NH1" <-> "NH2" Residue "W ARG 63": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X ARG 61": "NH1" <-> "NH2" Residue "Y PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 41": "NH1" <-> "NH2" Residue "Z ARG 79": "NH1" <-> "NH2" Residue "Z ARG 88": "NH1" <-> "NH2" Residue "Z ARG 109": "NH1" <-> "NH2" Residue "Z ARG 110": "NH1" <-> "NH2" Residue "Z ARG 113": "NH1" <-> "NH2" Residue "Z ARG 128": "NH1" <-> "NH2" Residue "Z ARG 131": "NH1" <-> "NH2" Residue "Z ARG 139": "NH1" <-> "NH2" Residue "a ARG 11": "NH1" <-> "NH2" Residue "a ARG 52": "NH1" <-> "NH2" Residue "a ARG 106": "NH1" <-> "NH2" Residue "c ARG 98": "NH1" <-> "NH2" Residue "c ARG 229": "NH1" <-> "NH2" Residue "e ARG 65": "NH1" <-> "NH2" Residue "e ARG 69": "NH1" <-> "NH2" Residue "e ARG 71": "NH1" <-> "NH2" Residue "e ARG 74": "NH1" <-> "NH2" Residue "f ARG 17": "NH1" <-> "NH2" Residue "f ARG 22": "NH1" <-> "NH2" Residue "f ARG 37": "NH1" <-> "NH2" Residue "f ARG 44": "NH1" <-> "NH2" Residue "f ARG 62": "NH1" <-> "NH2" Residue "h ARG 11": "NH1" <-> "NH2" Residue "h ARG 36": "NH1" <-> "NH2" Residue "j ARG 21": "NH1" <-> "NH2" Residue "j ARG 72": "NH1" <-> "NH2" Residue "k ARG 58": "NH1" <-> "NH2" Residue "m ARG 111": "NH1" <-> "NH2" Residue "m ARG 122": "NH1" <-> "NH2" Residue "n ARG 30": "NH1" <-> "NH2" Residue "o ARG 49": "NH1" <-> "NH2" Residue "o ARG 56": "NH1" <-> "NH2" Residue "p ARG 87": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 126561 Number of models: 1 Model: "" Number of chains: 91 Chain: "A" Number of atoms: 1985 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 254, 1922 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 238} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 254, 1922 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 238} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1901 Conformer: "C" Number of residues, atoms: 254, 1877 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 238} Unresolved chain links: 2 Unresolved chain link angles: 16 Unresolved chain link dihedrals: 26 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 1901 Chain: "B" Number of atoms: 3226 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 402, 3135 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 384} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 68 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 402, 3135 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 384} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 68 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 3101 Chain: "C" Number of atoms: 2824 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 366, 2808 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 348} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 366, 2808 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 348} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 2840 Chain: "D" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1220 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 3, 'TRANS': 164} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ARG:plan': 5, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "E" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1448 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 180} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1004 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "G" Number of atoms: 1746 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1730 Classifications: {'peptide': 220} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 220, 1730 Classifications: {'peptide': 220} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 1737 Chain: "H" Number of atoms: 1781 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 1757 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 209} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 221, 1757 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 209} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1765 Chain: "I" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1647 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 199} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1001 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 126} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 1164 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1154 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 144} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 149, 1154 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 144} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1161 Chain: "L" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1126 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "M" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1714 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 195} Chain: "N" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1454 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 11, 'TRANS': 178} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "O" Number of atoms: 1976 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 252, 1948 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 242} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 31 Conformer: "B" Number of residues, atoms: 252, 1948 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 242} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 31 bond proxies already assigned to first conformer: 1952 Chain: "P" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1539 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "Q" Number of atoms: 1452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1452 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 3, 'TRANS': 185} Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 103 Chain: "R" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1454 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 169} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1208 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 146} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "T" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1236 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 146} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "U" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 934 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "V" Number of atoms: 928 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 920 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 111} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Conformer: "B" Number of residues, atoms: 118, 920 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 111} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 926 Chain: "W" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "X" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 553 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 58} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Y" Number of atoms: 1039 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 1032 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 127} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Conformer: "B" Number of residues, atoms: 132, 1032 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 127} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 1044 Chain: "Z" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1067 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 135} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "a" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 985 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 121} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 30 Chain: "b" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 539 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 64} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1809 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 218} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "d" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 691 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 88} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "e" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 936 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 114} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "f" Number of atoms: 1048 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 130, 1040 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 130, 1040 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 1051 Chain: "g" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 998 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "h" Number of atoms: 1010 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 125, 1002 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 121} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 125, 1002 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 121} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 1009 Chain: "i" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 760 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 89} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "j" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 663 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "k" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 575 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 73} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "l" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 440 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "m" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "n" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 280 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 30} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "o" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 696 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 87} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "p" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 756 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "1" Number of atoms: 34631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1620, 34631 Inner-chain residues flagged as termini: ['pdbres=" G 11123 "'] Classifications: {'RNA': 1620} Modifications used: {'5*END': 1, 'rna2p': 2, 'rna2p_pur': 192, 'rna2p_pyr': 121, 'rna3p': 13, 'rna3p_pur': 723, 'rna3p_pyr': 559} Link IDs: {'rna2p': 314, 'rna3p': 1305} Chain breaks: 15 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' C%rna3p_pyr:plan': 2, ' A%rna3p_pur:plan2': 1, ' A%rna2p_pur:plan': 3, ' U%rna3p_pyr:plan': 1, ' C%rna2p_pyr:plan': 3, ' A%rna2p_pur:plan2': 3, ' C%rna3p_pyr:plan2': 2, ' G%rna3p_pur:plan': 1, ' A%rna3p_pur:plan': 1, ' U%rna2p_pyr:plan': 5, ' C%rna2p_pyr:plan2': 3} Unresolved non-hydrogen planarities: 144 Chain: "2" Number of atoms: 22996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 22996 Classifications: {'RNA': 1078} Modifications used: {'rna2p': 3, 'rna2p_pur': 112, 'rna2p_pyr': 77, 'rna3p': 21, 'rna3p_pur': 452, 'rna3p_pyr': 400} Link IDs: {'rna2p': 192, 'rna3p': 885} Chain breaks: 11 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' A%rna3p_pur:plan2': 2, ' G%rna2p_pur:plan2': 1, ' G%rna2p_pur:plan': 1, ' G%rna3p_pur:plan': 1, ' U%rna2p_pyr:plan': 4, ' A%rna3p_pur:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "3" Number of atoms: 3751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 3751 Classifications: {'RNA': 177} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 17, 'rna3p': 1, 'rna3p_pur': 72, 'rna3p_pyr': 72} Link IDs: {'rna2p': 31, 'rna3p': 145} Chain breaks: 5 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {' U%rna3p_pyr:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "4" Number of atoms: 3906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 3906 Classifications: {'RNA': 183} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 12, 'rna3p': 1, 'rna3p_pur': 84, 'rna3p_pyr': 72} Link IDs: {'rna2p': 25, 'rna3p': 157} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {' G%rna2p_pur:plan': 1, ' G%rna2p_pur:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "5" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2075 Classifications: {'RNA': 97} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 12, 'rna3p_pur': 47, 'rna3p_pyr': 33} Link IDs: {'rna2p': 16, 'rna3p': 80} Chain breaks: 3 Chain: "6" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1477 Classifications: {'RNA': 71} Modifications used: {'rna2p_pur': 16, 'rna2p_pyr': 14, 'rna3p_pur': 20, 'rna3p_pyr': 21} Link IDs: {'rna2p': 29, 'rna3p': 41} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' C%rna3p_pyr:plan2': 1, ' C%rna3p_pyr:plan': 1, ' U%rna3p_pyr:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "7" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 3465 Classifications: {'RNA': 163} Modifications used: {'5*END': 1, 'rna2p_pur': 16, 'rna2p_pyr': 11, 'rna3p': 2, 'rna3p_pur': 66, 'rna3p_pyr': 66} Link IDs: {'rna2p': 26, 'rna3p': 136} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {' U%rna3p_pyr:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "8" Number of atoms: 2511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2511 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 7, 'rna3p_pur': 53, 'rna3p_pyr': 50} Link IDs: {'rna2p': 14, 'rna3p': 103} Chain: "1" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 231 Unusual residues: {' MG': 21, 'PAR': 5} Classifications: {'undetermined': 26} Link IDs: {None: 25} Chain: "2" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 176 Unusual residues: {' MG': 8, 'PAR': 4} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {' MG': 2, 'PAR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "I" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "P" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "Q" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "c" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "f" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "h" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "j" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "l" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "p" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "1" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 442 Classifications: {'water': 442} Link IDs: {None: 441} Chain: "2" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 278 Classifications: {'water': 278} Link IDs: {None: 277} Chain: "3" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "4" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "5" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "6" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "8" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N ALYS A 28 " occ=0.33 ... (25 atoms not shown) pdb=" NZ CLYS A 28 " occ=0.33 residue: pdb=" N AARG B 58 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 58 " occ=0.50 residue: pdb=" N AARG B 115 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 115 " occ=0.50 residue: pdb=" N AARG B 249 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 249 " occ=0.50 residue: pdb=" N ALYS B 253 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 253 " occ=0.50 residue: pdb=" N AHIS K 198 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS K 198 " occ=0.50 residue: pdb=" N AHIS O 31 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS O 31 " occ=0.50 residue: pdb=" N AARG O 34 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG O 34 " occ=0.50 residue: pdb=" N AVAL O 70 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL O 70 " occ=0.50 Time building chain proxies: 54.66, per 1000 atoms: 0.43 Number of scatterers: 126561 At special positions: 0 Unit cell: (215.22, 248.88, 244.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 241 16.00 P 3505 15.00 Mg 34 11.99 O 33826 8.00 N 23645 7.00 C 65310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS j 19 " - pdb=" SG CYS j 22 " distance=2.04 Simple disulfide: pdb=" SG CYS j 22 " - pdb=" SG CYS j 34 " distance=2.05 Simple disulfide: pdb=" SG CYS j 22 " - pdb=" SG CYS j 37 " distance=2.03 Simple disulfide: pdb=" SG CYS m 96 " - pdb=" SG CYS m 115 " distance=2.05 Simple disulfide: pdb=" SG CYS m 110 " - pdb=" SG CYS m 115 " distance=2.03 Simple disulfide: pdb=" SG CYS o 39 " - pdb=" SG CYS o 42 " distance=2.05 Simple disulfide: pdb=" SG CYS o 39 " - pdb=" SG CYS o 57 " distance=2.05 Simple disulfide: pdb=" SG CYS o 39 " - pdb=" SG CYS o 60 " distance=2.06 Simple disulfide: pdb=" SG CYS o 42 " - pdb=" SG CYS o 57 " distance=2.05 Simple disulfide: pdb=" SG CYS o 42 " - pdb=" SG CYS o 60 " distance=2.08 Simple disulfide: pdb=" SG CYS o 57 " - pdb=" SG CYS o 60 " distance=1.99 Simple disulfide: pdb=" SG CYS p 12 " - pdb=" SG CYS p 17 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 50.48 Conformation dependent library (CDL) restraints added in 10.3 seconds 12700 Ramachandran restraints generated. 6350 Oldfield, 0 Emsley, 6350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12022 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 221 helices and 63 sheets defined 42.6% alpha, 13.8% beta 847 base pairs and 1952 stacking pairs defined. Time for finding SS restraints: 65.44 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 4.246A pdb=" N GLY A 11 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN A 12 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.504A pdb=" N ILE A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N THR A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.504A pdb=" N SER A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY A 191 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LYS A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 193 " --> pdb=" O PHE A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 4.008A pdb=" N ARG A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 205' Processing helix chain 'B' and resid 111 through 120 removed outlier: 4.052A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TYR B 119 " --> pdb=" O AARG B 115 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 140 removed outlier: 3.754A pdb=" N LYS B 134 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASN B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LYS B 140 " --> pdb=" O PHE B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 156 Processing helix chain 'B' and resid 167 through 172 removed outlier: 3.747A pdb=" N LEU B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ARG B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 167 through 172' Processing helix chain 'B' and resid 192 through 204 removed outlier: 3.602A pdb=" N ALA B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 214 removed outlier: 3.978A pdb=" N VAL B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.854A pdb=" N GLU B 359 " --> pdb=" O ARG B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 388 removed outlier: 3.601A pdb=" N LYS B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN B 385 " --> pdb=" O LYS B 381 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLY B 388 " --> pdb=" O ASN B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 403 removed outlier: 3.520A pdb=" N GLU B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 298 Proline residue: B 298 - end of helix No H-bonds generated for 'chain 'B' and resid 293 through 298' Processing helix chain 'C' and resid 25 through 30 removed outlier: 3.515A pdb=" N ALA C 29 " --> pdb=" O ALA C 25 " (cutoff:3.500A) Proline residue: C 30 - end of helix No H-bonds generated for 'chain 'C' and resid 25 through 30' Processing helix chain 'C' and resid 32 through 48 removed outlier: 3.944A pdb=" N LYS C 45 " --> pdb=" O THR C 41 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER C 47 " --> pdb=" O MET C 43 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ARG C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 133 removed outlier: 3.533A pdb=" N SER C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Proline residue: C 133 - end of helix Processing helix chain 'C' and resid 134 through 140 removed outlier: 3.506A pdb=" N ARG C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 removed outlier: 4.719A pdb=" N GLY C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 160' Processing helix chain 'C' and resid 162 through 174 removed outlier: 3.577A pdb=" N ALA C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 186 removed outlier: 3.786A pdb=" N VAL C 179 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP C 184 " --> pdb=" O ASN C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 removed outlier: 3.774A pdb=" N ARG C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 192 through 197' Processing helix chain 'C' and resid 216 through 221 removed outlier: 4.935A pdb=" N ASN C 221 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 240 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 251 through 263 removed outlier: 4.062A pdb=" N GLN C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU C 258 " --> pdb=" O ALA C 254 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LYS C 260 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 293 removed outlier: 3.707A pdb=" N ILE C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET C 291 " --> pdb=" O VAL C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 301 removed outlier: 4.642A pdb=" N VAL C 299 " --> pdb=" O GLU C 295 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 300 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 330 removed outlier: 3.526A pdb=" N LEU C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 345 removed outlier: 3.593A pdb=" N ALA C 338 " --> pdb=" O LYS C 334 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 341 " --> pdb=" O THR C 337 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ARG C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 369 removed outlier: 3.773A pdb=" N ALA C 351 " --> pdb=" O ALA C 347 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ALA C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA C 358 " --> pdb=" O LYS C 354 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N THR C 361 " --> pdb=" O MET C 357 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C 362 " --> pdb=" O ALA C 358 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 363 " --> pdb=" O ARG C 359 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 43 removed outlier: 3.781A pdb=" N THR D 33 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS D 37 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU D 40 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN D 41 " --> pdb=" O LYS D 37 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D 42 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 90 removed outlier: 4.005A pdb=" N GLU D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 143 removed outlier: 3.905A pdb=" N HIS D 142 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG D 143 " --> pdb=" O ARG D 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 138 through 143' Processing helix chain 'D' and resid 157 through 168 removed outlier: 3.852A pdb=" N LYS D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 removed outlier: 3.691A pdb=" N ASP D 113 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY D 115 " --> pdb=" O ILE D 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 85 removed outlier: 5.821A pdb=" N ILE E 66 " --> pdb=" O SER E 62 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS E 68 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU E 69 " --> pdb=" O PRO E 65 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASN E 70 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 165 removed outlier: 3.936A