Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 17:31:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az3_7025/04_2023/6az3_7025_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az3_7025/04_2023/6az3_7025.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az3_7025/04_2023/6az3_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_7025/04_2023/6az3_7025_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az3_7025/04_2023/6az3_7025_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az3_7025/04_2023/6az3_7025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az3_7025/04_2023/6az3_7025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az3_7025/04_2023/6az3_7025_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az3_7025/04_2023/6az3_7025_neut_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 119 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: 77 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: 6 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: 10 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: 24 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: 7 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: 54.06, 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: 49.37 Conformation dependent library (CDL) restraints added in 8.9 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 forstructures with more than 99999 atoms! 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: 52.53 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: 130.16 Time building geometry restraints manager: 53.51 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: 70122 35.94 - 71.89: 2944 71.89 - 107.83: 219 107.83 - 143.77: 26 143.77 - 179.72: 74 Dihedral angle restraints: 73385 sinusoidal: 54759 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 73382 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: 3.090 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 20.680 Check model and map are aligned: 1.450 Set scattering table: 0.860 Process input model: 381.450 Find NCS groups from input model: 2.840 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 422.450 ------------------------------------------------------------------------------- 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 : 16.536 179.716 61327 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 % 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 *********************** 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 : 6.560 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 19 residues processed: 1053 average time/residue: 2.3081 time to fit residues: 3287.2453 Evaluate side-chains 802 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 783 time to evaluate : 6.614 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 16 residues processed: 4 average time/residue: 1.6850 time to fit residues: 17.2420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 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: 10.0000 chunk 565 optimal weight: 2.9990 chunk 879 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 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 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 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 W 16 HIS W 18 GLN W 41 ASN W 97 HIS 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 177 GLN 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: 117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 135377 Z= 0.167 Angle : 0.834 27.140 199877 Z= 0.433 Chirality : 0.041 1.961 25096 Planarity : 0.008 0.132 12291 Dihedral : 17.166 179.835 48976 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.21 % Favored : 94.71 % Rotamer Outliers : 2.48 % 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: -2.52 (0.09), residues: 2115 sheet: -1.77 (0.16), residues: 836 loop : -1.79 (0.10), residues: 3399 *********************** 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 999 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 888 time to evaluate : 6.637 Fit side-chains revert: symmetry clash outliers start: 111 outliers final: 40 residues processed: 952 average time/residue: 2.1016 time to fit residues: 2775.9751 Evaluate side-chains 815 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 775 time to evaluate : 6.322 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 24 residues processed: 16 average time/residue: 1.3261 time to fit residues: 41.3331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 489 optimal weight: 8.9990 chunk 273 optimal weight: 7.9990 chunk 732 optimal weight: 10.0000 chunk 599 optimal weight: 20.0000 chunk 242 optimal weight: 10.0000 chunk 881 optimal weight: 10.0000 chunk 952 optimal weight: 10.0000 chunk 785 optimal weight: 10.0000 chunk 874 optimal weight: 10.0000 chunk 300 optimal weight: 20.0000 chunk 707 optimal weight: 10.0000 overall best weight: 9.3996 ------------------------------------------------------------------------------- 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 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 HIS B 284 ASN B 378 GLN C 93 ASN D 111 HIS E 123 GLN E 185 ASN F 56 GLN ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 335 HIS ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 GLN I 64 