Starting phenix.real_space_refine on Fri Dec 8 01:14:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp7_14114/12_2023/7qp7_14114_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp7_14114/12_2023/7qp7_14114.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp7_14114/12_2023/7qp7_14114_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp7_14114/12_2023/7qp7_14114_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp7_14114/12_2023/7qp7_14114_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp7_14114/12_2023/7qp7_14114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp7_14114/12_2023/7qp7_14114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp7_14114/12_2023/7qp7_14114_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp7_14114/12_2023/7qp7_14114_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 Zn 2 6.06 5 P 1812 5.49 5 S 284 5.16 5 C 60761 2.51 5 N 19996 2.21 5 O 25339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 492": "NH1" <-> "NH2" Residue "1 ARG 501": "NH1" <-> "NH2" Residue "1 ARG 505": "NH1" <-> "NH2" Residue "1 ARG 507": "NH1" <-> "NH2" Residue "1 ARG 550": "NH1" <-> "NH2" Residue "6 ARG 317": "NH1" <-> "NH2" Residue "6 ARG 330": "NH1" <-> "NH2" Residue "9 ARG 2": "NH1" <-> "NH2" Residue "9 ARG 23": "NH1" <-> "NH2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "C ARG 11": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C GLU 251": "OE1" <-> "OE2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "D ARG 17": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "E ARG 5": "NH1" <-> "NH2" Residue "E ARG 8": "NH1" <-> "NH2" Residue "E ARG 11": "NH1" <-> "NH2" Residue "E ARG 17": "NH1" <-> "NH2" Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 53": "OE1" <-> "OE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E ARG 107": "NH1" <-> "NH2" Residue "F ARG 105": "NH1" <-> "NH2" Residue "G GLU 18": "OE1" <-> "OE2" Residue "G GLU 20": "OE1" <-> "OE2" Residue "G GLU 29": "OE1" <-> "OE2" Residue "G GLU 50": "OE1" <-> "OE2" Residue "G ARG 57": "NH1" <-> "NH2" Residue "G ARG 78": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "G ARG 106": "NH1" <-> "NH2" Residue "G ARG 143": "NH1" <-> "NH2" Residue "H GLU 75": "OE1" <-> "OE2" Residue "H PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 103": "OE1" <-> "OE2" Residue "I ARG 104": "NH1" <-> "NH2" Residue "I ARG 114": "NH1" <-> "NH2" Residue "I ARG 121": "NH1" <-> "NH2" Residue "I GLU 142": "OE1" <-> "OE2" Residue "J GLU 49": "OE1" <-> "OE2" Residue "J PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 38": "OE1" <-> "OE2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "L GLU 92": "OE1" <-> "OE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L ARG 117": "NH1" <-> "NH2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 146": "OE1" <-> "OE2" Residue "L ARG 166": "NH1" <-> "NH2" Residue "L ARG 167": "NH1" <-> "NH2" Residue "L ARG 200": "NH1" <-> "NH2" Residue "L ARG 227": "NH1" <-> "NH2" Residue "L GLU 268": "OE1" <-> "OE2" Residue "M GLU 18": "OE1" <-> "OE2" Residue "M GLU 36": "OE1" <-> "OE2" Residue "M ARG 78": "NH1" <-> "NH2" Residue "M GLU 79": "OE1" <-> "OE2" Residue "M ARG 81": "NH1" <-> "NH2" Residue "M GLU 94": "OE1" <-> "OE2" Residue "N GLU 13": "OE1" <-> "OE2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 196": "OE1" <-> "OE2" Residue "O GLU 68": "OE1" <-> "OE2" Residue "O ARG 82": "NH1" <-> "NH2" Residue "O GLU 