pdb=" N ARG E 155 " --> pdb=" O GLU E 151 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA E 158 " --> pdb=" O SER E 154 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS E 164 " --> pdb=" O LEU E 160 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU E 165 " --> pdb=" O HIS E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 175 removed outlier: 4.161A pdb=" N LEU E 175 " --> pdb=" O ILE E 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 85 removed outlier: 4.089A pdb=" N VAL F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE F 85 " --> pdb=" O SER F 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 80 through 85' Processing helix chain 'F' and resid 147 through 168 removed outlier: 3.724A pdb=" N LYS F 155 " --> pdb=" O ALA F 151 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA F 160 " --> pdb=" O LYS F 156 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS F 167 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 181 removed outlier: 3.516A pdb=" N LYS F 174 " --> pdb=" O GLN F 170 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG F 179 " --> pdb=" O ALA F 175 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N VAL F 181 " --> pdb=" O TYR F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 194 removed outlier: 4.098A pdb=" N TRP F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN F 194 " --> pdb=" O PRO F 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 189 through 194' Processing helix chain 'G' and resid 138 through 154 removed outlier: 3.623A pdb=" N ARG G 145 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS G 146 " --> pdb=" O THR G 142 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG G 148 " --> pdb=" O GLN G 144 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG G 152 " --> pdb=" O ARG G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 166 removed outlier: 3.718A pdb=" N GLN G 162 " --> pdb=" O PRO G 158 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N PHE G 163 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR G 164 " --> pdb=" O LEU G 160 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL G 166 " --> pdb=" O GLN G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 183 removed outlier: 3.714A pdb=" N LYS G 177 " --> pdb=" O ASN G 173 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS G 181 " --> pdb=" O LYS G 177 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR G 182 " --> pdb=" O LEU G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 202 removed outlier: 4.787A pdb=" N ARG G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LYS G 196 " --> pdb=" O GLU G 192 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA G 197 " --> pdb=" O ARG G 193 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU G 199 " --> pdb=" O HIS G 195 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU G 200 " --> pdb=" O LYS G 196 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS G 201 " --> pdb=" O ALA G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 231 removed outlier: 3.833A pdb=" N THR G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG G 226 " --> pdb=" O GLN G 222 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS G 231 " --> pdb=" O ALA G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 259 Processing helix chain 'G' and resid 267 through 276 removed outlier: 6.018A pdb=" N LEU G 271 " --> pdb=" O ASP G 267 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY G 272 " --> pdb=" O MET G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 307 removed outlier: 3.685A pdb=" N GLU G 293 " --> pdb=" O ASN G 289 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA G 294 " --> pdb=" O ALA G 290 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N THR G 295 " --> pdb=" O GLU G 291 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU G 296 " --> pdb=" O ASP G 292 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA G 305 " --> pdb=" O ARG G 301 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG G 306 " --> pdb=" O SER G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 317 removed outlier: 4.065A pdb=" N ARG G 316 " --> pdb=" O ASP G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 339 removed outlier: 3.542A pdb=" N LEU G 331 " --> pdb=" O SER G 327 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS G 334 " --> pdb=" O GLU G 330 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG G 337 " --> pdb=" O LYS G 333 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN G 338 " --> pdb=" O LYS G 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 16 removed outlier: 4.156A pdb=" N ALA H 12 " --> pdb=" O ASP H 8 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER H 16 " --> pdb=" O ALA H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 48 removed outlier: 3.922A pdb=" N LEU H 46 " --> pdb=" O ALA H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 78 removed outlier: 3.966A pdb=" N LYS H 78 " --> pdb=" O GLN H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.821A pdb=" N GLY H 87 " --> pdb=" O ASN H 83 " (cutoff:3.500A) Proline residue: H 88 - end of helix No H-bonds generated for 'chain 'H' and resid 83 through 88' Processing helix chain 'H' and resid 93 through 107 removed outlier: 3.540A pdb=" N VAL H 99 " --> pdb=" O SER H 95 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET H 105 " --> pdb=" O THR H 101 " (cutoff:3.500A) Proline residue: H 107 - end of helix Processing helix chain 'H' and resid 110 through 121 removed outlier: 3.800A pdb=" N SER H 119 " --> pdb=" O LYS H 115 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU H 120 " --> pdb=" O ALA H 116 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL H 121 " --> pdb=" O LEU H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 134 removed outlier: 4.772A pdb=" N ARG H 132 " --> pdb=" O PRO H 128 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N THR H 133 " --> pdb=" O ASN H 129 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLY H 134 " --> pdb=" O VAL H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 148 removed outlier: 5.718A pdb=" N CYS H 147 " --> pdb=" O GLN H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 165 removed outlier: 3.525A pdb=" N LYS H 162 " --> pdb=" O GLY H 158 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N HIS H 163 " --> pdb=" O ASN H 159 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL H 164 " --> pdb=" O MET H 160 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY H 165 " --> pdb=" O CYS H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 208 removed outlier: 3.507A pdb=" N ARG H 179 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN H 190 " --> pdb=" O HIS H 186 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA H 191 " --> pdb=" O HIS H 187 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LYS H 192 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU H 193 " --> pdb=" O LYS H 189 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA H 196 " --> pdb=" O LYS H 192 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU H 203 " --> pdb=" O ALA H 199 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU H 205 " --> pdb=" O ARG H 201 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ALA H 206 " --> pdb=" O LYS H 202 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS H 207 " --> pdb=" O GLU H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 220 removed outlier: 3.713A pdb=" N VAL H 213 " --> pdb=" O PRO H 209 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU H 214 " --> pdb=" O LYS H 210 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL H 215 " --> pdb=" O HIS H 211 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU H 216 " --> pdb=" O ASN H 212 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE H 219 " --> pdb=" O VAL H 215 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY H 220 " --> pdb=" O LEU H 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 52 removed outlier: 3.551A pdb=" N PHE I 52 " --> pdb=" O ALA I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 removed outlier: 4.640A pdb=" N LYS I 86 " --> pdb=" O PRO I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 99 removed outlier: 3.585A pdb=" N ALA I 96 " --> pdb=" O PRO I 92 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR I 97 " --> pdb=" O GLN I 93 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE I 98 " --> pdb=" O TYR I 94 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY I 99 " --> pdb=" O ALA I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 128 removed outlier: 4.030A pdb=" N ASN I 117 " --> pdb=" O GLY I 113 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 151 removed outlier: 5.798A pdb=" N VAL I 148 " --> pdb=" O SER I 144 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA I 150 " --> pdb=" O GLU I 146 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA I 151 " --> pdb=" O GLU I 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 144 through 151' Processing helix chain 'I' and resid 159 through 164 removed outlier: 4.728A pdb=" N VAL I 163 " --> pdb=" O GLY I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 184 removed outlier: 4.392A pdb=" N SER I 183 " --> pdb=" O ALA I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 199 removed outlier: 4.031A pdb=" N PHE I 189 " --> pdb=" O CYS I 185 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL I 197 " --> pdb=" O ASN I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 213 removed outlier: 5.811A pdb=" N SER I 204 " --> pdb=" O PHE I 200 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG I 206 " --> pdb=" O ALA I 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA I 208 " --> pdb=" O SER I 204 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA I 212 " --> pdb=" O ALA I 208 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ALA I 213 " --> pdb=" O ARG I 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 129 removed outlier: 4.112A pdb=" N LEU J 127 " --> pdb=" O GLU J 123 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP J 128 " --> pdb=" O SER J 124 " (cutoff:3.500A) Proline residue: J 129 - end of helix Processing helix chain 'J' and resid 130 through 135 removed outlier: 3.593A pdb=" N HIS J 134 " --> pdb=" O LYS J 130 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA J 135 " --> pdb=" O ILE J 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 130 through 135' Processing helix chain 'K' and resid 110 through 115 removed outlier: 3.777A pdb=" N VAL K 114 " --> pdb=" O ASN K 110 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLU K 115 " --> pdb=" O LEU K 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 110 through 115' Processing helix chain 'K' and resid 128 through 140 removed outlier: 6.090A pdb=" N LEU K 132 " --> pdb=" O SER K 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LYS K 133 " --> pdb=" O ALA K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 149 removed outlier: 3.553A pdb=" N LYS K 147 " --> pdb=" O GLU K 143 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR K 148 " --> pdb=" O LYS K 144 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ARG K 149 " --> pdb=" O TYR K 145 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 163 removed outlier: 3.565A pdb=" N ALA K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA K 162 " --> pdb=" O LYS K 158 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 193 removed outlier: 5.218A pdb=" N LYS K 192 " --> pdb=" O GLU K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 209 removed outlier: 3.735A pdb=" N LEU K 202 " --> pdb=" O BHIS K 198 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS K 207 " --> pdb=" O LYS K 203 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LYS K 208 " --> pdb=" O LYS K 204 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 12 removed outlier: 3.945A pdb=" N HIS L 10 " --> pdb=" O LYS L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 48 Processing helix chain 'L' and resid 64 through 69 removed outlier: 4.126A pdb=" N MET L 68 " --> pdb=" O LYS L 64 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TRP L 69 " --> pdb=" O LYS L 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 64 through 69' Processing helix chain 'L' and resid 74 through 83 removed outlier: 3.718A pdb=" N LEU L 78 " --> pdb=" O ASN L 74 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER L 79 " --> pdb=" O LEU L 75 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ARG L 80 " --> pdb=" O ASN L 76 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU L 81 " --> pdb=" O ASN L 77 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE L 82 " --> pdb=" O LEU L 78 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ALA L 83 " --> pdb=" O SER L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 74 through 83' Processing helix chain 'L' and resid 84 through 91 removed outlier: 4.461A pdb=" N ALA L 88 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS L 89 " --> pdb=" O GLU L 85 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA L 90 " --> pdb=" O GLU L 86 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N THR L 91 " --> pdb=" O ALA L 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 84 through 91' Processing helix chain 'L' and resid 100 through 105 removed outlier: 4.139A pdb=" N SER L 104 " --> pdb=" O ASP L 100 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY L 105 " --> pdb=" O LEU L 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 100 through 105' Processing helix chain 'L' and resid 127 through 138 removed outlier: 4.033A pdb=" N LYS L 133 " --> pdb=" O LEU L 129 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS L 136 " --> pdb=" O LYS L 132 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA L 137 " --> pdb=" O LYS L 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 14 removed outlier: 4.124A pdb=" N TYR M 6 " --> pdb=" O GLY M 2 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU M 7 " --> pdb=" O ALA M 3 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS M 13 " --> pdb=" O GLU M 9 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LYS M 14 " --> pdb=" O LEU M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 34 removed outlier: 3.522A pdb=" N ARG M 31 " --> pdb=" O SER M 27 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS M 32 " --> pdb=" O TRP M 28 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN M 33 " --> pdb=" O GLU M 29 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N HIS M 34 " --> pdb=" O PHE M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 52 Processing helix chain 'M' and resid 83 through 88 removed outlier: 4.088A pdb=" N SER M 87 " --> pdb=" O LYS M 83 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLY M 88 " --> pdb=" O PRO M 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 83 through 88' Processing helix chain 'M' and resid 97 through 111 removed outlier: 3.717A pdb=" N ARG M 109 " --> pdb=" O ARG M 105 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY M 111 " --> pdb=" O GLY M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 145 Processing helix chain 'M' and resid 148 through 153 removed outlier: 4.581A pdb=" N VAL M 152 " --> pdb=" O ILE M 148 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASN M 153 " --> pdb=" O ASN M 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 148 through 153' Processing helix chain 'M' and resid 158 through 163 removed outlier: 3.929A pdb=" N ARG M 162 " --> pdb=" O HIS M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 173 removed outlier: 3.567A pdb=" N HIS M 171 " --> pdb=" O ALA M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 178 through 183 removed outlier: 3.690A pdb=" N SER M 182 " --> pdb=" O GLY M 178 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LYS M 183 " --> pdb=" O HIS M 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 178 through 183' Processing helix chain 'M' and resid 187 through 197 removed outlier: 3.543A pdb=" N ARG M 194 " --> pdb=" O ALA M 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 10 removed outlier: 4.706A pdb=" N TYR N 9 " --> pdb=" O PRO N 5 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG N 10 " --> pdb=" O SER N 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 5 through 10' Processing helix chain 'N' and resid 42 through 47 removed outlier: 4.596A pdb=" N PHE N 46 " --> pdb=" O THR N 42 " (cutoff:3.500A) Proline residue: N 47 - end of helix No H-bonds generated for 'chain 'N' and resid 42 through 47' Processing helix chain 'N' and resid 61 through 80 removed outlier: 3.568A pdb=" N GLN N 71 " --> pdb=" O ALA N 67 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS N 74 " --> pdb=" O ILE N 70 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 160 removed outlier: 3.928A pdb=" N ALA N 148 " --> pdb=" O TYR N 144 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU N 150 " --> pdb=" O PRO N 146 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET N 157 " --> pdb=" O ARG N 153 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS N 158 " --> pdb=" O ARG N 154 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE N 159 " --> pdb=" O ALA N 155 " (cutoff:3.500A) Proline residue: N 160 - end of helix Processing helix chain 'N' and resid 177 through 188 removed outlier: 5.233A pdb=" N GLU N 182 " --> pdb=" O ARG N 178 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA N 183 " --> pdb=" O THR N 179 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU N 184 " --> pdb=" O GLU N 180 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASP N 186 " --> pdb=" O GLU N 182 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA N 187 " --> pdb=" O ALA N 183 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY N 188 " --> pdb=" O LEU N 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 16 Processing helix chain 'O' and resid 20 through 26 removed outlier: 3.893A pdb=" N GLY O 26 " --> pdb=" O ARG O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 38 removed outlier: 4.145A pdb=" N GLN O 35 " --> pdb=" O AHIS O 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 87 removed outlier: 4.470A pdb=" N LEU O 83 " --> pdb=" O TYR O 79 " (cutoff:3.500A) Proline residue: O 84 - end of helix removed outlier: 3.511A pdb=" N GLY O 87 " --> pdb=" O LEU O 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 79 through 87' Processing helix chain 'O' and resid 94 through 114 removed outlier: 3.523A pdb=" N ALA O 100 " --> pdb=" O ALA O 96 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU O 110 " --> pdb=" O ALA O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 163 through 176 removed outlier: 3.956A pdb=" N GLY O 167 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL O 168 " --> pdb=" O ARG O 164 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU O 169 " --> pdb=" O VAL O 165 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS O 170 " --> pdb=" O PHE O 166 " (cutoff:3.500A) Processing helix chain 'O' and resid 197 through 207 removed outlier: 3.511A pdb=" N HIS O 201 " --> pdb=" O ASP O 197 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG O 204 " --> pdb=" O VAL O 200 " (cutoff:3.500A) Processing helix chain 'O' and resid 208 through 225 removed outlier: 3.801A pdb=" N TYR O 213 " --> pdb=" O HIS O 209 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN O 216 " --> pdb=" O GLU O 212 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER O 222 " --> pdb=" O LYS O 218 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER O 223 " --> pdb=" O GLU O 219 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASN O 224 " --> pdb=" O GLU O 220 " (cutoff:3.500A) Proline residue: O 225 - end of helix Processing helix chain 'O' and resid 232 through 239 removed outlier: 4.335A pdb=" N LYS O 239 " --> pdb=" O TYR O 235 " (cutoff:3.500A) Processing helix chain 'O' and resid 242 through 259 removed outlier: 7.273A pdb=" N GLU O 246 " --> pdb=" O PRO O 242 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY O 247 " --> pdb=" O GLU O 243 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N MET O 248 " --> pdb=" O SER O 244 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR O 249 " --> pdb=" O ILE O 245 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS O 250 " --> pdb=" O GLU O 246 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA O 254 " --> pdb=" O LYS O 250 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP O 259 " --> pdb=" O ALA O 255 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 13 removed outlier: 4.049A pdb=" N LYS P 11 " --> pdb=" O GLY P 7 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER P 12 " --> pdb=" O ILE P 8 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ARG P 13 " --> pdb=" O SER P 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 7 through 13' Processing helix chain 'P' and resid 23 through 40 removed outlier: 3.577A pdb=" N LYS P 27 " --> pdb=" O ASN P 23 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU P 28 " --> pdb=" O PRO P 24 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE P 35 " --> pdb=" O LYS P 31 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS P 38 " --> pdb=" O LYS P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 55 removed outlier: 3.634A pdb=" N LYS P 46 " --> pdb=" O SER P 42 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS P 54 " --> pdb=" O GLN P 50 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N SER P 55 " --> pdb=" O ARG P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 79 removed outlier: 3.516A pdb=" N VAL P 69 " --> pdb=" O SER P 65 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS P 72 " --> pdb=" O ALA P 68 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE P 77 " --> pdb=" O ARG P 73 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ALA P 79 " --> pdb=" O ALA P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 113 through 124 removed outlier: 3.610A pdb=" N GLN P 118 " --> pdb=" O LYS P 114 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA P 123 " --> pdb=" O SER P 119 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY P 124 " --> pdb=" O ILE P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 137 removed outlier: 3.959A pdb=" N MET P 135 " --> pdb=" O ASP P 131 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE P 136 " --> pdb=" O GLN P 132 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ALA P 137 " --> pdb=" O LEU P 133 " (cutoff:3.500A) Processing helix chain 'P' and resid 153 through 160 removed outlier: 5.872A pdb=" N GLY P 160 " --> pdb=" O VAL P 156 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 16 Processing helix chain 'Q' and resid 18 through 23 removed outlier: 5.865A pdb=" N TRP Q 23 " --> pdb=" O ARG Q 19 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 35 removed outlier: 3.634A pdb=" N GLN Q 33 " --> pdb=" O ALA Q 29 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN Q 34 " --> pdb=" O VAL Q 30 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ALA Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 48 Processing helix chain 'Q' and resid 60 through 73 removed outlier: 3.529A pdb=" N MET Q 66 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET Q 72 " --> pdb=" O GLU Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 82 removed outlier: 5.496A pdb=" N GLU Q 82 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 84 through 113 Proline residue: Q 90 - end of helix removed outlier: 6.657A pdb=" N GLU Q 93 " --> pdb=" O MET Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 116 through 130 removed outlier: 3.789A pdb=" N VAL Q 125 " --> pdb=" O ARG Q 121 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG Q 126 " --> pdb=" O ASP Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 