ASN K 126 ASN M 122 ASN M 171 HIS P 158 HIS P 168 HIS Q 75 HIS ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 134 HIS T 28 ASN T 50 GLN T 97 ASN T 121 GLN T 145 HIS ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 34 GLN ** V 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 123 ASN ** 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 l 18 ASN m 109 ASN o 21 ASN o 33 GLN o 37 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.111 135377 Z= 0.601 Angle : 1.047 25.687 199877 Z= 0.525 Chirality : 0.056 2.001 25096 Planarity : 0.010 0.151 12291 Dihedral : 17.442 179.967 48976 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.83 % Favored : 93.04 % Rotamer Outliers : 4.58 % 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: -2.63 (0.09), residues: 6350 helix: -1.83 (0.10), residues: 2120 sheet: -1.62 (0.16), residues: 846 loop : -1.67 (0.10), residues: 3384 *********************** 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 988 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 769 time to evaluate : 6.723 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 219 outliers final: 117 residues processed: 910 average time/residue: 2.1935 time to fit residues: 2811.0434 Evaluate side-chains 863 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 746 time to evaluate : 6.645 Switching outliers to nearest non-outliers outliers start: 117 outliers final: 82 residues processed: 37 average time/residue: 1.2554 time to fit residues: 84.4792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 457 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 420 optimal weight: 5.9990 chunk 591 optimal weight: 0.9980 chunk 884 optimal weight: 2.9990 chunk 936 optimal weight: 10.0000 chunk 462 optimal weight: 8.9990 chunk 838 optimal weight: 10.0000 chunk 252 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** C 93 ASN C 118 GLN E 123 GLN E 185 ASN F 56 GLN ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 ASN K 126 ASN M 23 GLN P 58 ASN ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 18 GLN W 41 ASN Z 42 HIS ** a 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 177 GLN c 226 GLN ** d 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 25 ASN j 76 ASN m 109 ASN o 33 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 135377 Z= 0.235 Angle : 0.814 26.434 199877 Z= 0.424 Chirality : 0.042 1.980 25096 Planarity : 0.008 0.131 12291 Dihedral : 16.992 179.792 48976 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.53 % Favored : 94.38 % Rotamer Outliers : 4.02 % 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: -2.02 (0.10), residues: 6350 helix: -1.07 (0.11), residues: 2149 sheet: -1.42 (0.17), residues: 854 loop : -1.45 (0.10), residues: 3347 *********************** 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 970 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 781 time to evaluate : 6.608 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 189 outliers final: 113 residues processed: 908 average time/residue: 2.0747 time to fit residues: 2648.7829 Evaluate side-chains 848 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 735 time to evaluate : 6.581 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 87 residues processed: 28 average time/residue: 1.2711 time to fit residues: 66.1031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 478 optimal weight: 5.9990 chunk 840 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 151 ASN B 167 GLN B 174 HIS C 93 ASN E 123 GLN ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 ASN I 108 ASN K 126 ASN L 77 ASN P 58 ASN Q 137 ASN T 110 ASN ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN ** V 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 41 ASN Y 21 HIS ** Z 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 87 GLN k 48 ASN l 33 ASN m 109 ASN n 31 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.097 135377 Z= 0.431 Angle : 0.916 25.976 199877 Z= 0.468 Chirality : 0.049 1.986 25096 Planarity : 0.009 0.141 12291 Dihedral : 17.114 179.483 48976 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.85 % Favored : 93.06 % Rotamer Outliers : 4.62 % 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: -1.95 (0.10), residues: 6350 helix: -0.98 (0.11), residues: 2149 sheet: -1.39 (0.17), residues: 833 loop : -1.43 (0.10), residues: 3368 *********************** 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 964 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 745 time to evaluate : 6.687 Fit side-chains revert: symmetry clash outliers start: 219 outliers final: 147 residues processed: 891 average time/residue: 2.0804 time to fit residues: 2607.8397 Evaluate side-chains 878 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 731 time to evaluate : 6.640 Switching outliers to nearest non-outliers outliers start: 147 outliers final: 104 residues processed: 45 average time/residue: 1.2570 time to fit residues: 101.5180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 315 optimal weight: 0.2980 chunk 843 optimal weight: 10.0000 chunk 185 optimal weight: 20.0000 chunk 549 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 chunk 937 optimal weight: 20.0000 chunk 778 optimal weight: 20.0000 chunk 434 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 310 optimal weight: 0.9980 chunk 492 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 E 123 GLN F 56 GLN ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 ASN I 108 ASN K 126 ASN L 77 ASN P 58 ASN T 110 ASN ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN ** V 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 41 ASN Z 14 GLN ** 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** j 76 ASN k 48 ASN m 109 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.099 135377 Z= 0.179 Angle : 0.779 26.439 199877 Z= 0.407 Chirality : 0.039 1.981 25096 Planarity : 0.007 0.128 12291 Dihedral : 16.790 179.827 48976 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.40 % Favored : 94.54 % Rotamer Outliers : 3.65 % 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: -1.50 (0.10), residues: 6350 helix: -0.45 (0.11), residues: 2152 sheet: -1.22 (0.17), residues: 861 loop : -1.24 (0.10), residues: 3337 *********************** 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 945 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 776 time to evaluate : 6.783 Fit side-chains outliers start: 169 outliers final: 110 residues processed: 907 average time/residue: 2.1213 time to fit residues: 2717.7385 Evaluate side-chains 851 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 741 time to evaluate : 6.640 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 99 residues processed: 13 average time/residue: 1.0312 time to fit residues: 31.7159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0010 chunk 534 optimal weight: 0.6980 chunk 684 optimal weight: 10.0000 chunk 530 optimal weight: 0.0040 chunk 789 optimal weight: 10.0000 chunk 523 optimal weight: 0.8980 chunk 933 optimal weight: 10.0000 chunk 584 optimal weight: 5.9990 chunk 569 optimal weight: 10.0000 chunk 431 optimal weight: 0.7980 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 108 HIS B 109 HIS 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 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 ASN I 108 ASN K 126 ASN O 81 HIS P 58 ASN ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 110 ASN ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN ** V 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 87 GLN k 48 ASN m 109 ASN o 33 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.077 135377 Z= 0.132 Angle : 0.767 26.686 199877 Z= 0.402 Chirality : 0.038 1.972 25096 Planarity : 0.007 0.124 12291 Dihedral : 16.756 179.838 48976 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.37 % Favored : 94.57 % Rotamer Outliers : 3.45 % 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: -1.25 (0.10), residues: 6350 helix: -0.14 (0.11), residues: 2147 sheet: -1.11 (0.17), residues: 860 loop : -1.17 (0.10), residues: 3343 *********************** 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 915 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 756 time to evaluate : 6.701 Fit side-chains revert: symmetry clash outliers start: 159 outliers final: 118 residues processed: 884 average time/residue: 2.0847 time to fit residues: 2617.6994 Evaluate side-chains 858 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 740 time to evaluate : 6.704 Switching outliers to nearest non-outliers outliers start: 118 outliers final: 100 residues processed: 19 average time/residue: 1.2805 time to fit residues: 48.0878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 577 optimal weight: 9.9990 chunk 372 optimal weight: 10.0000 chunk 557 optimal weight: 0.2980 chunk 281 optimal weight: 20.0000 chunk 183 optimal weight: 0.9980 chunk 180 optimal weight: 10.0000 chunk 593 optimal weight: 3.9990 chunk 636 optimal weight: 10.0000 chunk 461 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 734 optimal weight: 10.0000 overall best weight: 4.4586 ------------------------------------------------------------------------------- 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 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** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 GLN I 108 ASN K 126 ASN L 77 ASN P 58 ASN T 110 ASN T 121 GLN ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN ** V 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.090 135377 Z= 0.307 Angle : 0.824 26.168 199877 Z= 0.426 Chirality : 0.043 1.980 25096 Planarity : 0.008 0.134 12291 Dihedral : 16.771 179.999 48976 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.21 % Favored : 93.73 % Rotamer Outliers : 3.37 % 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: -1.28 (0.10), residues: 6350 helix: -0.18 (0.11), residues: 2140 sheet: -1.14 (0.17), residues: 864 loop : -1.17 (0.10), residues: 3346 *********************** 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 895 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 740 time to evaluate : 6.771 Fit side-chains outliers start: 155 outliers final: 116 residues processed: 861 average time/residue: 2.0421 time to fit residues: 2497.0423 Evaluate side-chains 849 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 733 time to evaluate : 6.663 Switching outliers to nearest non-outliers outliers start: 116 outliers final: 100 residues processed: 17 average time/residue: 0.9933 time to fit residues: 38.8294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 