190 removed outlier: 3.537A pdb=" N GLN Q 154 " --> pdb=" O LYS Q 150 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU Q 155 " --> pdb=" O LYS Q 151 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU Q 159 " --> pdb=" O LEU Q 155 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA Q 161 " --> pdb=" O GLU Q 157 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU Q 167 " --> pdb=" O HIS Q 163 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN Q 171 " --> pdb=" O GLU Q 167 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU Q 177 " --> pdb=" O ALA Q 173 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS Q 180 " --> pdb=" O GLN Q 176 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU Q 182 " --> pdb=" O LEU Q 178 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU Q 186 " --> pdb=" O GLU Q 182 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG Q 187 " --> pdb=" O LYS Q 183 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA Q 188 " --> pdb=" O GLU Q 184 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG Q 189 " --> pdb=" O ARG Q 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 51 Processing helix chain 'R' and resid 100 through 116 removed outlier: 3.720A pdb=" N ALA R 113 " --> pdb=" O TYR R 109 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER R 114 " --> pdb=" O HIS R 110 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS R 116 " --> pdb=" O LEU R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 124 removed outlier: 3.805A pdb=" N ILE R 123 " --> pdb=" O ARG R 119 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLU R 124 " --> pdb=" O TYR R 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 119 through 124' Processing helix chain 'R' and resid 138 through 146 removed outlier: 5.950A pdb=" N TYR R 144 " --> pdb=" O SER R 140 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N HIS R 145 " --> pdb=" O ILE R 141 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA R 146 " --> pdb=" O ALA R 142 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 32 removed outlier: 3.613A pdb=" N ILE S 30 " --> pdb=" O SER S 26 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR S 32 " --> pdb=" O SER S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 92 through 97 removed outlier: 4.308A pdb=" N VAL S 96 " --> pdb=" O ARG S 92 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ARG S 97 " --> pdb=" O PHE S 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 92 through 97' Processing helix chain 'S' and resid 102 through 121 removed outlier: 3.702A pdb=" N LYS S 108 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU S 116 " --> pdb=" O PHE S 112 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA S 117 " --> pdb=" O GLN S 113 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS S 119 " --> pdb=" O TYR S 115 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS S 120 " --> pdb=" O LEU S 116 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA S 121 " --> pdb=" O ALA S 117 " (cutoff:3.500A) Processing helix chain 'S' and resid 149 through 155 removed outlier: 4.590A pdb=" N TYR S 153 " --> pdb=" O ARG S 149 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU S 154 " --> pdb=" O VAL S 150 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA S 155 " --> pdb=" O ALA S 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 149 through 155' Processing helix chain 'T' and resid 10 through 15 removed outlier: 3.761A pdb=" N SER T 14 " --> pdb=" O VAL T 10 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ALA T 15 " --> pdb=" O SER T 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 10 through 15' Processing helix chain 'T' and resid 25 through 38 removed outlier: 4.995A pdb=" N GLU T 31 " --> pdb=" O LYS T 27 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL T 35 " --> pdb=" O GLU T 31 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE T 36 " --> pdb=" O THR T 32 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN T 37 " --> pdb=" O ALA T 33 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLY T 38 " --> pdb=" O ASN T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 54 removed outlier: 3.506A pdb=" N TYR T 48 " --> pdb=" O ALA T 44 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 106 removed outlier: 3.645A pdb=" N SER T 93 " --> pdb=" O VAL T 89 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU T 94 " --> pdb=" O ALA T 90 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS T 105 " --> pdb=" O ASN T 101 " (cutoff:3.500A) Processing helix chain 'T' and resid 70 through 76 removed outlier: 3.942A pdb=" N ALA T 73 " --> pdb=" O THR T 70 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS T 74 " --> pdb=" O ALA T 71 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU T 75 " --> pdb=" O GLN T 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 12 removed outlier: 3.965A pdb=" N ARG U 11 " --> pdb=" O LYS U 7 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N SER U 12 " --> pdb=" O VAL U 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 7 through 12' Processing helix chain 'U' and resid 30 through 37 removed outlier: 4.840A pdb=" N ALA U 34 " --> pdb=" O CYS U 30 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY U 37 " --> pdb=" O PRO U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 54 removed outlier: 5.070A pdb=" N GLY U 45 " --> pdb=" O GLU U 41 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN U 46 " --> pdb=" O ASP U 42 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU U 48 " --> pdb=" O LEU U 44 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN U 49 " --> pdb=" O GLY U 45 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE U 51 " --> pdb=" O PHE U 47 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN U 52 " --> pdb=" O GLU U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 86 through 102 removed outlier: 3.877A pdb=" N PHE U 90 " --> pdb=" O ARG U 86 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS U 91 " --> pdb=" O LYS U 87 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE U 97 " --> pdb=" O LEU U 93 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP U 102 " --> pdb=" O LEU U 98 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 67 removed outlier: 3.588A pdb=" N ALA V 61 " --> pdb=" O SER V 57 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ALA V 62 " --> pdb=" O LYS V 58 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N PHE V 63 " --> pdb=" O ASP V 59 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER V 64 " --> pdb=" O ILE V 60 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL V 65 " --> pdb=" O ALA V 61 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE V 66 " --> pdb=" O ALA V 62 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ARG V 67 " --> pdb=" O PHE V 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 57 through 67' Processing helix chain 'V' and resid 72 through 81 removed outlier: 3.587A pdb=" N GLU V 80 " --> pdb=" O MET V 76 " (cutoff:3.500A) Processing helix chain 'V' and resid 94 through 106 removed outlier: 4.453A pdb=" N TYR V 106 " --> pdb=" O MET V 102 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 143 removed outlier: 3.544A pdb=" N LYS V 141 " --> pdb=" O ASP V 137 " (cutoff:3.500A) Processing helix chain 'W' and resid 8 through 19 removed outlier: 3.701A pdb=" N PHE W 17 " --> pdb=" O ARG W 13 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA W 19 " --> pdb=" O ALA W 15 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 29 removed outlier: 4.136A pdb=" N VAL W 26 " --> pdb=" O HIS W 22 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER W 29 " --> pdb=" O ARG W 25 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 41 removed outlier: 3.668A pdb=" N ALA W 38 " --> pdb=" O LYS W 34 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS W 39 " --> pdb=" O GLU W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 102 removed outlier: 4.410A pdb=" N VAL W 101 " --> pdb=" O HIS W 97 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLU W 102 " --> pdb=" O PRO W 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 97 through 102' Processing helix chain 'W' and resid 109 through 120 removed outlier: 5.266A pdb=" N SER W 114 " --> pdb=" O HIS W 110 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE W 115 " --> pdb=" O HIS W 111 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU W 117 " --> pdb=" O LYS W 113 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG W 118 " --> pdb=" O SER W 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 47 Processing helix chain 'X' and resid 56 through 63 removed outlier: 3.571A pdb=" N ILE X 62 " --> pdb=" O THR X 58 " (cutoff:3.500A) Processing helix chain 'Y' and resid 58 through 67 removed outlier: 6.090A pdb=" N ALA Y 63 " --> pdb=" O LYS Y 59 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG Y 64 " --> pdb=" O GLN Y 60 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN Y 67 " --> pdb=" O ALA Y 63 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 81 removed outlier: 3.995A pdb=" N PHE Y 80 " --> pdb=" O ASN Y 76 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU Y 81 " --> pdb=" O HIS Y 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 76 through 81' Processing helix chain 'Y' and resid 90 through 98 removed outlier: 3.552A pdb=" N ARG Y 94 " --> pdb=" O SER Y 90 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY Y 95 " --> pdb=" O LYS Y 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS Y 96 " --> pdb=" O GLU Y 92 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE Y 97 " --> pdb=" O LEU Y 93 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASN Y 98 " --> pdb=" O ARG Y 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 90 through 98' Processing helix chain 'Y' and resid 102 through 123 removed outlier: 3.699A pdb=" N SER Y 106 " --> pdb=" O ALA Y 102 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER Y 108 " --> pdb=" O LYS Y 104 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU Y 111 " --> pdb=" O ARG Y 107 " (cutoff:3.500A) Processing helix chain 'Y' and resid 125 through 131 removed outlier: 4.013A pdb=" N PHE Y 129 " --> pdb=" O SER Y 125 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN Y 130 " --> pdb=" O MET Y 126 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ARG Y 131 " --> pdb=" O TRP Y 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 125 through 131' Processing helix chain 'Z' and resid 4 through 13 removed outlier: 3.717A pdb=" N ILE Z 10 " --> pdb=" O ASP Z 6 " (cutoff:3.500A) Processing helix chain 'Z' and resid 43 through 48 removed outlier: 3.941A pdb=" N ASN Z 47 " --> pdb=" O CYS Z 43 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLU Z 48 " --> pdb=" O GLY Z 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 43 through 48' Processing helix chain 'Z' and resid 73 through 78 removed outlier: 5.142A pdb=" N TYR Z 78 " --> pdb=" O PRO Z 74 " (cutoff:3.500A) Processing helix chain 'Z' and resid 88 through 100 removed outlier: 3.665A pdb=" N VAL Z 92 " --> pdb=" O ARG Z 88 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL Z 96 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL Z 99 " --> pdb=" O ALA Z 95 " (cutoff:3.500A) Processing helix chain 'Z' and resid 101 through 133 removed outlier: 5.468A pdb=" N ASP Z 105 " --> pdb=" O PRO Z 101 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL Z 106 " --> pdb=" O ASP Z 102 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER Z 107 " --> pdb=" O LEU Z 103 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG Z 109 " --> pdb=" O ASP Z 105 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA Z 122 " --> pdb=" O ALA Z 118 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA Z 125 " --> pdb=" O THR Z 121 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA Z 126 " --> pdb=" O ALA Z 122 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA Z 127 " --> pdb=" O LYS Z 123 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA Z 130 " --> pdb=" O ALA Z 126 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU Z 133 " --> pdb=" O LYS Z 129 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 13 removed outlier: 3.517A pdb=" N LEU a 10 " --> pdb=" O LYS a 6 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU a 12 " --> pdb=" O LYS a 8 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LYS a 13 " --> pdb=" O ASP a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 14 through 39 removed outlier: 3.528A pdb=" N TYR a 25 " --> pdb=" O THR a 21 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL a 34 " --> pdb=" O SER a 30 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL a 35 " --> pdb=" O GLN a 31 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN a 37 " --> pdb=" O ARG a 33 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY a 39 " --> pdb=" O VAL a 35 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 78 removed outlier: 4.758A pdb=" N GLY a 46 " --> pdb=" O GLU a 42 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG a 47 " --> pdb=" O THR a 43 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE a 48 " --> pdb=" O ARG a 44 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ARG a 49 " --> pdb=" O LEU a 45 " (cutoff:3.500A) Proline residue: a 50 - end of helix removed outlier: 3.508A pdb=" N ASN a 69 " --> pdb=" O ASN a 65 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE a 73 " --> pdb=" O ASN a 69 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ASP a 76 " --> pdb=" O MET a 72 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ARG a 77 " --> pdb=" O PHE a 73 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LYS a 78 " --> pdb=" O TYR a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 89 removed outlier: 3.643A pdb=" N ARG a 88 " --> pdb=" O PRO a 84 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ALA a 89 " --> pdb=" O LYS a 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 84 through 89' Processing helix chain 'a' and resid 92 through 98 removed outlier: 3.671A pdb=" N LEU a 97 " --> pdb=" O HIS a 93 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 106 removed outlier: 3.900A pdb=" N LYS a 104 " --> pdb=" O LYS a 100 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASN a 105 " --> pdb=" O GLU a 101 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG a 106 " --> pdb=" O ASN a 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 100 through 106' Processing helix chain 'a' and resid 108 through 118 removed outlier: 3.616A pdb=" N ALA a 115 " --> pdb=" O GLN a 111 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 20 removed outlier: 3.623A pdb=" N HIS b 17 " --> pdb=" O SER b 13 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG b 18 " --> pdb=" O SER b 14 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASN b 19 " --> pdb=" O LYS b 15 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY b 20 " --> pdb=" O ASN b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 26 through 31 removed outlier: 5.437A pdb=" N HIS b 30 " --> pdb=" O PRO b 26 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ASN b 31 " --> pdb=" O LEU b 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 26 through 31' Processing helix chain 'b' and resid 38 through 69 removed outlier: 3.681A pdb=" N HIS b 50 " --> pdb=" O ARG b 46 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS b 53 " --> pdb=" O LYS b 49 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA b 64 " --> pdb=" O ARG b 60 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE b 66 " --> pdb=" O ARG b 62 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA b 68 " --> pdb=" O ALA b 64 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS b 69 " --> pdb=" O ALA b 65 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 83 removed outlier: 4.056A pdb=" N GLN c 31 " --> pdb=" O ALA c 27 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR c 33 " --> pdb=" O LYS c 29 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS c 38 " --> pdb=" O GLU c 34 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL c 41 " --> pdb=" O LYS c 37 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA c 48 " --> pdb=" O LYS c 44 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG c 57 " --> pdb=" O THR c 53 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER c 62 " --> pdb=" O ALA c 58 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU c 69 " --> pdb=" O TYR c 65 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU c 72 " --> pdb=" O ALA c 68 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL c 73 " --> pdb=" O GLU c 69 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS c 82 " --> pdb=" O GLN c 78 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY c 83 " --> pdb=" O ALA c 79 " (cutoff:3.500A) Processing helix chain 'c' and resid 106 through 117 removed outlier: 3.693A pdb=" N ARG c 117 " --> pdb=" O LEU c 113 " (cutoff:3.500A) Processing helix chain 'c' and resid 130 through 141 removed outlier: 3.685A pdb=" N MET c 136 " --> pdb=" O PRO c 132 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA c 139 " --> pdb=" O ASN c 135 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL c 140 " --> pdb=" O MET c 136 " (cutoff:3.500A) Processing helix chain 'c' and resid 150 through 160 Processing helix chain 'c' and resid 175 through 184 removed outlier: 3.584A pdb=" N ILE c 179 " --> pdb=" O ASP c 175 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN c 184 " --> pdb=" O LYS c 180 " (cutoff:3.500A) Processing helix chain 'c' and resid 190 through 201 removed outlier: 3.621A pdb=" N MET c 194 " --> pdb=" O CYS c 190 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS c 201 " --> pdb=" O GLN c 197 " (cutoff:3.500A) Processing helix chain 'c' and resid 204 through 213 removed outlier: 5.169A pdb=" N TRP c 213 " --> pdb=" O THR c 209 " (cutoff:3.500A) Processing helix chain 'c' and resid 243 through 252 removed outlier: 3.796A pdb=" N PHE c 247 " --> pdb=" O LEU c 243 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG c 250 " --> pdb=" O ARG c 246 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET c 251 " --> pdb=" O PHE c 247 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 22 removed outlier: 3.514A pdb=" N ASN d 13 " --> pdb=" O VAL d 9 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU d 18 " --> pdb=" O ALA d 14 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL d 19 " --> pdb=" O LYS d 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 28 through 39 removed outlier: 4.012A pdb=" N THR d 34 " --> pdb=" O GLN d 30 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR d 35 " --> pdb=" O GLN d 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY d 39 " --> pdb=" O THR d 35 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 66 removed outlier: 3.685A pdb=" N THR d 63 " --> pdb=" O GLU d 59 " (cutoff:3.500A) Processing helix chain 'd' and resid 75 through 84 removed outlier: 3.636A pdb=" N CYS d 83 " --> pdb=" O LEU d 79 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY d 84 " --> pdb=" O GLY d 80 " (cutoff:3.500A) Processing helix chain 'e' and resid 64 through 69 removed outlier: 4.171A pdb=" N LEU e 68 " --> pdb=" O THR e 64 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG e 69 " --> pdb=" O ARG e 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 64 through 69' Processing helix chain 'e' and resid 86 through 92 removed outlier: 4.424A pdb=" N LEU e 90 " --> pdb=" O HIS e 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS e 92 " --> pdb=" O SER e 88 " (cutoff:3.500A) Processing helix chain 'e' and resid 95 through 116 removed outlier: 3.642A pdb=" N ARG e 99 " --> pdb=" O THR e 95 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ALA e 100 " --> pdb=" O PHE e 96 " (cutoff:3.500A) Proline residue: e 101 - end of helix removed outlier: 3.723A pdb=" N ILE e 104 " --> pdb=" O ALA e 100 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS e 105 " --> pdb=" O PRO e 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG e 106 " --> pdb=" O LEU e 102 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU e 114 " --> pdb=" O PHE e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 123 through 132 removed outlier: 4.766A pdb=" N ASN e 127 " --> pdb=" O ASP e 123 " (cutoff:3.500A) Processing helix chain 'f' and resid 22 through 27 removed outlier: 4.646A pdb=" N PHE f 26 " --> pdb=" O ARG f 22 " (cutoff:3.500A) Proline residue: f 27 - end of helix No H-bonds generated for 'chain 'f' and resid 22 through 27' Processing helix chain 'f' and resid 41 through 46 Processing helix chain 'f' and resid 79 through 90 removed outlier: 4.310A pdb=" N LEU f 83 " --> pdb=" O ASN f 79 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR f 84 " --> pdb=" O VAL f 80 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N MET f 85 " --> pdb=" O GLU f 81 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU f 86 " --> pdb=" O ASP f 82 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL f 87 " --> pdb=" O LEU f 83 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N MET f 88 " --> pdb=" O TYR f 84 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLN f 89 " --> pdb=" O MET f 85 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN f 90 " --> pdb=" O LEU f 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 79 through 90' Processing helix chain 'f' and resid 102 through 117 removed outlier: 4.066A pdb=" N LYS f 107 " --> pdb=" O ALA f 103 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA f 108 " --> pdb=" O ARG f 104 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS f 112 " --> pdb=" O ALA f 108 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET f 114 " --> pdb=" O ALA f 110 " (cutoff:3.500A) Processing helix chain 'f' and resid 124 through 131 removed outlier: 3.564A pdb=" N LYS f 129 " --> pdb=" O ALA f 125 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE f 130 " --> pdb=" O LYS f 126 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA f 131 " --> pdb=" O LEU f 127 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 71 removed outlier: 3.834A pdb=" N TRP g 69 " --> pdb=" O GLU g 65 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR g 70 " --> pdb=" O ASP g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 89 through 94 Proline residue: g 94 - end of helix No H-bonds generated for 'chain 'g' and resid 89 through 94' Processing helix chain 'h' and resid 62 through 68 removed outlier: 3.949A pdb=" N ARG h 66 " --> pdb=" O HIS h 62 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA h 68 " --> pdb=" O ASP h 64 " (cutoff:3.500A) Processing helix chain 'h' and resid 69 through 74 removed outlier: 4.353A pdb=" N LYS h 73 " --> pdb=" O SER h 69 " (cutoff:3.500A) Processing helix chain 'h' and resid 84 through 127 removed outlier: 3.721A pdb=" N ARG h 89 " --> pdb=" O HIS h 85 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP h 90 " --> pdb=" O ASP h 86 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG h 91 " --> pdb=" O GLN h 87 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG h 94 " --> pdb=" O ASP h 90 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU h 99 " --> pdb=" O ALA h 95 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG h 102 " --> pdb=" O VAL h 98 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG h 120 " --> pdb=" O LEU h 116 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR h 121 " --> pdb=" O SER h 117 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA h 122 " --> pdb=" O HIS h 118 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASN h 123 " --> pdb=" O LYS h 119 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS h 124 " --> pdb=" O ARG h 120 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS h 125 " --> pdb=" O THR h 121 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS h 126 " --> pdb=" O ALA h 122 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N SER h 127 " --> pdb=" O ASN h 123 " (cutoff:3.500A) Processing helix chain 'i' and resid 37 through 52 removed outlier: 3.573A pdb=" N ALA i 42 " --> pdb=" O LYS i 38 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY i 52 " --> pdb=" O ALA i 48 " (cutoff:3.500A) Processing helix chain 'i' and resid 54 through 67 removed outlier: 3.609A pdb=" N GLN i 61 " --> pdb=" O GLU i 57 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE i 63 " --> pdb=" O ARG i 59 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG i 65 " --> pdb=" O GLN i 61 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL i 66 " --> pdb=" O GLU i 62 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY i 67 " --> pdb=" O PHE i 63 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 80 Processing helix chain 'i' and resid 82 through 99 removed outlier: 3.562A pdb=" N GLU i 95 " --> pdb=" O SER i 91 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA i 96 " --> pdb=" O LYS i 92 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N HIS i 99 " --> pdb=" O GLU i 95 " (cutoff:3.500A) Processing helix chain 'j' and resid 4 through 11 removed outlier: 3.640A pdb=" N MET j 8 " --> pdb=" O GLY j 4 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN j 10 " --> pdb=" O THR j 6 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG j 11 " --> pdb=" O SER j 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 4 through 11' Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.543A pdb=" N ARG j 58 " --> pdb=" O ILE j 54 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 77 removed outlier: 4.256A pdb=" N VAL j 69 " --> pdb=" O ARG j 65 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 18 removed outlier: 3.722A pdb=" N PHE k 11 " --> pdb=" O THR k 7 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA k 13 " --> pdb=" O LYS k 9 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG k 17 " --> pdb=" O ALA k 13 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYS k 18 " --> pdb=" O ILE k 14 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 61 removed outlier: 3.911A pdb=" N ASP k 54 " --> pdb=" O LYS k 50 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS k 55 " --> pdb=" O LYS k 51 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER k 59 " --> pdb=" O LYS k 55 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE k 60 " --> pdb=" O ILE k 56 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HIS k 61 " --> pdb=" O GLU k 57 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 21 removed outlier: 3.551A pdb=" N LYS l 12 " --> pdb=" O ALA l 8 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET l 17 " --> pdb=" O TYR l 13 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LYS l 21 " --> pdb=" O MET l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 removed outlier: 4.068A pdb=" N ARG l 28 " --> pdb=" O PRO l 24 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU l 29 " --> pdb=" O TYR l 25 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG l 30 " --> pdb=" O TRP l 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 24 through 30' Processing helix chain 'm' and resid 79 through 91 removed outlier: 3.533A pdb=" N ALA m 84 " --> pdb=" O PRO m 80 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU m 85 " --> pdb=" O THR m 81 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR m 89 " --> pdb=" O LEU m 85 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 34 removed outlier: 5.896A pdb=" N LYS n 17 " --> pdb=" O LYS n 13 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG n 18 " --> pdb=" O TRP n 14 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER n 33 " --> pdb=" O MET n 29 " (cutoff:3.500A) Processing helix chain 'o' and resid 19 through 35 removed outlier: 3.642A pdb=" N LYS o 28 " --> pdb=" O LYS o 24 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU o 29 " --> pdb=" O ARG o 25 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER o 32 " --> pdb=" O LYS o 28 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS o 34 " --> pdb=" O GLU o 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 73 through 91 removed outlier: 3.790A pdb=" N SER o 77 " --> pdb=" O THR o 73 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR o 78 " --> pdb=" O PRO o 74 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA o 90 " --> pdb=" O LEU o 86 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS o 91 " --> pdb=" O ARG o 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 37 through 49 removed outlier: 3.509A pdb=" N SER p 48 " --> pdb=" O ASP p 44 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLY p 49 " --> pdb=" O ARG p 45 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.782A pdb=" N SER A 47 " --> pdb=" O ARG A 60 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL A 88 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL A 45 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN A 86 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N GLY A 99 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N PHE A 89 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 110 through 114 removed outlier: 4.047A pdb=" N CYS A 111 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG A 147 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 58 through 64 Processing sheet with id= 4, first strand: chain 'A' and resid 145 through 150 removed outlier: 4.355A pdb=" N GLN A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 41 through 44 removed outlier: 3.598A pdb=" N THR B 44 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLN B 187 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N HIS B 182 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ILE B 160 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE B 163 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS B 206 " --> pdb=" O ILE B 86 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 45 through 50 removed outlier: 4.519A pdb=" N ARG B 341 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU B 218 " --> pdb=" O ILE B 287 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 53 through 58 removed outlier: 3.839A pdb=" N TYR B 328 " --> pdb=" O GLY B 291 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 98 through 102 removed outlier: 6.957A pdb=" N GLY B 91 " --> pdb=" O ILE B 102 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 88 through 93 Processing sheet with id= 10, first strand: chain 'C' and resid 6 through 9 removed outlier: 3.618A pdb=" N GLY C 19 " --> pdb=" O VAL C 9 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 225 through 229 removed outlier: 6.137A pdb=" N VAL C 209 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 47 through 51 removed outlier: 3.561A pdb=" N VAL D 48 " --> pdb=" O HIS D 70 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ILE D 67 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 25 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS D 18 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N CYS D 24 " --> pdb=" O GLY D 126 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N GLY D 126 " --> pdb=" O CYS D 24 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE D 104 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU D 133 " --> pdb=" O GLY D 102 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLY D 102 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 5 through 12 removed outlier: 3.592A pdb=" N CYS E 8 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ARG E 52 " --> pdb=" O ILE E 12 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR E 53 " --> pdb=" O ASP E 48 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 17 through 20 Processing sheet with id= 15, first strand: chain 'E' and resid 101 through 104 Processing sheet with id= 16, first strand: chain 'E' and resid 129 through 134 removed outlier: 4.860A pdb=" N GLU E 142 " --> pdb=" O THR E 134 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'E' and resid 86 through 90 No H-bonds generated for sheet with id= 17 Processing sheet with id= 18, first strand: chain 'F' and resid 37 through 42 removed outlier: 4.340A pdb=" N VAL F 37 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG F 49 " --> pdb=" O ILE F 41 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL F 64 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS F 55 " --> pdb=" O VAL F 64 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'F' and resid 63 through 66 Processing sheet with id= 20, first strand: chain 'G' and resid 261 through 265 Processing sheet with id= 21, first strand: chain 'H' and resid 24 through 28 Processing sheet with id= 22, first strand: chain 'I' and resid 61 through 65 removed outlier: 6.018A pdb=" N LYS I 73 " --> pdb=" O CYS I 65 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'J' and resid 34 through 38 removed outlier: 7.203A pdb=" N ASN J 100 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN J 26 " --> pdb=" O ASN J 100 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE J 104 " --> pdb=" O ALA J 28 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN J 77 " --> pdb=" O VAL J 105 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 86 through 89 removed outlier: 4.061A pdb=" N THR J 93 " --> pdb=" O ARG J 89 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'J' and resid 81 through 84 removed outlier: 4.235A pdb=" N ARG J 84 " --> pdb=" O ASP J 99 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ASP J 99 " --> pdb=" O ARG J 84 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'K' and resid 69 through 73 removed outlier: 4.363A pdb=" N ARG K 69 " --> pdb=" O ILE K 85 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG K 81 " --> pdb=" O ILE K 73 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'L' and resid 70 through 73 No H-bonds generated for sheet with id= 27 Processing sheet with id= 28, first strand: chain 'L' and resid 119 through 122 removed outlier: 3.555A pdb=" N ALA L 140 " --> pdb=" O CYS L 119 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'M' and resid 35 through 39 removed outlier: 6.470A pdb=" N THR M 35 " --> pdb=" O ARG M 65 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL M 61 " --> pdb=" O LEU M 39 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N GLY M 58 " --> pdb=" O ASP M 136 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N THR M 126 " --> pdb=" O ARG M 68 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE M 133 " --> pdb=" O LEU M 116 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'M' and resid 118 through 121 removed outlier: 6.691A pdb=" N TRP M 129 " --> pdb=" O VAL M 121 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'N' and resid 85 through 90 removed outlier: 5.210A pdb=" N LEU N 135 " --> pdb=" O ARG N 90 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU N 136 " --> pdb=" O VAL N 52 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N CYS N 49 " --> pdb=" O SER N 168 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ARG N 162 " --> pdb=" O ARG N 55 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'N' and resid 189 through 192 removed outlier: 6.660A pdb=" N LYS N 189 " --> pdb=" O ILE N 200 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'O' and resid 60 through 66 Processing sheet with id= 34, first strand: chain 'P' and resid 86 through 89 Processing sheet with id= 35, first strand: chain 'R' and resid 26 through 32 removed outlier: 6.384A pdb=" N VAL R 12 " --> pdb=" O LEU R 61 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'R' and resid 88 through 97 removed outlier: 3.609A pdb=" N GLY R 88 " --> pdb=" O SER R 84 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER R 84 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS R 94 " --> pdb=" O VAL R 78 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN R 75 " --> pdb=" O ILE R 131 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS R 129 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'R' and resid 8 through 12 removed outlier: 4.854A pdb=" N HIS R 8 " --> pdb=" O VAL R 66 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'S' and resid 39 through 42 removed outlier: 3.936A pdb=" N ARG S 60 " --> pdb=" O VAL S 42 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'S' and resid 65 through 68 removed outlier: 3.722A pdb=" N ASN S 66 " --> pdb=" O GLY S 73 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY S 71 " --> pdb=" O THR S 68 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'T' and resid 16 through 19 removed outlier: 4.023A pdb=" N VAL T 146 " --> pdb=" O VAL T 19 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLN T 111 " --> pdb=" O LYS T 153 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'T' and resid 124 through 131 No H-bonds generated for sheet with id= 41 Processing sheet with id= 42, first strand: chain 'U' and resid 76 through 81 removed outlier: 5.493A pdb=" N GLY U 115 " --> pdb=" O VAL U 25 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'V' and resid 83 through 89 removed outlier: 6.488A pdb=" N ASN V 83 " --> pdb=" O LEU V 129 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU V 129 " --> pdb=" O ASN V 83 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS V 123 " --> pdb=" O VAL V 89 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU V 122 " --> pdb=" O ARG V 118 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS V 112 " --> pdb=" O ARG V 128 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'W' and resid 69 through 72 Processing sheet with id= 45, first strand: chain 'W' and resid 83 through 86 removed outlier: 4.820A pdb=" N SER W 90 " --> pdb=" O LYS W 86 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'X' and resid 3 through 6 removed outlier: 4.667A pdb=" N PHE X 11 " --> pdb=" O CYS X 6 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'X' and resid 18 through 22 Processing sheet with id= 48, first strand: chain 'Y' and resid 10 through 13 removed outlier: 3.889A pdb=" N HIS Y 21 " --> pdb=" O VAL Y 13 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'Y' and resid 27 through 30 removed outlier: 3.570A pdb=" N GLN Y 27 " --> pdb=" O LEU Y 42 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'Z' and resid 18 through 21 removed outlier: 6.390A pdb=" N PHE Z 18 " --> pdb=" O ASN Z 29 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN Z 20 " --> pdb=" O MET Z 27 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'Z' and resid 49 through 55 removed outlier: 4.869A pdb=" N ILE Z 61 " --> pdb=" O HIS Z 83 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'c' and resid 143 through 148 removed outlier: 7.327A pdb=" N TYR c 143 " --> pdb=" O ILE c 99 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASN c 123 " --> pdb=" O ARG c 98 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N PHE c 122 " --> pdb=" O LEU c 217 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'd' and resid 24 through 27 removed outlier: 5.847A pdb=" N LYS d 24 " --> pdb=" O THR d 95 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU d 43 " --> pdb=" O VAL d 94 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'e' and resid 119 through 122 removed outlier: 4.569A pdb=" N ASP e 119 " --> pdb=" O PHE e 161 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL e 79 " --> pdb=" O ARG e 148 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER e 80 " --> pdb=" O VAL e 181 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'f' and resid 72 through 78 Processing sheet with id= 56, first strand: chain 'g' and resid 37 through 40 removed outlier: 6.924A pdb=" N LEU g 55 " --> pdb=" O ALA g 40 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG g 118 " --> pdb=" O THR g 108 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TRP g 104 " --> pdb=" O ASN g 122 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR g 99 " --> pdb=" O GLY g 81 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS g 73 " --> pdb=" O VAL g 107 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ARG g 74 " --> pdb=" O TYR g 138 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'g' and resid 34 through 38 Processing sheet with id= 58, first strand: chain 'h' and resid 20 through 25 removed outlier: 5.630A pdb=" N ARG h 20 " --> pdb=" O ARG h 36 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN h 34 " --> pdb=" O LYS h 22 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'k' and resid 2 through 5 removed outlier: 3.544A pdb=" N THR k 44 " --> pdb=" O ARG k 3 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N VAL k 46 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N CYS k 22 " --> pdb=" O ARG k 37 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N HIS k 27 " --> pdb=" O VAL k 69 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'm' and resid 100 through 103 removed outlier: 3.995A pdb=" N ALA m 101 " --> pdb=" O CYS m 96 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS m 96 " --> pdb=" O ALA m 101 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ASN m 120 " --> pdb=" O ARG m 97 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'o' and resid 46 through 50 removed outlier: 7.860A pdb=" N ALA o 46 " --> pdb=" O ASP o 58 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE o 54 " --> pdb=" O LYS o 50 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLY o 53 " --> pdb=" O GLY o 66 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS o 62 " --> pdb=" O CYS o 57 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'p' and resid 2 through 6 removed outlier: 4.146A pdb=" N LYS p 6 " --> pdb=" O ASN p 94 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'p' and resid 7 through 10 removed outlier: 7.633A pdb=" N SER p 22 " --> pdb=" O SER p 75 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LYS p 71 " --> pdb=" O VAL p 26 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL p 69 " --> pdb=" O TYR p 28 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS p 74 " --> pdb=" O SER p 79 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER p 79 " --> pdb=" O CYS p 74 " (cutoff:3.500A) 1683 hydrogen bonds defined for protein. 4976 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2083 hydrogen bonds 3404 hydrogen bond angles 0 basepair planarities 847 basepair parallelities 1952 stacking parallelities Total time for adding SS restraints: 128.39 Time building geometry restraints manager: 55.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 29751 1.34 - 1.49: 63549 1.49 - 1.64: 41671 1.64 - 1.79: 270 1.79 - 1.94: 136 Bond restraints: 135377 Sorted by residual: bond pdb=" C2' A2M 21186 " pdb=" C1' A2M 21186 " ideal model delta sigma weight residual 1.305 1.569 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C2' A2M 1 858 " pdb=" C1' A2M 1 858 " ideal model delta sigma weight residual 1.305 1.563 -0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C2' A2M 2 527 " pdb=" C1' A2M 2 527 " ideal model delta sigma weight residual 1.305 1.559 -0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C2' A2M 1 681 " pdb=" C1' A2M 1 681 " ideal model delta sigma weight residual 1.305 1.557 -0.252 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C2' A2M 2 572 " pdb=" C1' A2M 2 572 " ideal model delta sigma weight residual 1.305 1.550 -0.245 2.00e-02 2.50e+03 1.51e+02 ... (remaining 135372 not shown) Histogram of bond angle deviations from ideal: 81.56 - 92.65: 3 92.65 - 103.74: 11386 103.74 - 114.83: 97005 114.83 - 125.93: 79227 125.93 - 137.02: 12256 Bond angle restraints: 199877 Sorted by residual: angle pdb=" C1' A2M 21385 " pdb=" N9 A2M 21385 " pdb=" C8 A2M 21385 " ideal model delta sigma weight residual 88.50 130.08 -41.58 3.00e+00 1.11e-01 1.92e+02 angle pdb=" C1' A2M 21068 " pdb=" N9 A2M 21068 " pdb=" C8 A2M 21068 " ideal model delta sigma weight residual 88.50 129.96 -41.46 3.00e+00 1.11e-01 1.91e+02 angle pdb=" C1' A2M 2 572 " pdb=" N9 A2M 2 572 " pdb=" C8 A2M 2 572 " ideal model delta sigma weight residual 88.50 129.21 -40.71 3.00e+00 1.11e-01 1.84e+02 angle pdb=" C1' A2M 1 697 " pdb=" N9 A2M 1 697 " pdb=" C8 A2M 1 697 " ideal model delta sigma weight residual 88.50 129.09 -40.59 3.00e+00 1.11e-01 1.83e+02 angle pdb=" C1' A2M 1 69 " pdb=" N9 A2M 1 69 " pdb=" C8 A2M 1 69 " ideal model delta sigma weight residual 88.50 128.71 -40.21 3.00e+00 1.11e-01 1.80e+02 ... (remaining 199872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 76890 35.94 - 71.89: 8474 71.89 - 107.83: 983 107.83 - 143.77: 32 143.77 - 179.72: 74 Dihedral angle restraints: 86453 sinusoidal: 67827 harmonic: 18626 Sorted by residual: dihedral pdb=" O4' C 3 128 " pdb=" C1' C 3 128 " pdb=" N1 C 3 128 " pdb=" C2 C 3 128 " ideal model delta sinusoidal sigma weight residual 200.00 20.28 179.72 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 21191 " pdb=" C1' U 21191 " pdb=" N1 U 21191 " pdb=" C2 U 21191 " ideal model delta sinusoidal sigma weight residual 200.00 21.68 178.32 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 1 778 " pdb=" C1' C 1 778 " pdb=" N1 C 1 778 " pdb=" C2 C 1 778 " ideal model delta sinusoidal sigma weight residual -160.00 13.75 -173.75 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 86450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.400: 25083 0.400 - 0.800: 12 0.800 - 1.200: 0 1.200 - 1.600: 0 1.600 - 2.000: 1 Chirality restraints: 25096 Sorted by residual: chirality pdb=" P C 2 668 " pdb=" OP1 C 2 668 " pdb=" OP2 C 2 668 " pdb=" O5' C 2 668 " both_signs ideal model delta sigma weight residual True 2.41 0.41 2.00 2.00e-01 2.50e+01 1.00e+02 chirality pdb=" CB VAL H 54 " pdb=" CA VAL H 54 " pdb=" CG1 VAL H 54 " pdb=" CG2 VAL H 54 " both_signs ideal model delta sigma weight residual False -2.63 -2.09 -0.54 2.00e-01 2.50e+01 7.31e+00 chirality pdb=" C1' A 11670 " pdb=" O4' A 11670 " pdb=" C2' A 11670 " pdb=" N9 A 11670 " both_signs ideal model delta sigma weight residual False 2.46 1.95 0.51 2.00e-01 2.50e+01 6.53e+00 ... (remaining 25093 not shown) Planarity restraints: 12291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG 2 71 " -0.116 2.00e-02 2.50e+03 6.38e-01 9.16e+03 pdb=" C4' OMG 2 71 " -0.448 2.00e-02 2.50e+03 pdb=" O4' OMG 2 71 " -0.580 2.00e-02 2.50e+03 pdb=" C3' OMG 2 71 " 0.592 2.00e-02 2.50e+03 pdb=" O3' OMG 2 71 " 0.765 2.00e-02 2.50e+03 pdb=" C2' OMG 2 71 " 0.117 2.00e-02 2.50e+03 pdb=" O2' OMG 2 71 " -1.089 2.00e-02 2.50e+03 pdb=" C1' OMG 2 71 " -0.208 2.00e-02 2.50e+03 pdb=" N9 OMG 2 71 " 0.967 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG 2 641 " -0.091 2.00e-02 2.50e+03 6.28e-01 8.88e+03 pdb=" C4' OMG 2 641 " -0.475 2.00e-02 2.50e+03 pdb=" O4' OMG 2 641 " -0.675 2.00e-02 2.50e+03 pdb=" C3' OMG 2 641 " 0.584 2.00e-02 2.50e+03 pdb=" O3' OMG 2 641 " 0.703 2.00e-02 2.50e+03 pdb=" C2' OMG 2 641 " 0.163 2.00e-02 2.50e+03 pdb=" O2' OMG 2 641 " -0.991 2.00e-02 2.50e+03 pdb=" C1' OMG 2 641 " -0.205 2.00e-02 2.50e+03 pdb=" N9 OMG 2 641 " 0.987 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG 11190 " 0.109 2.00e-02 2.50e+03 6.25e-01 8.80e+03 pdb=" C4' OMG 11190 " 0.431 2.00e-02 2.50e+03 pdb=" O4' OMG 11190 " 0.558 2.00e-02 2.50e+03 pdb=" C3' OMG 11190 " -0.602 2.00e-02 2.50e+03 pdb=" O3' OMG 11190 " -0.735 2.00e-02 2.50e+03 pdb=" C2' OMG 11190 " -0.121 2.00e-02 2.50e+03 pdb=" O2' OMG 11190 " 1.079 2.00e-02 2.50e+03 pdb=" C1' OMG 11190 " 0.221 2.00e-02 2.50e+03 pdb=" N9 OMG 11190 " -0.940 2.00e-02 2.50e+03 ... (remaining 12288 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 16 2.06 - 2.77: 24364 2.77 - 3.48: 153960 3.48 - 4.19: 417469 4.19 - 4.90: 584406 Nonbonded interactions: 1180215 Sorted by model distance: nonbonded pdb=" NH2BARG H 112 " pdb=" O HOH H 301 " model vdw 1.349 2.520 nonbonded pdb=" NH2AARG H 112 " pdb=" O HOH H 301 " model vdw 1.471 2.520 nonbonded pdb=" OP2 U 21312 " pdb=" O HOH 21801 " model vdw 1.659 2.440 nonbonded pdb=" NH2 ARG A 242 " pdb=" O THR A 243 " model vdw 1.870 2.520 nonbonded pdb=" OP2 U 2 54 " pdb="MG MG 11818 " model vdw 1.938 2.170 ... (remaining 1180210 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.33 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: 2.280 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: 0.090 Extract box with map and model: 17.130 Check model and map are aligned: 1.420 Set scattering table: 0.880 Process input model: 399.820 Find NCS groups from input model: 2.880 Set up NCS constraints: 0.320 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:9.