849 optimal weight: 9.9990 chunk 894 optimal weight: 10.0000 chunk 816 optimal weight: 9.9990 chunk 870 optimal weight: 20.0000 chunk 523 optimal weight: 0.8980 chunk 379 optimal weight: 0.9980 chunk 683 optimal weight: 10.0000 chunk 267 optimal weight: 8.9990 chunk 786 optimal weight: 10.0000 chunk 823 optimal weight: 10.0000 chunk 867 optimal weight: 10.0000 overall best weight: 6.1786 ------------------------------------------------------------------------------- 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 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS C 93 ASN C 158 GLN ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 GLN ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 ASN J 106 ASN K 126 ASN L 34 ASN L 77 ASN ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 110 ASN ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN ** V 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 41 ASN 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 o 21 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.096 135377 Z= 0.407 Angle : 0.894 25.911 199877 Z= 0.458 Chirality : 0.048 1.988 25096 Planarity : 0.009 0.140 12291 Dihedral : 16.939 179.770 48976 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.45 % Favored : 93.47 % Rotamer Outliers : 3.20 % 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: -1.48 (0.10), residues: 6350 helix: -0.40 (0.11), residues: 2146 sheet: -1.22 (0.17), residues: 859 loop : -1.25 (0.10), residues: 3345 *********************** 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 893 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 747 time to evaluate : 6.899 Fit side-chains outliers start: 146 outliers final: 119 residues processed: 868 average time/residue: 2.0670 time to fit residues: 2538.1468 Evaluate side-chains 857 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 738 time to evaluate : 6.613 Switching outliers to nearest non-outliers outliers start: 119 outliers final: 104 residues processed: 16 average time/residue: 1.1386 time to fit residues: 39.0890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 571 optimal weight: 3.9990 chunk 920 optimal weight: 10.0000 chunk 561 optimal weight: 0.9990 chunk 436 optimal weight: 9.9990 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: 3.9990 chunk 593 optimal weight: 7.9990 chunk 471 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 GLN ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 ASN K 126 ASN ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN ** V 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** i 39 HIS j 76 ASN k 48 ASN m 109 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 135377 Z= 0.272 Angle : 0.845 26.376 199877 Z= 0.437 Chirality : 0.043 1.977 25096 Planarity : 0.008 0.135 12291 Dihedral : 16.922 179.910 48976 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.21 % Favored : 93.73 % Rotamer Outliers : 2.83 % 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: -1.41 (0.10), residues: 6350 helix: -0.30 (0.11), residues: 2148 sheet: -1.23 (0.17), residues: 854 loop : -1.24 (0.10), residues: 3348 ********************** 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 878 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 751 time to evaluate : 7.013 Fit side-chains outliers start: 127 outliers final: 113 residues processed: 868 average time/residue: 2.0722 time to fit residues: 2541.1747 Evaluate side-chains 855 residues out of total 5373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 742 time to evaluate : 6.718 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 105 residues processed: 9 average time/residue: 1.1206 time to fit residues: 24.9572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 610 optimal weight: 5.9990 chunk 818 optimal weight: 10.0000 chunk 235 optimal weight: 6.9990 chunk 708 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 213 optimal weight: 10.0000 chunk 769 optimal weight: 10.0000 chunk 322 optimal weight: 2.9990 chunk 790 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 GLN ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 ASN I 108 ASN K 126 ASN ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 155 GLN ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN ** V 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN k 48 ASN m 109 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.158251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.130573 restraints weight = 271777.998| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.23 r_work: 0.3510 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.094 135377 Z= 0.340 Angle : 0.858 26.052 199877 Z= 0.442 Chirality : 0.045 1.988 25096 Planarity : 0.008 0.137 12291 Dihedral : 16.882 179.709 48976 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.32 % Favored : 93.61 % Rotamer Outliers : 3.04 % 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: -1.41 (0.10), residues: 6350 helix: -0.30 (0.11), residues: 2149 sheet: -1.23 (0.17), residues: 857 loop : -1.23 (0.10), residues: 3344 =============================================================================== Job complete usr+sys time: 39141.58 seconds wall clock time: 680 minutes 57.19 seconds (40857.19 seconds total)