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 433.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 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 : 0.012 0.264 135377 Z= 0.713 Angle : 1.289 41.576 199877 Z= 0.589 Chirality : 0.058 2.000 25096 Planarity : 0.027 0.638 12291 Dihedral : 23.107 179.716 74395 Min Nonbonded Distance : 1.349 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.43 % Favored : 93.39 % Rotamer: Outliers : 0.96 % Allowed : 4.43 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.39 % 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: -4.53 (0.08), residues: 6350 helix: -4.34 (0.06), residues: 2071 sheet: -2.27 (0.15), residues: 831 loop : -2.29 (0.09), residues: 3448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.005 TRP B 260 HIS 0.034 0.004 HIS Y 77 PHE 0.069 0.005 PHE C 121 TYR 0.067 0.005 TYR Y 85 ARG 0.025 0.002 ARG M 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12700 Ramachandran restraints generated. 6350 Oldfield, 0 Emsley, 6350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12700 Ramachandran restraints generated. 6350 Oldfield, 0 Emsley, 6350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1028 time to evaluate : 5.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7631 (mm-30) REVERT: A 119 LYS cc_start: 0.8258 (ptpp) cc_final: 0.8049 (ptpp) REVERT: A 194 ASN cc_start: 0.8353 (t0) cc_final: 0.8142 (t0) REVERT: B 39 GLN cc_start: 0.7245 (mm110) cc_final: 0.6935 (mm110) REVERT: B 84 MET cc_start: 0.8776 (mtm) cc_final: 0.8467 (mtp) REVERT: B 185 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8449 (mt-10) REVERT: B 201 LYS cc_start: 0.7334 (mtpm) cc_final: 0.7081 (mtpt) REVERT: B 236 LYS cc_start: 0.8121 (mmmm) cc_final: 0.7757 (mmmt) REVERT: B 330 MET cc_start: 0.8041 (ttp) cc_final: 0.7768 (ttm) REVERT: B 351 PRO cc_start: 0.7836 (Cg_exo) cc_final: 0.7622 (Cg_endo) REVERT: C 164 LYS cc_start: 0.7947 (pttt) cc_final: 0.7644 (ptmt) REVERT: C 217 ARG cc_start: 0.7414 (ptm160) cc_final: 0.7022 (ttt180) REVERT: C 273 LYS cc_start: 0.7985 (mttt) cc_final: 0.7421 (mmtm) REVERT: D 146 LYS cc_start: 0.7732 (mtpt) cc_final: 0.7465 (mtmm) REVERT: H 60 ASN cc_start: 0.8774 (m110) cc_final: 0.8510 (m110) REVERT: L 68 MET cc_start: 0.7906 (ptm) cc_final: 0.7643 (ptp) REVERT: L 81 LEU cc_start: 0.8010 (mt) cc_final: 0.7793 (mp) REVERT: N 115 MET cc_start: 0.6992 (ttt) cc_final: 0.6666 (ttt) REVERT: N 141 LYS cc_start: 0.7885 (mttp) cc_final: 0.7590 (mttp) REVERT: N 164 ILE cc_start: 0.8461 (pt) cc_final: 0.8221 (pp) REVERT: O 89 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6991 (mm-30) REVERT: O 126 ASP cc_start: 0.7222 (m-30) cc_final: 0.6596 (m-30) REVERT: O 158 ARG cc_start: 0.7669 (ttm170) cc_final: 0.7258 (ttm170) REVERT: O 199 LYS cc_start: 0.8141 (ttpt) cc_final: 0.7521 (ttpt) REVERT: O 202 ARG cc_start: 0.7257 (tmt170) cc_final: 0.6975 (ttp80) REVERT: O 203 ASP cc_start: 0.7136 (m-30) cc_final: 0.6503 (m-30) REVERT: Q 65 LYS cc_start: 0.7975 (ttpm) cc_final: 0.7703 (ptpp) REVERT: Q 96 MET cc_start: 0.8724 (mtm) cc_final: 0.8423 (mtm) REVERT: R 91 ARG cc_start: 0.7804 (tmm160) cc_final: 0.7498 (ttp-170) REVERT: S 21 LYS cc_start: 0.8574 (mmtt) cc_final: 0.8346 (mmtm) REVERT: S 35 LYS cc_start: 0.7783 (ttpt) cc_final: 0.7180 (ttmm) REVERT: S 134 MET cc_start: 0.5757 (mpm) cc_final: 0.5513 (mmm) REVERT: U 31 SER cc_start: 0.7537 (m) cc_final: 0.7233 (t) REVERT: V 114 ASN cc_start: 0.8677 (m-40) cc_final: 0.8473 (m-40) REVERT: W 82 VAL cc_start: 0.8566 (t) cc_final: 0.8319 (m) REVERT: W 113 LYS cc_start: 0.8104 (mtmt) cc_final: 0.7827 (mtmt) REVERT: Y 119 ARG cc_start: 0.7202 (mpt90) cc_final: 0.6980 (mmt90) REVERT: Z 123 LYS cc_start: 0.7293 (tppp) cc_final: 0.7013 (tmtt) REVERT: a 21 THR cc_start: 0.8602 (t) cc_final: 0.8317 (p) REVERT: a 47 ARG cc_start: 0.7228 (mmp-170) cc_final: 0.6957 (mmp-170) REVERT: c 66 ARG cc_start: 0.6740 (tpp-160) cc_final: 0.5761 (ttp80) REVERT: c 181 ASP cc_start: 0.7320 (m-30) cc_final: 0.7010 (m-30) REVERT: d 42 LYS cc_start: 0.7635 (mptt) cc_final: 0.7428 (mmtm) REVERT: e 119 ASP cc_start: 0.8239 (t0) cc_final: 0.7908 (t70) REVERT: f 117 ASP cc_start: 0.7736 (t70) cc_final: 0.7450 (t70) REVERT: h 30 LYS cc_start: 0.8011 (ptmt) cc_final: 0.7652 (ptmt) REVERT: h 102 ARG cc_start: 0.7489 (mtm-85) cc_final: 0.7271 (ptp-170) REVERT: k 65 LYS cc_start: 0.7937 (ttmt) cc_final: 0.7227 (tttt) REVERT: m 108 THR cc_start: 0.8713 (m) cc_final: 0.8342 (p) REVERT: p 81 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.7017 (ttt180) REVERT: p 90 HIS cc_start: 0.7467 (t-170) cc_final: 0.6468 (m90) outliers start: 33 outliers final: 19 residues processed: 1053 average time/residue: 2.2571 time to fit residues: 3207.0472 Evaluate side-chains 812 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 792 time to evaluate : 5.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain U residue 110 LEU Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain c residue 163 TYR Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain e residue 144 VAL Chi-restraints excluded: chain e residue 177 THR Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain p residue 81 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 818 optimal weight: 0.8980 chunk 734 optimal weight: 0.9980 chunk 407 optimal weight: 6.9990 chunk 250 optimal weight: 3.9990 chunk 495 optimal weight: 1.9990 chunk 392 optimal weight: 0.7980 chunk 759 optimal weight: 8.9990 chunk 293 optimal weight: 4.9990 chunk 461 optimal weight: 7.9990 chunk 565 optimal weight: 5.9990 chunk 879 optimal weight: 9.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 21 HIS A 50 HIS A 100 ASN A 115 ASN A 140 ASN A 194 ASN A 209 HIS A 228 HIS B 24 GLN B 55 HIS B 282 GLN B 284 ASN B 299 ASN B 352 GLN B 378 GLN C 46 ASN C 61 HIS C 158 GLN C 197 ASN ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS D 154 HIS E 75 HIS E 123 GLN E 152 GLN E 162 GLN E 185 ASN F 60 ASN G 144 GLN G 222 GLN G 258 ASN G 335 HIS H 68 ASN H 118 ASN I 12 HIS I 23 GLN I 36 GLN I 70 HIS I 108 ASN I 134 ASN J 100 ASN ** K 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 ASN K 126 ASN K 198 HIS B L 28 HIS L 34 ASN L 41 HIS L 62 HIS L 74 ASN L 114 HIS L 144 GLN M 32 HIS M 98 ASN M 153 ASN M 196 ASN N 33 ASN N 71 GLN N 81 ASN N 192 GLN N 196 HIS O 63 GLN O 90 HIS O 253 HIS Q 118 HIS Q 137 ASN Q 141 HIS R 5 HIS R 10 GLN R 75 ASN R 110 HIS R 116 HIS R 134 HIS R 155 GLN S 3 HIS S 111 GLN S 142 ASN T 37 ASN ** T 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 121 GLN V 34 GLN V 114 ASN W 18 GLN W 41 ASN W 88 ASN W 97 HIS ** Z 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 47 ASN Z 72 ASN a 3 HIS a 69 ASN b 7 HIS b 9 ASN b 11 ASN b 17 HIS b 30 HIS b 51 ASN c 135 ASN c 239 ASN ** d 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 96 ASN e 120 ASN e 132 HIS e 167 ASN f 55 ASN ** f 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 99 HIS g 25 ASN g 49 GLN g 111 HIS g 122 ASN h 19 ASN h 41 GLN h 51 HIS h 62 HIS j 10 GLN j 25 ASN j 28 HIS m 109 ASN m 120 ASN o 75 ASN p 3 ASN p 20 HIS p 73 GLN p 82 GLN Total number of N/Q/H flips: 120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 135377 Z= 0.185 Angle : 0.840 27.028 199877 Z= 0.434 Chirality : 0.041 1.954 25096 Planarity : 0.008 0.132 12291 Dihedral : 24.323 179.813 62077 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.34 % Favored : 94.57 % Rotamer: Outliers : 2.61 % Allowed : 11.08 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.03 % 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: -3.12 (0.09), residues: 6350 helix: -2.50 (0.09), residues: 2115 sheet: -1.78 (0.16), residues: 836 loop : -1.80 (0.09), residues: 3399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 260 HIS 0.013 0.001 HIS B 248 PHE 0.023 0.002 PHE C 121 TYR 0.024 0.002 TYR O 213 ARG 0.007 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12700 Ramachandran restraints generated. 6350 Oldfield, 0 Emsley, 6350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12700 Ramachandran restraints generated. 6350 Oldfield, 0 Emsley, 6350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 882 time to evaluate : 6.346 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7787 (mm-30) REVERT: A 62 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7292 (mm-30) REVERT: A 198 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.8010 (mtpp) REVERT: B 39 GLN cc_start: 0.7031 (mm110) cc_final: 0.6755 (mm110) REVERT: B 80 GLU cc_start: 0.8388 (tt0) cc_final: 0.7979 (tt0) REVERT: B 201 LYS cc_start: 0.7152 (mtpm) cc_final: 0.6912 (mtpt) REVERT: B 326 ASN cc_start: 0.8275 (m110) cc_final: 0.7772 (m110) REVERT: B 343 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.7371 (mmt) REVERT: C 164 LYS cc_start: 0.7946 (pttt) cc_final: 0.7613 (ptmt) REVERT: C 273 LYS cc_start: 0.7935 (mttt) cc_final: 0.7379 (mmtm) REVERT: D 146 LYS cc_start: 0.7657 (mtpt) cc_final: 0.7393 (mtmm) REVERT: E 185 ASN cc_start: 0.7781 (m110) cc_final: 0.7357 (m-40) REVERT: G 331 LEU cc_start: 0.7752 (mm) cc_final: 0.7551 (mp) REVERT: H 60 ASN cc_start: 0.8763 (m110) cc_final: 0.8390 (m110) REVERT: H 176 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7215 (mt-10) REVERT: H 188 GLU cc_start: 0.6851 (tp30) cc_final: 0.6425 (mt-10) REVERT: H 207 LYS cc_start: 0.7140 (mtpp) cc_final: 0.6900 (mtpt) REVERT: I 75 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8384 (ptt-90) REVERT: L 68 MET cc_start: 0.7946 (ptm) cc_final: 0.7664 (ptp) REVERT: M 147 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7313 (ptt-90) REVERT: N 40 ARG cc_start: 0.6730 (mtp180) cc_final: 0.6428 (ttm-80) REVERT: O 126 ASP cc_start: 0.7136 (m-30) cc_final: 0.6514 (m-30) REVERT: O 199 LYS cc_start: 0.7803 (ttpt) cc_final: 0.6897 (ttpt) REVERT: O 203 ASP cc_start: 0.6829 (m-30) cc_final: 0.6186 (m-30) REVERT: O 243 GLU cc_start: 0.7056 (tt0) cc_final: 0.6610 (pm20) REVERT: O 250 LYS cc_start: 0.7921 (mtmt) cc_final: 0.6864 (tttp) REVERT: P 46 LYS cc_start: 0.7688 (mptp) cc_final: 0.6841 (mttp) REVERT: Q 5 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7205 (mtpp) REVERT: Q 96 MET cc_start: 0.8673 (mtm) cc_final: 0.8448 (mtm) REVERT: Q 136 ARG cc_start: 0.6528 (ttp-170) cc_final: 0.5774 (ttp-170) REVERT: R 91 ARG cc_start: 0.7688 (tmm160) cc_final: 0.7307 (ttp-170) REVERT: S 21 LYS cc_start: 0.8543 (mmtt) cc_final: 0.8298 (mmtm) REVERT: S 74 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8246 (t) REVERT: S 134 MET cc_start: 0.5755 (mpm) cc_final: 0.5524 (mmm) REVERT: S 144 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7386 (mt-10) REVERT: T 31 GLU cc_start: 0.7803 (mp0) cc_final: 0.7165 (mp0) REVERT: T 111 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7371 (mp10) REVERT: T 125 MET cc_start: 0.7285 (mtp) cc_final: 0.7037 (mtt) REVERT: U 110 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6508 (tp) REVERT: V 104 LYS cc_start: 0.8163 (tttp) cc_final: 0.7776 (tttm) REVERT: W 113 LYS cc_start: 0.8056 (mtmt) cc_final: 0.7789 (mtmt) REVERT: X 53 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8118 (mt) REVERT: Z 29 ASN cc_start: 0.7765 (t0) cc_final: 0.7561 (t0) REVERT: Z 79 ARG cc_start: 0.7368 (mmt90) cc_final: 0.6582 (mmm-85) REVERT: Z 100 ARG cc_start: 0.7559 (mtp180) cc_final: 0.7143 (mmm-85) REVERT: Z 112 ARG cc_start: 0.7235 (ttt-90) cc_final: 0.6967 (ttp80) REVERT: Z 123 LYS cc_start: 0.7459 (tppp) cc_final: 0.7211 (tmtt) REVERT: a 21 THR cc_start: 0.8497 (t) cc_final: 0.8268 (m) REVERT: c 66 ARG cc_start: 0.6518 (tpp-160) cc_final: 0.6024 (ttm-80) REVERT: c 109 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7146 (mm-40) REVERT: d 25 TYR cc_start: 0.8320 (p90) cc_final: 0.7966 (p90) REVERT: e 81 MET cc_start: 0.8246 (ptp) cc_final: 0.7857 (ptm) REVERT: e 119 ASP cc_start: 0.8297 (t0) cc_final: 0.7897 (t70) REVERT: e 162 TYR cc_start: 0.8460 (p90) cc_final: 0.7843 (p90) REVERT: f 114 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.6756 (ttm) REVERT: f 117 ASP cc_start: 0.7509 (t70) cc_final: 0.7188 (t70) REVERT: g 38 THR cc_start: 0.8501 (m) cc_final: 0.8239 (p) REVERT: h 30 LYS cc_start: 0.8061 (ptmt) cc_final: 0.7710 (ptmt) REVERT: h 72 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7309 (mp0) REVERT: h 102 ARG cc_start: 0.7701 (mtm-85) cc_final: 0.7389 (ptp90) REVERT: k 65 LYS cc_start: 0.7886 (ttmt) cc_final: 0.7157 (tttt) REVERT: m 108 THR cc_start: 0.8739 (m) cc_final: 0.8464 (p) REVERT: p 90 HIS cc_start: 0.7493 (t-170) cc_final: 0.6422 (m90) outliers start: 118 outliers final: 45 residues processed: 952 average time/residue: 2.0939 time to fit residues: 2753.3886 Evaluate side-chains 833 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 775 time to evaluate : 6.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 176 GLU Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain L residue 129 LEU Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain M residue 147 ARG Chi-restraints excluded: chain N residue 78 LYS Chi-restraints excluded: chain N residue 166 VAL Chi-restraints excluded: chain N residue 176 ILE Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain Q residue 5 LYS Chi-restraints excluded: chain Q residue 40 SER Chi-restraints excluded: chain R residue 7 ARG Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 76 ILE Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain T residue 111 GLN Chi-restraints excluded: chain U residue 110 LEU Chi-restraints excluded: chain W residue 88 ASN Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Z residue 27 MET Chi-restraints excluded: chain Z residue 35 ASN Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain c residue 41 VAL Chi-restraints excluded: chain c residue 72 LEU Chi-restraints excluded: chain c residue 109 GLN Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain e residue 144 VAL Chi-restraints excluded: chain e residue 177 THR Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 114 MET Chi-restraints excluded: chain f residue 127 LEU Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 81 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 489 optimal weight: 5.9990 chunk 273 optimal weight: 7.9990 chunk 732 optimal weight: 10.0000 chunk 599 optimal weight: 20.0000 chunk 242 optimal weight: 8.9990 chunk 881 optimal weight: 9.9990 chunk 952 optimal weight: 10.0000 chunk 785 optimal weight: 10.0000 chunk 874 optimal weight: 9.9990 chunk 300 optimal weight: 1.9990 chunk 707 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 8 HIS B 248 HIS B 284 ASN B 378 GLN C 93 ASN C 118 GLN E 123 GLN F 56 GLN ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN H 190 GLN I 64 ASN K 126 ASN M 171 HIS P 158 HIS Q 75 HIS T 28 ASN T 50 GLN ** T 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 121 GLN T 145 HIS ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 34 GLN W 41 ASN ** Z 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 72 ASN ** a 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 105 ASN c 109 GLN c 123 ASN ** d 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 25 ASN j 76 ASN l 18 ASN m 109 ASN o 21 ASN o 33 GLN o 37 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 135377 Z= 0.461 Angle : 0.945 25.939 199877 Z= 0.480 Chirality : 0.050 1.979 25096 Planarity : 0.009 0.144 12291 Dihedral : 24.232 179.903 62065 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.48 % Favored : 93.41 % Rotamer: Outliers : 4.08 % Allowed : 12.68 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.09), residues: 6350 helix: -1.70 (0.10), residues: 2127 sheet: -1.62 (0.16), residues: 851 loop : -1.61 (0.10), residues: 3372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 260 HIS 0.015 0.002 HIS B 248 PHE 0.046 0.003 PHE B 387 TYR 0.035 0.003 TYR Y 85 ARG 0.011 0.001 ARG G 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12700 Ramachandran restraints generated. 6350 Oldfield, 0 Emsley, 6350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12700 Ramachandran restraints generated. 6350 Oldfield, 0 Emsley, 6350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 781 time to evaluate : 6.885 Fit side-chains REVERT: A 49 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7716 (mm-30) REVERT: A 74 GLU cc_start: 0.7323 (tp30) cc_final: 0.6946 (tp30) REVERT: A 106 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.6951 (mp10) REVERT: A 149 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7893 (tttt) REVERT: A 198 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7892 (mtpt) REVERT: A 245 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6892 (tmt170) REVERT: B 94 GLN cc_start: 0.8069 (mt0) cc_final: 0.7439 (mm-40) REVERT: B 201 LYS cc_start: 0.7217 (mtpm) cc_final: 0.6982 (mtpt) REVERT: C 164 LYS cc_start: 0.8168 (pttt) cc_final: 0.7745 (ptmt) REVERT: C 217 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7033 (ptm160) REVERT: C 273 LYS cc_start: 0.8017 (mttt) cc_final: 0.7351 (mmtm) REVERT: D 146 LYS cc_start: 0.7744 (mtpt) cc_final: 0.7332 (mtmm) REVERT: H 176 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: H 188 GLU cc_start: 0.6873 (tp30) cc_final: 0.6602 (tp30) REVERT: I 54 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7783 (ptm160) REVERT: I 75 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8501 (ptt-90) REVERT: L 68 MET cc_start: 0.7920 (ptm) cc_final: 0.7621 (ptp) REVERT: M 19 MET cc_start: 0.8192 (mmm) cc_final: 0.7709 (mmp) REVERT: M 97 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8238 (p0) REVERT: M 189 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.6207 (tmt-80) REVERT: N 78 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7005 (ttpt) REVERT: N 115 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6458 (ttt) REVERT: N 153 ARG cc_start: 0.6532 (tmm160) cc_final: 0.6180 (tmt170) REVERT: N 156 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7583 (ptpt) REVERT: O 76 MET cc_start: 0.7264 (tpp) cc_final: 0.6911 (tpp) REVERT: O 89 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6866 (mm-30) REVERT: O 203 ASP cc_start: 0.7048 (m-30) cc_final: 0.6279 (m-30) REVERT: O 243 GLU cc_start: 0.7109 (tt0) cc_final: 0.6583 (pm20) REVERT: Q 5 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7350 (mtpp) REVERT: R 97 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7360 (ttm-80) REVERT: S 21 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8335 (mmtm) REVERT: S 35 LYS cc_start: 0.7727 (ttpt) cc_final: 0.7151 (ttmt) REVERT: S 134 MET cc_start: 0.5642 (mpm) cc_final: 0.5290 (mmm) REVERT: S 144 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7371 (mt-10) REVERT: W 3 SER cc_start: 0.6952 (t) cc_final: 0.6324 (m) REVERT: W 113 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7751 (mtmt) REVERT: X 53 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8212 (mt) REVERT: Z 27 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7369 (ttp) REVERT: Z 54 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6274 (mmpt) REVERT: Z 112 ARG cc_start: 0.7362 (ttt-90) cc_final: 0.6932 (ttp80) REVERT: a 6 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7237 (ptpt) REVERT: c 66 ARG cc_start: 0.6569 (tpp-160) cc_final: 0.5999 (ttm-80) REVERT: c 159 TYR cc_start: 0.7804 (m-80) cc_final: 0.7593 (m-80) REVERT: c 177 GLN cc_start: 0.7758 (tp-100) cc_final: 0.6691 (tm-30) REVERT: c 181 ASP cc_start: 0.7373 (m-30) cc_final: 0.6423 (m-30) REVERT: c 224 MET cc_start: 0.6970 (mtm) cc_final: 0.6669 (mtm) REVERT: f 56 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.6865 (pmmt) REVERT: f 114 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.6792 (ttm) REVERT: f 117 ASP cc_start: 0.7552 (t70) cc_final: 0.7182 (t70) REVERT: h 30 LYS cc_start: 0.8096 (ptmt) cc_final: 0.7711 (ptpp) REVERT: k 66 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8328 (mtpm) REVERT: m 108 THR cc_start: 0.8724 (m) cc_final: 0.8427 (p) REVERT: o 48 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7084 (mmm-85) REVERT: p 7 LYS cc_start: 0.7743 (mtpp) cc_final: 0.7515 (mtpp) outliers start: 193 outliers final: 98 residues processed: 902 average time/residue: 2.0661 time to fit residues: 2569.4095 Evaluate side-chains 878 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 756 time to evaluate : 6.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 176 GLU Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 129 LEU Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 97 ASN Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain M residue 147 ARG Chi-restraints excluded: chain M residue 189 ARG Chi-restraints excluded: chain N residue 78 LYS Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 166 VAL Chi-restraints excluded: chain N residue 176 ILE Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 161 THR Chi-restraints excluded: chain O residue 205 ILE Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain Q residue 5 LYS Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 40 SER Chi-restraints excluded: chain Q residue 91 SER Chi-restraints excluded: chain Q residue 113 LYS Chi-restraints excluded: chain Q residue 140 GLU Chi-restraints excluded: chain R residue 7 ARG Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 103 GLU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain U residue 25 VAL Chi-restraints excluded: chain U residue 44 LEU Chi-restraints excluded: chain U residue 110 LEU Chi-restraints excluded: chain V residue 34 GLN Chi-restraints excluded: chain W residue 88 ASN Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Z residue 27 MET Chi-restraints excluded: chain Z residue 35 ASN Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 90 SER Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain c residue 41 VAL Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 164 LEU Chi-restraints excluded: chain c residue 188 ILE Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 130 ILE Chi-restraints excluded: chain e residue 144 VAL Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 177 THR Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain f residue 114 MET Chi-restraints excluded: chain f residue 127 LEU Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 119 VAL Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 142 SER Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 87 GLN Chi-restraints excluded: chain j residue 22 CYS Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 66 LYS Chi-restraints excluded: chain m residue 105 VAL Chi-restraints excluded: chain o residue 48 ARG Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 81 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 870 optimal weight: 10.0000 chunk 662 optimal weight: 10.0000 chunk 457 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 420 optimal weight: 2.9990 chunk 591 optimal weight: 0.6980 chunk 884 optimal weight: 7.9990 chunk 936 optimal weight: 10.0000 chunk 462 optimal weight: 5.9990 chunk 838 optimal weight: 9.9990 chunk 252 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 ASN C 93 ASN E 123 GLN F 56 GLN ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 126 ASN P 58 ASN ** T 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 34 GLN W 18 GLN W 41 ASN W 88 ASN ** Z 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 42 HIS ** a 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 109 GLN c 226 GLN ** d 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 122 ASN j 25 ASN j 76 ASN m 109 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 135377 Z= 0.264 Angle : 0.821 26.400 199877 Z= 0.427 Chirality : 0.042 1.972 25096 Planarity : 0.008 0.132 12291 Dihedral : 24.050 179.521 62065 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.67 % Favored : 94.25 % Rotamer: Outliers : 4.19 % Allowed : 13.90 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.98 (0.10), residues: 6350 helix: -1.03 (0.11), residues: 2150 sheet: -1.41 (0.17), residues: 854 loop : -1.42 (0.10), residues: 3346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 260 HIS 0.013 0.001 HIS R 134 PHE 0.022 0.002 PHE T 149 TYR 0.027 0.002 TYR M 188 ARG 0.008 0.001 ARG V 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12700 Ramachandran restraints generated. 6350 Oldfield, 0 Emsley, 6350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12700 Ramachandran restraints generated. 6350 Oldfield, 0 Emsley, 6350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 787 time to evaluate : 6.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7758 (mm-30) REVERT: A 62 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7574 (mm-30) REVERT: A 106 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.6849 (mp10) REVERT: A 198 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8040 (mtpp) REVERT: B 10 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7296 (ptp-170) REVERT: B 94 GLN cc_start: 0.8077 (mt0) cc_final: 0.7442 (mm-40) REVERT: B 343 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7222 (mmt) REVERT: C 164 LYS cc_start: 0.8145 (pttt) cc_final: 0.7728 (ptmt) REVERT: C 217 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6973 (ptm160) REVERT: C 273 LYS cc_start: 0.8001 (mttt) cc_final: 0.7402 (mmtm) REVERT: C 284 ASN cc_start: 0.7305 (m110) cc_final: 0.7073 (m110) REVERT: D 146 LYS cc_start: 0.7743 (mtpt) cc_final: 0.7329 (mtmm) REVERT: G 337 ARG cc_start: 0.7139 (ttp-110) cc_final: 0.6916 (ptp90) REVERT: H 117 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7474 (tm) REVERT: H 176 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7008 (mt-10) REVERT: H 188 GLU cc_start: 0.6845 (tp30) cc_final: 0.6620 (tp30) REVERT: H 207 LYS cc_start: 0.7264 (mtpp) cc_final: 0.7055 (mtpt) REVERT: I 54 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7755 (ptm160) REVERT: I 75 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8347 (ptt-90) REVERT: L 68 MET cc_start: 0.7950 (ptm) cc_final: 0.7658 (ptp) REVERT: M 26 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.6605 (mtt90) REVERT: M 189 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.6290 (tmt-80) REVERT: N 153 ARG cc_start: 0.6456 (tmm160) cc_final: 0.6155 (tmt170) REVERT: N 156 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7597 (ptpt) REVERT: N 178 ARG cc_start: 0.6217 (mtp180) cc_final: 0.5855 (mmm-85) REVERT: O 89 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6923 (mm-30) REVERT: O 126 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.6758 (m-30) REVERT: O 203 ASP cc_start: 0.6828 (m-30) cc_final: 0.6170 (m-30) REVERT: O 243 GLU cc_start: 0.7101 (tt0) cc_final: 0.6685 (pm20) REVERT: P 46 LYS cc_start: 0.7702 (mptp) cc_final: 0.7044 (mttt) REVERT: Q 5 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.6911 (mtpt) REVERT: Q 133 ARG cc_start: 0.7804 (mpt90) cc_final: 0.7569 (mtp-110) REVERT: S 21 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8321 (mmtm) REVERT: S 35 LYS cc_start: 0.7707 (ttpt) cc_final: 0.7239 (ttmm) REVERT: S 134 MET cc_start: 0.5749 (mpm) cc_final: 0.5438 (mmm) REVERT: S 144 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7494 (mt-10) REVERT: T 31 GLU cc_start: 0.7857 (mp0) cc_final: 0.7335 (mp0) REVERT: T 124 ARG cc_start: 0.7878 (mtt90) cc_final: 0.7618 (mtt90) REVERT: T 140 MET cc_start: 0.7590 (mmm) cc_final: 0.7302 (mmm) REVERT: V 104 LYS cc_start: 0.8120 (tttp) cc_final: 0.7665 (tttm) REVERT: W 3 SER cc_start: 0.6707 (t) cc_final: 0.6133 (m) REVERT: W 35 GLU cc_start: 0.7271 (pp20) cc_final: 0.7038 (pp20) REVERT: W 113 LYS cc_start: 0.8087 (mtmt) cc_final: 0.7754 (mtmt) REVERT: X 53 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8152 (mt) REVERT: Z 54 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6311 (mmpt) REVERT: Z 79 ARG cc_start: 0.7418 (mmt90) cc_final: 0.6469 (mmm-85) REVERT: Z 112 ARG cc_start: 0.7277 (ttt-90) cc_final: 0.6783 (ttp80) REVERT: Z 123 LYS cc_start: 0.7211 (tmtt) cc_final: 0.6922 (tttt) REVERT: a 6 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7130 (ptpt) REVERT: c 66 ARG cc_start: 0.6553 (tpp-160) cc_final: 0.6010 (ttm-80) REVERT: c 76 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.5815 (mtp180) REVERT: c 224 MET cc_start: 0.6817 (mtm) cc_final: 0.6611 (mtm) REVERT: f 56 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.6903 (pmmt) REVERT: f 114 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.6716 (ttm) REVERT: f 117 ASP cc_start: 0.7443 (t70) cc_final: 0.7098 (t70) REVERT: g 143 GLN cc_start: 0.7605 (mm-40) cc_final: 0.7283 (mm-40) REVERT: h 30 LYS cc_start: 0.8070 (ptmt) cc_final: 0.7700 (ptpp) REVERT: h 102 ARG cc_start: 0.7796 (mtm-85) cc_final: 0.7463 (mtm-85) REVERT: j 25 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8449 (t0) REVERT: k 65 LYS cc_start: 0.7978 (ttmt) cc_final: 0.7184 (tttt) REVERT: m 108 THR cc_start: 0.8687 (m) cc_final: 0.8391 (p) REVERT: o 25 ARG cc_start: 0.7119 (mtm-85) cc_final: 0.6831 (ttp-170) REVERT: o 48 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7083 (mmm-85) REVERT: p 7 LYS cc_start: 0.7778 (mtpp) cc_final: 0.7553 (mtpp) REVERT: p 89 LYS cc_start: 0.8063 (mttm) cc_final: 0.7790 (mttm) outliers start: 198 outliers final: 111 residues processed: 916 average time/residue: 2.0243 time to fit residues: 2573.4140 Evaluate side-chains 893 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 759 time to evaluate : 6.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 176 GLU Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 147 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 129 LEU Chi-restraints excluded: chain M residue 26 ARG Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain M residue 189 ARG Chi-restraints excluded: chain N residue 78 LYS Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 166 VAL Chi-restraints excluded: chain N residue 176 ILE Chi-restraints excluded: chain O residue 82 GLU Chi-restraints excluded: chain O residue 126 ASP Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 161 THR Chi-restraints excluded: chain O residue 205 ILE Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain Q residue 5 LYS Chi-restraints excluded: chain Q residue 40 SER Chi-restraints excluded: chain Q residue 91 SER Chi-restraints excluded: chain Q residue 137 ASN Chi-restraints excluded: chain Q residue 140 GLU Chi-restraints excluded: chain R residue 7 ARG Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 103 GLU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 64 ASN Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain W residue 77 ILE Chi-restraints excluded: chain W residue 88 ASN Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Z residue 35 ASN Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 90 SER Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 92 THR Chi-restraints excluded: chain c residue 41 VAL Chi-restraints excluded: chain c residue 72 LEU Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 76 ARG Chi-restraints excluded: chain c residue 109 GLN Chi-restraints excluded: chain c residue 188 ILE Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 85 ILE Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 130 ILE Chi-restraints excluded: chain e residue 144 VAL Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 177 THR Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain f residue 114 MET Chi-restraints excluded: chain f residue 127 LEU Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 119 VAL Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 142 SER Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain j residue 22 CYS Chi-restraints excluded: chain j residue 25 ASN Chi-restraints excluded: chain m residue 105 VAL Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain o residue 48 ARG Chi-restraints excluded: chain o residue 57 CYS Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 81 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 780 optimal weight: 10.0000 chunk 531 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 697 optimal weight: 10.0000 chunk 386 optimal weight: 9.9990 chunk 799 optimal weight: 10.0000 chunk 647 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 478 optimal weight: 5.9990 chunk 840 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN B 278 HIS C 93 ASN E 123 GLN ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 ASN K 126 ASN L 77 ASN P 58 ASN T 97 ASN ** T 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN V 34 GLN W 41 ASN W 88 ASN ** Z 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 87 GLN j 25 ASN l 33 ASN m 109 ASN n 31 GLN o 33 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 135377 Z= 0.446 Angle : 0.921 25.895 199877 Z= 0.470 Chirality : 0.049 1.981 25096 Planarity : 0.009 0.142 12291 Dihedral : 24.099 179.362 62063 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.86 % Favored : 93.04 % Rotamer: Outliers : 4.74 % Allowed : 14.51 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.94 (0.10), residues: 6350 helix: -0.97 (0.11), residues: 2147 sheet: -1.36 (0.17), residues: 845 loop : -1.44 (0.10), residues: 3358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 260 HIS 0.013 0.002 HIS R 134 PHE 0.032 0.002 PHE i 63 TYR 0.032 0.003 TYR M 188 ARG 0.009 0.001 ARG h 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12700 Ramachandran restraints generated. 6350 Oldfield, 0 Emsley, 6350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12700 Ramachandran restraints generated. 6350 Oldfield, 0 Emsley, 6350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 768 time to evaluate : 6.543 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7847 (mm-30) REVERT: A 106 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.6895 (mp10) REVERT: A 149 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7958 (tttt) REVERT: A 198 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7889 (mtpt) REVERT: A 245 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.6926 (tmt170) REVERT: B 10 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7095 (ptp-170) REVERT: B 94 GLN cc_start: 0.8096 (mt0) cc_final: 0.7437 (mm-40) REVERT: B 201 LYS cc_start: 0.7165 (mtpp) cc_final: 0.6944 (mtpt) REVERT: C 108 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8261 (ttt90) REVERT: C 164 LYS cc_start: 0.8143 (pttt) cc_final: 0.7717 (ptmt) REVERT: C 217 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7040 (ptm160) REVERT: C 273 LYS cc_start: 0.8035 (mttt) cc_final: 0.7361 (mmtm) REVERT: D 146 LYS cc_start: 0.7795 (mtpt) cc_final: 0.7371 (mtmm) REVERT: F 82 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7879 (mmp80) REVERT: G 143 MET cc_start: 0.7442 (mmt) cc_final: 0.7214 (mmt) REVERT: H 117 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7536 (tm) REVERT: H 188 GLU cc_start: 0.6835 (tp30) cc_final: 0.6624 (tp30) REVERT: I 28 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7254 (tttm) REVERT: I 54 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7743 (ptm160) REVERT: I 75 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8495 (ptt-90) REVERT: I 184 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7327 (ttt) REVERT: L 29 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6897 (pm20) REVERT: L 68 MET cc_start: 0.7987 (ptm) cc_final: 0.7637 (ptm) REVERT: M 19 MET cc_start: 0.8186 (mmm) cc_final: 0.7734 (mmp) REVERT: M 26 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6545 (mtt90) REVERT: M 77 LYS cc_start: 0.8021 (mtmt) cc_final: 0.7418 (mtmt) REVERT: M 189 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.6225 (tmt-80) REVERT: N 19 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6332 (mtpp) REVERT: N 78 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7027 (ttpt) REVERT: N 115 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6518 (ttt) REVERT: N 153 ARG cc_start: 0.6471 (tmm160) cc_final: 0.6170 (tmt170) REVERT: N 156 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7591 (ptpt) REVERT: O 89 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6988 (mm-30) REVERT: O 203 ASP cc_start: 0.6984 (m-30) cc_final: 0.6297 (m-30) REVERT: O 243 GLU cc_start: 0.7172 (tt0) cc_final: 0.6727 (pm20) REVERT: P 46 LYS cc_start: 0.7718 (mptp) cc_final: 0.6991 (mttt) REVERT: Q 5 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7257 (mtmt) REVERT: Q 19 ARG cc_start: 0.8517 (tpm-80) cc_final: 0.8253 (tpm-80) REVERT: Q 133 ARG cc_start: 0.7850 (mtt90) cc_final: 0.7579 (mtp-110) REVERT: R 97 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7520 (ttm-80) REVERT: R 134 HIS cc_start: 0.8563 (p-80) cc_final: 0.8312 (p90) REVERT: S 21 LYS cc_start: 0.8611 (mmtt) cc_final: 0.8336 (mmtm) REVERT: S 35 LYS cc_start: 0.7648 (ttpt) cc_final: 0.7048 (ttmt) REVERT: S 92 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7945 (ttt180) REVERT: S 144 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: T 124 ARG cc_start: 0.7978 (mtt90) cc_final: 0.7703 (mtt90) REVERT: W 3 SER cc_start: 0.6937 (t) cc_final: 0.6343 (m) REVERT: W 35 GLU cc_start: 0.7240 (pp20) cc_final: 0.7017 (pp20) REVERT: W 113 LYS cc_start: 0.8076 (mtmt) cc_final: 0.7727 (mtmt) REVERT: X 53 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8185 (mt) REVERT: Z 54 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6353 (mmpt) REVERT: Z 79 ARG cc_start: 0.7375 (mmt90) cc_final: 0.6415 (mmm-85) REVERT: Z 123 LYS cc_start: 0.7055 (tmtt) cc_final: 0.6705 (tttt) REVERT: Z 133 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.5384 (pp20) REVERT: a 6 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7228 (ptpt) REVERT: c 66 ARG cc_start: 0.6425 (tpp-160) cc_final: 0.5868 (ttm-80) REVERT: c 76 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.5808 (mtp180) REVERT: c 181 ASP cc_start: 0.7500 (m-30) cc_final: 0.7298 (m-30) REVERT: c 224 MET cc_start: 0.7070 (mtm) cc_final: 0.6719 (mtm) REVERT: f 56 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.6951 (pmmt) REVERT: f 114 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.6793 (ttm) REVERT: f 117 ASP cc_start: 0.7516 (t70) cc_final: 0.7153 (t70) REVERT: g 143 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7168 (mm-40) REVERT: h 30 LYS cc_start: 0.8091 (ptmt) cc_final: 0.7716 (ptpp) REVERT: h 100 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: k 66 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8341 (mtpm) REVERT: m 108 THR cc_start: 0.8662 (m) cc_final: 0.8365 (p) REVERT: o 48 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7220 (mmm-85) REVERT: p 18 ASN cc_start: 0.7919 (OUTLIER) cc_final: 0.7465 (t0) REVERT: p 81 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6817 (mtp85) outliers start: 225 outliers final: 135 residues processed: 911 average time/residue: 2.0260 time to fit residues: 2566.6737 Evaluate side-chains 914 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 743 time to evaluate : 6.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 82 ARG Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 184 MET Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 147 LYS Chi-restraints excluded: chain L residue 8 CYS Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 129 LEU Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain M residue 26 ARG Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain M residue 147 ARG Chi-restraints excluded: chain M residue 189 ARG Chi-restraints excluded: chain N residue 19 LYS Chi-restraints excluded: chain N residue 78 LYS Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 166 VAL Chi-restraints excluded: chain N residue 176 ILE Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 161 THR Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain Q residue 5 LYS Chi-restraints excluded: chain Q residue 40 SER Chi-restraints excluded: chain Q residue 91 SER Chi-restraints excluded: chain Q residue 137 ASN Chi-restraints excluded: chain Q residue 140 GLU Chi-restraints excluded: chain R residue 7 ARG Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 76 ILE Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain S residue 103 GLU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain T residue 2 THR Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 64 ASN Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain U residue 25 VAL Chi-restraints excluded: chain W residue 50 ASP Chi-restraints excluded: chain W residue 66 LYS Chi-restraints excluded: chain W residue 77 ILE Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Z residue 35 ASN Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 90 SER Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain a residue 3 HIS Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain c residue 41 VAL Chi-restraints excluded: chain c residue 72 LEU Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 76 ARG Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 164 LEU Chi-restraints excluded: chain c residue 188 ILE Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 85 ILE Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 130 ILE Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain e residue 144 VAL Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 177 THR Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 15 THR Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 114 MET Chi-restraints excluded: chain f residue 127 LEU Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 119 VAL Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 135 ILE Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 142 SER Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 87 GLN Chi-restraints excluded: chain h residue 100 GLU Chi-restraints excluded: chain j residue 22 CYS Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 66 LYS Chi-restraints excluded: chain m residue 105 VAL Chi-restraints excluded: chain n residue 22 LEU Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain o residue 48 ARG Chi-restraints excluded: chain o residue 57 CYS Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 18 ASN Chi-restraints excluded: chain p residue 81 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 315 optimal weight: 7.9990 chunk 843 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 549 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 937 optimal weight: 20.0000 chunk 778 optimal weight: 20.0000 chunk 434 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 310 optimal weight: 6.9990 chunk 492 optimal weight: 0.8980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS C 93 ASN C 243 HIS E 123 GLN F 56 GLN ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 ASN K 126 ASN L 77 ASN P 58 ASN S 113 GLN ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN V 34 GLN W 41 ASN c 109 GLN ** d 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 87 GLN j 76 ASN k 48 ASN m 109 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 135377 Z= 0.237 Angle : 0.809 26.417 199877 Z= 0.421 Chirality : 0.041 1.972 25096 Planarity : 0.008 0.131 12291 Dihedral : 23.984 179.943 62063 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.72 % Favored : 94.20 % Rotamer: Outliers : 4.50 % Allowed : 15.19 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.61 (0.10), residues: 6350 helix: -0.57 (0.11), residues: 2153 sheet: -1.27 (0.17), residues: 862 loop : -1.30 (0.10), residues: 3335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 122 HIS 0.012 0.001 HIS R 134 PHE 0.021 0.002 PHE i 63 TYR 0.028 0.002 TYR M 188 ARG 0.007 0.000 ARG S 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12700 Ramachandran restraints generated. 6350 Oldfield, 0 Emsley, 6350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12700 Ramachandran restraints generated. 6350 Oldfield, 0 Emsley, 6350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 766 time to evaluate : 6.514 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7780 (mm-30) REVERT: A 62 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7506 (mm-30) REVERT: A 80 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7674 (tt0) REVERT: A 106 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.6715 (mp10) REVERT: A 149 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7811 (tttt) REVERT: A 198 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8040 (mtpp) REVERT: A 245 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6920 (tmt170) REVERT: B 10 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7250 (ptp-170) REVERT: B 94 GLN cc_start: 0.8073 (mt0) cc_final: 0.7413 (mm-40) REVERT: B 149 THR cc_start: 0.7843 (t) cc_final: 0.7289 (m) REVERT: C 164 LYS cc_start: 0.8107 (pttt) cc_final: 0.7682 (ptmt) REVERT: C 217 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7033 (ptm160) REVERT: C 273 LYS cc_start: 0.7975 (mttt) cc_final: 0.7357 (mmtm) REVERT: D 93 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7348 (pp) REVERT: D 146 LYS cc_start: 0.7766 (mtpt) cc_final: 0.7345 (mtmm) REVERT: G 143 MET cc_start: 0.7352 (mmt) cc_final: 0.7120 (mmt) REVERT: H 117 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7839 (tp) REVERT: I 28 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7237 (tttm) REVERT: I 49 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8063 (mtpp) REVERT: I 54 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7698 (ptm160) REVERT: I 75 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8373 (ptt-90) REVERT: I 184 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7323 (ttt) REVERT: L 68 MET cc_start: 0.7994 (ptm) cc_final: 0.7641 (ptm) REVERT: M 19 MET cc_start: 0.8252 (mmm) cc_final: 0.7726 (mmp) REVERT: M 26 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6722 (mtt90) REVERT: M 77 LYS cc_start: 0.7984 (mtmt) cc_final: 0.7396 (mtmt) REVERT: M 189 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.6294 (tmt-80) REVERT: N 19 LYS cc_start: 0.6729 (OUTLIER) cc_final: 0.6114 (mtpp) REVERT: N 153 ARG cc_start: 0.6462 (tmm160) cc_final: 0.6126 (tmt170) REVERT: N 156 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7538 (ptpt) REVERT: O 89 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6969 (mm-30) REVERT: O 203 ASP cc_start: 0.6855 (m-30) cc_final: 0.6215 (m-30) REVERT: O 243 GLU cc_start: 0.7173 (tt0) cc_final: 0.6744 (pm20) REVERT: P 46 LYS cc_start: 0.7687 (mptp) cc_final: 0.6945 (mttt) REVERT: Q 5 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7263 (mtmt) REVERT: Q 133 ARG cc_start: 0.7793 (mtt90) cc_final: 0.7563 (mtp-110) REVERT: R 97 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7332 (ttm-80) REVERT: S 21 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8321 (mmtm) REVERT: S 35 LYS cc_start: 0.7547 (ttpt) cc_final: 0.7043 (ttmt) REVERT: S 144 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7496 (mt-10) REVERT: T 31 GLU cc_start: 0.7770 (mp0) cc_final: 0.7247 (mp0) REVERT: T 111 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7363 (mp10) REVERT: T 124 ARG cc_start: 0.7910 (mtt90) cc_final: 0.7632 (mtt90) REVERT: W 3 SER cc_start: 0.6844 (t) cc_final: 0.6277 (m) REVERT: W 113 LYS cc_start: 0.8132 (mtmt) cc_final: 0.7764 (mtmt) REVERT: X 53 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8113 (mt) REVERT: X 61 ARG cc_start: 0.7223 (mtm180) cc_final: 0.6767 (mtp85) REVERT: Z 54 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.6333 (mmpt) REVERT: Z 79 ARG cc_start: 0.7390 (mmt90) cc_final: 0.6441 (mmm-85) REVERT: Z 112 ARG cc_start: 0.7218 (ttt-90) cc_final: 0.6701 (ttp80) REVERT: Z 133 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.5481 (pp20) REVERT: c 66 ARG cc_start: 0.6386 (tpp-160) cc_final: 0.5434 (ttp-110) REVERT: c 76 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.5804 (mtp180) REVERT: c 224 MET cc_start: 0.6890 (mtm) cc_final: 0.6589 (mtm) REVERT: c 242 THR cc_start: 0.6590 (OUTLIER) cc_final: 0.6390 (t) REVERT: f 56 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.6781 (pmmt) REVERT: f 114 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.6665 (ttm) REVERT: f 117 ASP cc_start: 0.7459 (t70) cc_final: 0.7169 (t70) REVERT: g 143 GLN cc_start: 0.7512 (mm-40) cc_final: 0.7191 (mm-40) REVERT: h 30 LYS cc_start: 0.8090 (ptmt) cc_final: 0.7730 (ptpp) REVERT: h 102 ARG cc_start: 0.7736 (mtm-85) cc_final: 0.7496 (mtm-85) REVERT: m 108 THR cc_start: 0.8603 (m) cc_final: 0.8322 (p) REVERT: n 10 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.6452 (mtm) REVERT: o 25 ARG cc_start: 0.7148 (mtm-85) cc_final: 0.6809 (ttp-170) REVERT: o 48 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7098 (mmm-85) REVERT: o 84 ARG cc_start: 0.7854 (ttp-110) cc_final: 0.7633 (ttm110) outliers start: 213 outliers final: 129 residues processed: 909 average time/residue: 2.0305 time to fit residues: 2565.6718 Evaluate side-chains 904 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 745 time to evaluate : 6.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain I residue 49 LYS Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 184 MET Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 147 LYS Chi-restraints excluded: chain L residue 8 CYS Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 129 LEU Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain M residue 26 ARG Chi-restraints excluded: chain M residue 60 CYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain M residue 189 ARG Chi-restraints excluded: chain N residue 19 LYS Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 166 VAL Chi-restraints excluded: chain N residue 176 ILE Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 161 THR Chi-restraints excluded: chain O residue 205 ILE Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain Q residue 5 LYS Chi-restraints excluded: chain Q residue 40 SER Chi-restraints excluded: chain Q residue 91 SER Chi-restraints excluded: chain Q residue 137 ASN Chi-restraints excluded: chain Q residue 140 GLU Chi-restraints excluded: chain R residue 7 ARG Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 85 LEU Chi-restraints excluded: chain S residue 90 CYS Chi-restraints excluded: chain S residue 103 GLU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain T residue 2 THR Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 64 ASN Chi-restraints excluded: chain T residue 111 GLN Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain W residue 50 ASP Chi-restraints excluded: chain W residue 66 LYS Chi-restraints excluded: chain W residue 88 ASN Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Z residue 35 ASN Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 90 SER Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain a residue 3 HIS Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 92 THR Chi-restraints excluded: chain c residue 41 VAL Chi-restraints excluded: chain c residue 72 LEU Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 76 ARG Chi-restraints excluded: chain c residue 109 GLN Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 164 LEU Chi-restraints excluded: chain c residue 188 ILE Chi-restraints excluded: chain c residue 242 THR Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 85 ILE Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 130 ILE Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain e residue 144 VAL Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 177 THR Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain f residue 114 MET Chi-restraints excluded: chain f residue 127 LEU Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 119 VAL Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 135 ILE Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 142 SER Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain h residue 64 ASP Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 87 GLN Chi-restraints excluded: chain j residue 22 CYS Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain n residue 10 MET Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain o residue 48 ARG Chi-restraints excluded: chain o residue 57 CYS Chi-restraints excluded: chain o residue 78 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 903 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 534 optimal weight: 4.9990 chunk 684 optimal weight: 10.0000 chunk 530 optimal weight: 0.0970 chunk 789 optimal weight: 10.0000 chunk 523 optimal weight: 0.8980 chunk 933 optimal weight: 10.0000 chunk 584 optimal weight: 4.9990 chunk 569 optimal weight: 3.9990 chunk 431 optimal weight: 9.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS C 93 ASN C 158 GLN E 123 GLN F 56 GLN ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN H 74 GLN I 108 ASN K 126 ASN P 58 ASN S 113 GLN ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN V 34 GLN W 41 ASN ** d 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 87 GLN k 48 ASN m 109 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 135377 Z= 0.219 Angle : 0.790 26.444 199877 Z= 0.412 Chirality : 0.040 1.969 25096 Planarity : 0.008 0.128 12291 Dihedral : 23.891 179.930 62059 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer: Outliers : 4.41 % Allowed : 15.76 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.35 (0.10), residues: 6350 helix: -0.27 (0.11), residues: 2147 sheet: -1.16 (0.17), residues: 854 loop : -1.19 (0.10), residues: 3349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 59 HIS 0.013 0.001 HIS R 134 PHE 0.029 0.002 PHE U 97 TYR 0.027 0.002 TYR M 188 ARG 0.008 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12700 Ramachandran restraints generated. 6350 Oldfield, 0 Emsley, 6350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12700 Ramachandran restraints generated. 6350 Oldfield, 0 Emsley, 6350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 772 time to evaluate : 6.385 Fit side-chains REVERT: A 49 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7741 (mm-30) REVERT: A 76 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7390 (mtt) REVERT: A 106 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.6691 (mp10) REVERT: A 149 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7909 (ttpt) REVERT: A 198 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8025 (mtpp) REVERT: A 245 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.6979 (tmt170) REVERT: B 10 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7294 (ptp-170) REVERT: B 94 GLN cc_start: 0.8064 (mt0) cc_final: 0.7414 (mm-40) REVERT: B 149 THR cc_start: 0.7872 (t) cc_final: 0.7339 (m) REVERT: C 164 LYS cc_start: 0.8074 (pttt) cc_final: 0.7644 (ptmt) REVERT: C 217 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6960 (ptm160) REVERT: C 273 LYS cc_start: 0.7967 (mttt) cc_final: 0.7388 (mmtm) REVERT: D 93 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7169 (pp) REVERT: D 146 LYS cc_start: 0.7768 (mtpt) cc_final: 0.7344 (mtmm) REVERT: E 108 ASN cc_start: 0.7046 (OUTLIER) cc_final: 0.6831 (m110) REVERT: G 143 MET cc_start: 0.7343 (mmt) cc_final: 0.7111 (mmt) REVERT: H 117 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7844 (tp) REVERT: H 188 GLU cc_start: 0.6956 (tp30) cc_final: 0.6301 (mt-10) REVERT: I 28 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7244 (tttm) REVERT: I 49 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8142 (mtpp) REVERT: I 54 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7671 (ptm160) REVERT: I 75 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8329 (ptt-90) REVERT: I 184 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7348 (ttt) REVERT: L 68 MET cc_start: 0.8010 (ptm) cc_final: 0.7643 (ptm) REVERT: M 19 MET cc_start: 0.8242 (mmm) cc_final: 0.7714 (mmp) REVERT: M 77 LYS cc_start: 0.7917 (mtmt) cc_final: 0.7563 (mtmt) REVERT: M 189 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.6210 (tmt-80) REVERT: N 19 LYS cc_start: 0.6826 (OUTLIER) cc_final: 0.6172 (mtpp) REVERT: N 40 ARG cc_start: 0.6799 (mtp180) cc_final: 0.6513 (ttm-80) REVERT: N 153 ARG cc_start: 0.6342 (tmm160) cc_final: 0.6086 (tmt170) REVERT: N 156 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7497 (ptpt) REVERT: O 89 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6991 (mm-30) REVERT: O 203 ASP cc_start: 0.6791 (m-30) cc_final: 0.6258 (m-30) REVERT: O 243 GLU cc_start: 0.7125 (tt0) cc_final: 0.6701 (pm20) REVERT: P 46 LYS cc_start: 0.7668 (mptp) cc_final: 0.7027 (mttt) REVERT: Q 5 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7268 (mtmt) REVERT: R 138 HIS cc_start: 0.7613 (m90) cc_final: 0.7339 (m90) REVERT: S 21 LYS cc_start: 0.8631 (mmtt) cc_final: 0.8350 (mmtm) REVERT: S 35 LYS cc_start: 0.7515 (ttpt) cc_final: 0.7072 (ttmt) REVERT: S 74 VAL cc_start: 0.8624 (OUTLIER) cc_final: 0.8370 (t) REVERT: S 144 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7528 (mt-10) REVERT: T 31 GLU cc_start: 0.7601 (mp0) cc_final: 0.7151 (mp0) REVERT: T 124 ARG cc_start: 0.7906 (mtt90) cc_final: 0.7625 (mtt90) REVERT: T 151 SER cc_start: 0.7818 (OUTLIER) cc_final: 0.7616 (m) REVERT: V 102 MET cc_start: 0.7404 (tpp) cc_final: 0.7200 (tpt) REVERT: W 3 SER cc_start: 0.6671 (t) cc_final: 0.6122 (m) REVERT: W 113 LYS cc_start: 0.8106 (mtmt) cc_final: 0.7741 (mtmt) REVERT: X 53 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8100 (mt) REVERT: Z 79 ARG cc_start: 0.7366 (mmt90) cc_final: 0.6446 (mmm-85) REVERT: Z 100 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7241 (mmm-85) REVERT: Z 112 ARG cc_start: 0.7128 (ttt-90) cc_final: 0.6927 (ttp80) REVERT: Z 123 LYS cc_start: 0.7055 (tmtt) cc_final: 0.6753 (tttt) REVERT: Z 133 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.5489 (pp20) REVERT: a 6 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7097 (ptpt) REVERT: b 53 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7910 (mmtm) REVERT: c 66 ARG cc_start: 0.6398 (tpp-160) cc_final: 0.5523 (ttp-110) REVERT: c 76 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.5919 (mtp180) REVERT: c 108 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7651 (tttp) REVERT: c 224 MET cc_start: 0.6848 (mtm) cc_final: 0.6618 (mtm) REVERT: c 242 THR cc_start: 0.6528 (OUTLIER) cc_final: 0.6323 (t) REVERT: f 114 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.6629 (ttm) REVERT: f 117 ASP cc_start: 0.7354 (t70) cc_final: 0.7102 (t70) REVERT: g 38 THR cc_start: 0.8570 (m) cc_final: 0.8208 (p) REVERT: g 143 GLN cc_start: 0.7479 (mm-40) cc_final: 0.7168 (mm-40) REVERT: h 30 LYS cc_start: 0.8145 (ptmt) cc_final: 0.7790 (ptpp) REVERT: k 66 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8318 (mtpm) REVERT: m 108 THR cc_start: 0.8600 (m) cc_final: 0.8353 (p) REVERT: o 25 ARG cc_start: 0.7115 (mtm-85) cc_final: 0.6792 (ttp-170) REVERT: p 7 LYS cc_start: 0.7850 (mtpp) cc_final: 0.7611 (mtpp) REVERT: p 18 ASN cc_start: 0.7731 (OUTLIER) cc_final: 0.7267 (t0) outliers start: 208 outliers final: 132 residues processed: 913 average time/residue: 1.9821 time to fit residues: 2514.8245 Evaluate side-chains 919 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 754 time to evaluate : 6.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain I residue 49 LYS Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 184 MET Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 147 LYS Chi-restraints excluded: chain L residue 8 CYS Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 129 LEU Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain M residue 60 CYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain M residue 189 ARG Chi-restraints excluded: chain N residue 19 LYS Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 166 VAL Chi-restraints excluded: chain N residue 176 ILE Chi-restraints excluded: chain O residue 82 GLU Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 161 THR Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain Q residue 5 LYS Chi-restraints excluded: chain Q residue 40 SER Chi-restraints excluded: chain Q residue 91 SER Chi-restraints excluded: chain Q residue 137 ASN Chi-restraints excluded: chain Q residue 140 GLU Chi-restraints excluded: chain R residue 7 ARG Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 92 MET Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 90 CYS Chi-restraints excluded: chain S residue 103 GLU Chi-restraints excluded: chain S residue 128 LEU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 64 ASN Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain W residue 50 ASP Chi-restraints excluded: chain W residue 66 LYS Chi-restraints excluded: chain W residue 88 ASN Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Z residue 35 ASN Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 90 SER Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 100 ARG Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain a residue 3 HIS Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain b residue 53 LYS Chi-restraints excluded: chain c residue 41 VAL Chi-restraints excluded: chain c residue 72 LEU Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 76 ARG Chi-restraints excluded: chain c residue 108 LYS Chi-restraints excluded: chain c residue 129 MET Chi-restraints excluded: chain c residue 164 LEU Chi-restraints excluded: chain c residue 188 ILE Chi-restraints excluded: chain c residue 242 THR Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 85 ILE Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 130 ILE Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain e residue 144 VAL Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 177 THR Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 15 THR Chi-restraints excluded: chain f residue 114 MET Chi-restraints excluded: chain f residue 127 LEU Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 119 VAL Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 135 ILE Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 142 SER Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain h residue 64 ASP Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 114 MET Chi-restraints excluded: chain j residue 22 CYS Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain k residue 66 LYS Chi-restraints excluded: chain m residue 105 VAL Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain o residue 57 CYS Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 18 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 577 optimal weight: 8.9990 chunk 372 optimal weight: 9.9990 chunk 557 optimal weight: 1.9990 chunk 281 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 593 optimal weight: 3.9990 chunk 636 optimal weight: 10.0000 chunk 461 optimal weight: 0.0270 chunk 87 optimal weight: 9.9990 chunk 734 optimal weight: 10.0000 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS C 93 ASN C 158 GLN E 123 GLN F 56 GLN ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN H 74 GLN I 108 ASN K 126 ASN L 77 ASN P 58 ASN Q 137 ASN S 113 GLN ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN V 34 GLN W 41 ASN Z 14 GLN Z 29 ASN ** Z 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 48 ASN m 109 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 135377 Z= 0.216 Angle : 0.780 26.552 199877 Z= 0.406 Chirality : 0.040 1.965 25096 Planarity : 0.007 0.128 12291 Dihedral : 23.801 179.794 62059 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.51 % Favored : 94.43 % Rotamer: Outliers : 4.23 % Allowed : 16.36 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.16 (0.10), residues: 6350 helix: -0.04 (0.11), residues: 2145 sheet: -1.13 (0.17), residues: 873 loop : -1.11 (0.10), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 59 HIS 0.014 0.001 HIS R 134 PHE 0.024 0.001 PHE a 73 TYR 0.026 0.002 TYR M 188 ARG 0.009 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12700 Ramachandran restraints generated. 6350 Oldfield, 0 Emsley, 6350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12700 Ramachandran restraints generated. 6350 Oldfield, 0 Emsley, 6350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 764 time to evaluate : 6.442 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7788 (mm-30) REVERT: A 76 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7379 (mtt) REVERT: A 80 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7654 (tt0) REVERT: A 106 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.6688 (mp10) REVERT: A 245 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7081 (tmt-80) REVERT: B 10 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7287 (ptp-170) REVERT: B 94 GLN cc_start: 0.8061 (mt0) cc_final: 0.7409 (mm-40) REVERT: B 149 THR cc_start: 0.7971 (t) cc_final: 0.7447 (m) REVERT: B 304 THR cc_start: 0.7940 (OUTLIER) cc_final: 0.7732 (t) REVERT: B 343 MET cc_start: 0.7307 (mmt) cc_final: 0.7003 (mmt) REVERT: C 164 LYS cc_start: 0.8055 (pttt) cc_final: 0.7635 (ptmt) REVERT: C 217 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6973 (ptm160) REVERT: C 273 LYS cc_start: 0.7966 (mttt) cc_final: 0.7389 (mmtm) REVERT: D 93 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7233 (pp) REVERT: D 146 LYS cc_start: 0.7808 (mtpt) cc_final: 0.7505 (mtmm) REVERT: E 108 ASN cc_start: 0.7028 (OUTLIER) cc_final: 0.6798 (m110) REVERT: G 143 MET cc_start: 0.7365 (mmt) cc_final: 0.7140 (mmt) REVERT: H 117 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7813 (tp) REVERT: H 176 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7012 (mm-30) REVERT: H 188 GLU cc_start: 0.6803 (tp30) cc_final: 0.6194 (mt-10) REVERT: I 28 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7249 (tttm) REVERT: I 49 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8147 (mtpp) REVERT: I 54 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7792 (ptm160) REVERT: I 75 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8334 (ptt-90) REVERT: I 86 LYS cc_start: 0.7948 (ttpt) cc_final: 0.7426 (ttpp) REVERT: I 184 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7306 (ttt) REVERT: J 59 MET cc_start: 0.8591 (ttp) cc_final: 0.8309 (ttm) REVERT: L 68 MET cc_start: 0.8040 (ptm) cc_final: 0.7705 (ptm) REVERT: M 19 MET cc_start: 0.8249 (mmm) cc_final: 0.7710 (mmp) REVERT: M 77 LYS cc_start: 0.7922 (mtmt) cc_final: 0.7562 (mtmt) REVERT: M 189 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.6236 (tmt-80) REVERT: N 40 ARG cc_start: 0.6798 (mtp180) cc_final: 0.6512 (ttm-80) REVERT: N 153 ARG cc_start: 0.6339 (tmm160) cc_final: 0.6101 (tmt170) REVERT: N 156 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7518 (ptpt) REVERT: N 178 ARG cc_start: 0.6255 (mtp180) cc_final: 0.5920 (mmm-85) REVERT: O 89 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6944 (mm-30) REVERT: O 203 ASP cc_start: 0.6821 (m-30) cc_final: 0.6281 (m-30) REVERT: O 243 GLU cc_start: 0.7157 (tt0) cc_final: 0.6726 (pm20) REVERT: P 46 LYS cc_start: 0.7610 (mptp) cc_final: 0.6957 (mttt) REVERT: S 21 LYS cc_start: 0.8669 (mmtt) cc_final: 0.8390 (mmtm) REVERT: S 35 LYS cc_start: 0.7514 (ttpt) cc_final: 0.7068 (ttmt) REVERT: S 74 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8372 (t) REVERT: S 144 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7504 (mt-10) REVERT: T 31 GLU cc_start: 0.7582 (mp0) cc_final: 0.7198 (mp0) REVERT: T 111 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: T 124 ARG cc_start: 0.7910 (mtt90) cc_final: 0.7628 (mtt90) REVERT: U 72 MET cc_start: 0.4879 (tpt) cc_final: 0.1760 (mtm) REVERT: U 100 LYS cc_start: 0.7223 (tptt) cc_final: 0.6889 (tttp) REVERT: V 102 MET cc_start: 0.7418 (tpp) cc_final: 0.7189 (tpt) REVERT: W 3 SER cc_start: 0.6657 (t) cc_final: 0.6108 (m) REVERT: W 113 LYS cc_start: 0.8139 (mtmt) cc_final: 0.7769 (mtmt) REVERT: X 53 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8074 (mt) REVERT: X 61 ARG cc_start: 0.7215 (mtm180) cc_final: 0.6752 (mtp85) REVERT: Z 79 ARG cc_start: 0.7322 (mmt90) cc_final: 0.6440 (mmm-85) REVERT: Z 100 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7352 (mmm-85) REVERT: Z 123 LYS cc_start: 0.7159 (tmtt) cc_final: 0.6811 (tttt) REVERT: Z 133 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.5486 (pp20) REVERT: b 53 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7933 (mmtm) REVERT: c 66 ARG cc_start: 0.6344 (tpp-160) cc_final: 0.5497 (ttp-110) REVERT: c 76 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.5931 (mtp180) REVERT: c 108 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7646 (ttpm) REVERT: c 224 MET cc_start: 0.6802 (mtm) cc_final: 0.6519 (mtm) REVERT: e 162 TYR cc_start: 0.8530 (p90) cc_final: 0.7783 (p90) REVERT: f 56 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.6847 (pmmt) REVERT: f 114 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.6611 (ttm) REVERT: g 38 THR cc_start: 0.8545 (m) cc_final: 0.8180 (p) REVERT: g 143 GLN cc_start: 0.7424 (mm-40) cc_final: 0.7126 (mm-40) REVERT: h 30 LYS cc_start: 0.8139 (ptmt) cc_final: 0.7787 (ptpp) REVERT: k 65 LYS cc_start: 0.8032 (ttmt) cc_final: 0.7225 (tttt) REVERT: k 66 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8310 (mtpm) REVERT: m 108 THR cc_start: 0.8605 (m) cc_final: 0.8377 (p) REVERT: o 25 ARG cc_start: 0.7096 (mtm-85) cc_final: 0.6787 (ttp-170) REVERT: p 18 ASN cc_start: 0.7775 (OUTLIER) cc_final: 0.7511 (t0) outliers start: 199 outliers final: 130 residues processed: 900 average time/residue: 1.9739 time to fit residues: 2468.1916 Evaluate side-chains 909 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 750 time to evaluate : 5.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain I residue 49 LYS Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 184 MET Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain L residue 8 CYS Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 129 LEU Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain M residue 60 CYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain M residue 189 ARG Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 166 VAL Chi-restraints excluded: chain N residue 176 ILE Chi-restraints excluded: chain O residue 82 GLU Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 161 THR Chi-restraints excluded: chain O residue 205 ILE Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain Q residue 40 SER Chi-restraints excluded: chain Q residue 91 SER Chi-restraints excluded: chain R residue 7 ARG Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 92 MET Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 90 CYS Chi-restraints excluded: chain S residue 103 GLU Chi-restraints excluded: chain S residue 128 LEU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain T residue 2 THR Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 64 ASN Chi-restraints excluded: chain T residue 111 GLN Chi-restraints excluded: chain W residue 50 ASP Chi-restraints excluded: chain W residue 66 LYS Chi-restraints excluded: chain W residue 77 ILE Chi-restraints excluded: chain W residue 88 ASN Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Z residue 35 ASN Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 90 SER Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 100 ARG Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain a residue 3 HIS Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 53 LYS Chi-restraints excluded: chain c residue 41 VAL Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 76 ARG Chi-restraints excluded: chain c residue 108 LYS Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 164 LEU Chi-restraints excluded: chain c residue 188 ILE Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 85 ILE Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 97 SER Chi-restraints excluded: chain e residue 130 ILE Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain e residue 144 VAL Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 177 THR Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 15 THR Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain f residue 114 MET Chi-restraints excluded: chain f residue 127 LEU Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 119 VAL Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 135 ILE Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 142 SER Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain h residue 64 ASP Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain j residue 22 CYS Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain k residue 66 LYS Chi-restraints excluded: chain m residue 105 VAL Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain o residue 57 CYS Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 18 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 849 optimal weight: 10.0000 chunk 894 optimal weight: 10.0000 chunk 816 optimal weight: 9.9990 chunk 870 optimal weight: 20.0000 chunk 523 optimal weight: 0.9980 chunk 379 optimal weight: 0.9980 chunk 683 optimal weight: 20.0000 chunk 267 optimal weight: 6.9990 chunk 786 optimal weight: 10.0000 chunk 823 optimal weight: 9.9990 chunk 867 optimal weight: 9.9990 overall best weight: 5.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN B 108 HIS ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS C 93 ASN C 158 GLN E 123 GLN ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS G 222 GLN H 74 GLN I 108 ASN J 106 ASN K 126 ASN L 77 ASN P 58 ASN ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN V 34 GLN W 41 ASN W 88 ASN Y 21 HIS Z 14 GLN Z 29 ASN ** Z 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 106 ASN ** d 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 87 GLN k 48 ASN m 109 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 135377 Z= 0.389 Angle : 0.878 26.047 199877 Z= 0.450 Chirality : 0.046 1.975 25096 Planarity : 0.008 0.138 12291 Dihedral : 23.899 179.780 62059 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.42 % Favored : 93.50 % Rotamer: Outliers : 4.23 % Allowed : 16.54 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.35 (0.10), residues: 6350 helix: -0.26 (0.11), residues: 2143 sheet: -1.16 (0.17), residues: 845 loop : -1.20 (0.10), residues: 3362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP U 106 HIS 0.015 0.002 HIS R 134 PHE 0.037 0.002 PHE i 63 TYR 0.032 0.002 TYR M 188 ARG 0.011 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12700 Ramachandran restraints generated. 6350 Oldfield, 0 Emsley, 6350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12700 Ramachandran restraints generated. 6350 Oldfield, 0 Emsley, 6350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 754 time to evaluate : 6.587 Fit side-chains REVERT: A 49 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7851 (mm-30) REVERT: A 76 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7370 (mtt) REVERT: A 106 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.6851 (mp10) REVERT: A 245 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6907 (tmt170) REVERT: B 10 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7118 (ptp-170) REVERT: B 94 GLN cc_start: 0.8081 (mt0) cc_final: 0.7430 (mm-40) REVERT: B 132 ARG cc_start: 0.7193 (mtm180) cc_final: 0.6992 (mmm160) REVERT: B 149 THR cc_start: 0.7886 (t) cc_final: 0.7353 (m) REVERT: C 164 LYS cc_start: 0.8127 (pttt) cc_final: 0.7676 (ptmt) REVERT: C 217 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7030 (ptm160) REVERT: C 273 LYS cc_start: 0.7968 (mttt) cc_final: 0.7331 (mmtm) REVERT: D 93 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7280 (pp) REVERT: D 146 LYS cc_start: 0.7932 (mtpt) cc_final: 0.7512 (mtmm) REVERT: E 108 ASN cc_start: 0.7045 (OUTLIER) cc_final: 0.6809 (m110) REVERT: G 143 MET cc_start: 0.7452 (mmt) cc_final: 0.7213 (mmt) REVERT: H 117 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7592 (tm) REVERT: H 176 GLU cc_start: 0.7722 (mm-30) cc_final: 0.6944 (mm-30) REVERT: H 188 GLU cc_start: 0.6923 (tp30) cc_final: 0.6294 (mt-10) REVERT: I 28 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7240 (tttm) REVERT: I 49 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8082 (mtpp) REVERT: I 54 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7673 (ptm160) REVERT: I 75 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8451 (ptt-90) REVERT: I 184 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7316 (ttt) REVERT: L 68 MET cc_start: 0.8059 (ptm) cc_final: 0.7696 (ptm) REVERT: M 77 LYS cc_start: 0.7972 (mtmt) cc_final: 0.7410 (mtmt) REVERT: M 189 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.6386 (tmt-80) REVERT: N 19 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6329 (mtpp) REVERT: N 153 ARG cc_start: 0.6467 (tmm160) cc_final: 0.6075 (tmt170) REVERT: N 156 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7598 (ptpt) REVERT: O 89 GLU cc_start: 0.7300 (mm-30) cc_final: 0.7051 (mm-30) REVERT: O 203 ASP cc_start: 0.6926 (m-30) cc_final: 0.6332 (m-30) REVERT: O 243 GLU cc_start: 0.7224 (tt0) cc_final: 0.6778 (pm20) REVERT: P 46 LYS cc_start: 0.7687 (mptp) cc_final: 0.7024 (mtmt) REVERT: Q 19 ARG cc_start: 0.8493 (tpm-80) cc_final: 0.8237 (tpm-80) REVERT: S 18 LYS cc_start: 0.8090 (mmtt) cc_final: 0.7875 (mmtm) REVERT: S 21 LYS cc_start: 0.8641 (mmtt) cc_final: 0.8357 (mmtm) REVERT: S 35 LYS cc_start: 0.7550 (ttpt) cc_final: 0.6996 (ttmt) REVERT: S 134 MET cc_start: 0.5825 (mpm) cc_final: 0.5404 (mmm) REVERT: S 144 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7371 (mt-10) REVERT: T 31 GLU cc_start: 0.7630 (mp0) cc_final: 0.7158 (mp0) REVERT: T 124 ARG cc_start: 0.7968 (mtt90) cc_final: 0.7678 (mtt90) REVERT: V 102 MET cc_start: 0.7446 (tpp) cc_final: 0.7216 (tpt) REVERT: W 3 SER cc_start: 0.6884 (t) cc_final: 0.6300 (m) REVERT: W 113 LYS cc_start: 0.8054 (mtmt) cc_final: 0.7782 (mtmt) REVERT: X 53 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8167 (mt) REVERT: X 61 ARG cc_start: 0.7229 (mtm180) cc_final: 0.6760 (mtp85) REVERT: Z 54 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6363 (mmpt) REVERT: Z 100 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7398 (mmm-85) REVERT: Z 123 LYS cc_start: 0.7162 (tmtt) cc_final: 0.6842 (tttt) REVERT: Z 133 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.5430 (pp20) REVERT: a 6 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7173 (ptpt) REVERT: c 66 ARG cc_start: 0.6362 (tpp-160) cc_final: 0.5475 (ttp-110) REVERT: c 76 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.5909 (mtp180) REVERT: f 56 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.6959 (pmmt) REVERT: f 114 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.6691 (ttm) REVERT: g 143 GLN cc_start: 0.7501 (mm-40) cc_final: 0.7127 (mm-40) REVERT: h 30 LYS cc_start: 0.8087 (ptmt) cc_final: 0.7720 (ptpp) REVERT: h 100 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7237 (mm-30) REVERT: h 102 ARG cc_start: 0.7720 (mtm-85) cc_final: 0.7360 (mtm-85) REVERT: k 66 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8366 (mtpm) REVERT: m 108 THR cc_start: 0.8629 (m) cc_final: 0.8364 (p) REVERT: o 25 ARG cc_start: 0.7111 (mtm-85) cc_final: 0.6789 (ttp-170) REVERT: o 48 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7083 (mmm-85) REVERT: o 79 VAL cc_start: 0.7777 (t) cc_final: 0.7454 (t) REVERT: o 84 ARG cc_start: 0.7859 (ttp-110) cc_final: 0.7640 (ttm110) REVERT: p 18 ASN cc_start: 0.7828 (OUTLIER) cc_final: 0.7347 (t0) outliers start: 200 outliers final: 139 residues processed: 893 average time/residue: 2.0335 time to fit residues: 2529.2183 Evaluate side-chains 913 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 745 time to evaluate : 6.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain I residue 49 LYS Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 146 GLU Chi-restraints excluded: chain I residue 184 MET Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 8 CYS Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 129 LEU Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain M residue 60 CYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain M residue 189 ARG Chi-restraints excluded: chain N residue 19 LYS Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 166 VAL Chi-restraints excluded: chain N residue 176 ILE Chi-restraints excluded: chain O residue 82 GLU Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 161 THR Chi-restraints excluded: chain O residue 205 ILE Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain Q residue 40 SER Chi-restraints excluded: chain Q residue 91 SER Chi-restraints excluded: chain R residue 7 ARG Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 92 MET Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 76 ILE Chi-restraints excluded: chain S residue 85 LEU Chi-restraints excluded: chain S residue 90 CYS Chi-restraints excluded: chain S residue 103 GLU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain T residue 2 THR Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 64 ASN Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain W residue 50 ASP Chi-restraints excluded: chain W residue 66 LYS Chi-restraints excluded: chain W residue 77 ILE Chi-restraints excluded: chain W residue 88 ASN Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Z residue 29 ASN Chi-restraints excluded: chain Z residue 35 ASN Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 90 SER Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 100 ARG Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain a residue 3 HIS Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain b residue 53 LYS Chi-restraints excluded: chain c residue 41 VAL Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 76 ARG Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 164 LEU Chi-restraints excluded: chain c residue 188 ILE Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 85 ILE Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 97 SER Chi-restraints excluded: chain e residue 130 ILE Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain e residue 144 VAL Chi-restraints excluded: chain e residue 166 SER Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 177 THR Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 15 THR Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain f residue 114 MET Chi-restraints excluded: chain f residue 127 LEU Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 119 VAL Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 142 SER Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain h residue 45 THR Chi-restraints excluded: chain h residue 64 ASP Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 87 GLN Chi-restraints excluded: chain h residue 100 GLU Chi-restraints excluded: chain j residue 22 CYS Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 66 LYS Chi-restraints excluded: chain m residue 105 VAL Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain o residue 48 ARG Chi-restraints excluded: chain o residue 57 CYS Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 18 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 571 optimal weight: 0.9980 chunk 920 optimal weight: 10.0000 chunk 561 optimal weight: 0.0010 chunk 436 optimal weight: 5.9990 chunk 639 optimal weight: 10.0000 chunk 965 optimal weight: 10.0000 chunk 888 optimal weight: 30.0000 chunk 768 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 593 optimal weight: 4.9990 chunk 471 optimal weight: 7.9990 overall best weight: 2.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS C 93 ASN C 158 GLN E 123 GLN F 56 GLN ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN H 74 GLN I 108 ASN K 126 ASN P 58 ASN ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN V 34 GLN W 41 ASN Z 14 GLN ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 177 GLN ** d 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 39 HIS k 48 ASN m 109 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.163 135377 Z= 0.290 Angle : 0.896 59.194 199877 Z= 0.470 Chirality : 0.043 1.983 25096 Planarity : 0.009 0.148 12291 Dihedral : 23.900 179.736 62059 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.37 % Favored : 93.57 % Rotamer: Outliers : 3.94 % Allowed : 17.12 % Favored : 78.94 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.10), residues: 6350 helix: -0.25 (0.11), residues: 2143 sheet: -1.17 (0.17), residues: 845 loop : -1.20 (0.10), residues: 3362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP U 106 HIS 0.013 0.002 HIS R 134 PHE 0.033 0.002 PHE i 63 TYR 0.029 0.002 TYR M 188 ARG 0.009 0.001 ARG B 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12700 Ramachandran restraints generated. 6350 Oldfield, 0 Emsley, 6350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12700 Ramachandran restraints generated. 6350 Oldfield, 0 Emsley, 6350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 744 time to evaluate : 6.435 Fit side-chains REVERT: A 49 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7845 (mm-30) REVERT: A 76 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7351 (mtt) REVERT: A 106 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.6847 (mp10) REVERT: A 245 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6902 (tmt170) REVERT: B 10 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7109 (ptp-170) REVERT: B 94 GLN cc_start: 0.8085 (mt0) cc_final: 0.7429 (mm-40) REVERT: B 132 ARG cc_start: 0.7213 (mtm180) cc_final: 0.7007 (mmm160) REVERT: B 149 THR cc_start: 0.7878 (t) cc_final: 0.7343 (m) REVERT: C 164 LYS cc_start: 0.8124 (pttt) cc_final: 0.7672 (ptmt) REVERT: C 217 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.7017 (ptm160) REVERT: C 273 LYS cc_start: 0.7962 (mttt) cc_final: 0.7326 (mmtm) REVERT: D 93 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7275 (pp) REVERT: D 146 LYS cc_start: 0.7926 (mtpt) cc_final: 0.7275 (mtmt) REVERT: E 108 ASN cc_start: 0.7040 (OUTLIER) cc_final: 0.6804 (m110) REVERT: G 143 MET cc_start: 0.7437 (mmt) cc_final: 0.7197 (mmt) REVERT: H 117 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7845 (tp) REVERT: H 176 GLU cc_start: 0.7716 (mm-30) cc_final: 0.6940 (mm-30) REVERT: H 188 GLU cc_start: 0.6904 (tp30) cc_final: 0.6283 (mt-10) REVERT: I 28 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7229 (tttm) REVERT: I 49 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8077 (mtpp) REVERT: I 54 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7670 (ptm160) REVERT: I 75 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8440 (ptt-90) REVERT: I 184 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7312 (ttt) REVERT: L 68 MET cc_start: 0.8052 (ptm) cc_final: 0.7689 (ptm) REVERT: M 77 LYS cc_start: 0.7965 (mtmt) cc_final: 0.7403 (mtmt) REVERT: M 189 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.6377 (tmt-80) REVERT: N 19 LYS cc_start: 0.6846 (OUTLIER) cc_final: 0.6284 (mtpp) REVERT: N 153 ARG cc_start: 0.6458 (tmm160) cc_final: 0.6066 (tmt170) REVERT: N 156 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7596 (ptpt) REVERT: O 89 GLU cc_start: 0.7300 (mm-30) cc_final: 0.7053 (mm-30) REVERT: O 203 ASP cc_start: 0.6904 (m-30) cc_final: 0.6319 (m-30) REVERT: O 243 GLU cc_start: 0.7218 (tt0) cc_final: 0.6774 (pm20) REVERT: P 46 LYS cc_start: 0.7684 (mptp) cc_final: 0.7020 (mtmt) REVERT: S 18 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7870 (mmtm) REVERT: S 21 LYS cc_start: 0.8635 (mmtt) cc_final: 0.8351 (mmtm) REVERT: S 35 LYS cc_start: 0.7542 (ttpt) cc_final: 0.6991 (ttmt) REVERT: S 144 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7369 (mt-10) REVERT: T 31 GLU cc_start: 0.7692 (mp0) cc_final: 0.7164 (mp0) REVERT: T 124 ARG cc_start: 0.7980 (mtt90) cc_final: 0.7684 (mtt90) REVERT: V 102 MET cc_start: 0.7469 (tpp) cc_final: 0.7243 (tpt) REVERT: W 3 SER cc_start: 0.6876 (t) cc_final: 0.6293 (m) REVERT: W 113 LYS cc_start: 0.8051 (mtmt) cc_final: 0.7776 (mtmt) REVERT: X 53 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8162 (mt) REVERT: X 61 ARG cc_start: 0.7232 (mtm180) cc_final: 0.6760 (mtp85) REVERT: Z 54 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.6357 (mmpt) REVERT: Z 100 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7395 (mmm-85) REVERT: Z 123 LYS cc_start: 0.7151 (tmtt) cc_final: 0.6834 (tttt) REVERT: Z 133 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.5429 (pp20) REVERT: a 6 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7167 (ptpt) REVERT: c 66 ARG cc_start: 0.6360 (tpp-160) cc_final: 0.5470 (ttp-110) REVERT: c 76 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.5901 (mtp180) REVERT: c 224 MET cc_start: 0.6878 (mtm) cc_final: 0.6646 (mtm) REVERT: f 56 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.6947 (pmmt) REVERT: f 114 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.6614 (ttm) REVERT: g 143 GLN cc_start: 0.7493 (mm-40) cc_final: 0.7122 (mm-40) REVERT: h 30 LYS cc_start: 0.8077 (ptmt) cc_final: 0.7710 (ptpp) REVERT: h 100 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7221 (mm-30) REVERT: k 66 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8363 (mtpm) REVERT: m 108 THR cc_start: 0.8620 (m) cc_final: 0.8360 (p) REVERT: o 25 ARG cc_start: 0.7101 (mtm-85) cc_final: 0.6783 (ttp-170) REVERT: o 48 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7069 (mmm-85) REVERT: o 79 VAL cc_start: 0.7753 (t) cc_final: 0.7438 (t) REVERT: o 84 ARG cc_start: 0.7852 (ttp-110) cc_final: 0.7635 (ttm110) REVERT: p 18 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7340 (t0) outliers start: 185 outliers final: 139 residues processed: 870 average time/residue: 2.0347 time to fit residues: 2466.8920 Evaluate side-chains 905 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 737 time to evaluate : 6.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain I residue 49 LYS Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 184 MET Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 8 CYS Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 129 LEU Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain M residue 60 CYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain M residue 189 ARG Chi-restraints excluded: chain N residue 19 LYS Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 166 VAL Chi-restraints excluded: chain N residue 176 ILE Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 161 THR Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain Q residue 40 SER Chi-restraints excluded: chain Q residue 91 SER Chi-restraints excluded: chain Q residue 137 ASN Chi-restraints excluded: chain R residue 7 ARG Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 92 MET Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 76 ILE Chi-restraints excluded: chain S residue 85 LEU Chi-restraints excluded: chain S residue 90 CYS Chi-restraints excluded: chain S residue 103 GLU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain T residue 2 THR Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 64 ASN Chi-restraints excluded: chain T residue 69 ARG Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain W residue 50 ASP Chi-restraints excluded: chain W residue 66 LYS Chi-restraints excluded: chain W residue 77 ILE Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Z residue 35 ASN Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 90 SER Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 100 ARG Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain a residue 3 HIS Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain b residue 53 LYS Chi-restraints excluded: chain c residue 41 VAL Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 76 ARG Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 129 MET Chi-restraints excluded: chain c residue 164 LEU Chi-restraints excluded: chain c residue 188 ILE Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 85 ILE Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 97 SER Chi-restraints excluded: chain e residue 130 ILE Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain e residue 144 VAL Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 177 THR Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 15 THR Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain f residue 114 MET Chi-restraints excluded: chain f residue 127 LEU Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 119 VAL Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 142 SER Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain h residue 64 ASP Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 100 GLU Chi-restraints excluded: chain j residue 22 CYS Chi-restraints excluded: chain j residue 31 TRP Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 66 LYS Chi-restraints excluded: chain m residue 105 VAL Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain o residue 48 ARG Chi-restraints excluded: chain o residue 57 CYS Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 18 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 610 optimal weight: 2.9990 chunk 818 optimal weight: 10.0000 chunk 235 optimal weight: 5.9990 chunk 708 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 213 optimal weight: 9.9990 chunk 769 optimal weight: 10.0000 chunk 322 optimal weight: 5.9990 chunk 790 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 141 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS C 93 ASN C 158 GLN E 123 GLN ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN H 74 GLN I 108 ASN K 126 ASN P 58 ASN ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN V 34 GLN W 41 ASN Z 14 GLN ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 87 GLN k 48 ASN m 109 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.158471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.132262 restraints weight = 271423.159| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.19 r_work: 0.3500 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.163 135377 Z= 0.290 Angle : 0.896 59.194 199877 Z= 0.470 Chirality : 0.043 1.983 25096 Planarity : 0.009 0.148 12291 Dihedral : 23.900 179.736 62059 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.37 % Favored : 93.57 % Rotamer: Outliers : 3.72 % Allowed : 17.28 % Favored : 79.00 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.10), residues: 6350 helix: -0.25 (0.11), residues: 2143 sheet: -1.17 (0.17), residues: 845 loop : -1.20 (0.10), residues: 3362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP U 106 HIS 0.013 0.002 HIS R 134 PHE 0.033 0.002 PHE i 63 TYR 0.029 0.002 TYR M 188 ARG 0.009 0.001 ARG B 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38921.73 seconds wall clock time: 676 minutes 27.41 seconds (40587.41 seconds total)