89": "OE1" <-> "OE2" Residue "O PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 151": "NH1" <-> "NH2" Residue "O ARG 162": "NH1" <-> "NH2" Residue "O ARG 165": "NH1" <-> "NH2" Residue "O GLU 198": "OE1" <-> "OE2" Residue "O ARG 213": "NH1" <-> "NH2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P ARG 117": "NH1" <-> "NH2" Residue "P ARG 141": "NH1" <-> "NH2" Residue "P ARG 150": "NH1" <-> "NH2" Residue "Q ARG 10": "NH1" <-> "NH2" Residue "Q GLU 55": "OE1" <-> "OE2" Residue "Q ARG 85": "NH1" <-> "NH2" Residue "Q ARG 87": "NH1" <-> "NH2" Residue "Q ARG 89": "NH1" <-> "NH2" Residue "R ARG 25": "NH1" <-> "NH2" Residue "R ARG 41": "NH1" <-> "NH2" Residue "R TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 114": "OE1" <-> "OE2" Residue "R GLU 133": "OE1" <-> "OE2" Residue "R GLU 135": "OE1" <-> "OE2" Residue "R TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 151": "OE1" <-> "OE2" Residue "R GLU 164": "OE1" <-> "OE2" Residue "R TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 196": "OE1" <-> "OE2" Residue "S GLU 44": "OE1" <-> "OE2" Residue "S ARG 131": "NH1" <-> "NH2" Residue "S ARG 132": "NH1" <-> "NH2" Residue "S GLU 150": "OE1" <-> "OE2" Residue "S GLU 165": "OE1" <-> "OE2" Residue "S ARG 178": "NH1" <-> "NH2" Residue "S GLU 204": "OE1" <-> "OE2" Residue "S GLU 205": "OE1" <-> "OE2" Residue "S GLU 219": "OE1" <-> "OE2" Residue "T ARG 20": "NH1" <-> "NH2" Residue "T ARG 41": "NH1" <-> "NH2" Residue "T ARG 61": "NH1" <-> "NH2" Residue "V ARG 62": "NH1" <-> "NH2" Residue "V ARG 71": "NH1" <-> "NH2" Residue "V ARG 81": "NH1" <-> "NH2" Residue "V GLU 123": "OE1" <-> "OE2" Residue "V ARG 127": "NH1" <-> "NH2" Residue "V ARG 135": "NH1" <-> "NH2" Residue "V GLU 160": "OE1" <-> "OE2" Residue "V ARG 164": "NH1" <-> "NH2" Residue "V GLU 176": "OE1" <-> "OE2" Residue "Y GLU 43": "OE1" <-> "OE2" Residue "Y ARG 45": "NH1" <-> "NH2" Residue "Y ARG 62": "NH1" <-> "NH2" Residue "Y ARG 125": "NH1" <-> "NH2" Residue "Y ARG 126": "NH1" <-> "NH2" Residue "Y ARG 138": "NH1" <-> "NH2" Residue "Y ARG 140": "NH1" <-> "NH2" Residue "Z ARG 9": "NH1" <-> "NH2" Residue "Z GLU 20": "OE1" <-> "OE2" Residue "Z GLU 61": "OE1" <-> "OE2" Residue "Z GLU 81": "OE1" <-> "OE2" Residue "Z GLU 85": "OE1" <-> "OE2" Residue "Z GLU 89": "OE1" <-> "OE2" Residue "Z ARG 94": "NH1" <-> "NH2" Residue "Z ARG 117": "NH1" <-> "NH2" Residue "Z ARG 143": "NH1" <-> "NH2" Residue "Z TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 216": "OE1" <-> "OE2" Residue "a GLU 18": "OE1" <-> "OE2" Residue "a ARG 65": "NH1" <-> "NH2" Residue "a GLU 88": "OE1" <-> "OE2" Residue "b GLU 31": "OE1" <-> "OE2" Residue "b ARG 61": "NH1" <-> "NH2" Residue "b GLU 66": "OE1" <-> "OE2" Residue "b GLU 71": "OE1" <-> "OE2" Residue "b GLU 110": "OE1" <-> "OE2" Residue "c GLU 3": "OE1" <-> "OE2" Residue "c ARG 47": "NH1" <-> "NH2" Residue "c GLU 49": "OE1" <-> "OE2" Residue "c ARG 57": "NH1" <-> "NH2" Residue "c ARG 100": "NH1" <-> "NH2" Residue "c GLU 149": "OE1" <-> "OE2" Residue "c GLU 223": "OE1" <-> "OE2" Residue "c PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 262": "OE1" <-> "OE2" Residue "c GLU 269": "OE1" <-> "OE2" Residue "c GLU 273": "OE1" <-> "OE2" Residue "d GLU 13": "OE1" <-> "OE2" Residue "d GLU 44": "OE1" <-> "OE2" Residue "d GLU 50": "OE1" <-> "OE2" Residue "d ARG 62": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d ARG 121": "NH1" <-> "NH2" Residue "e GLU 75": "OE1" <-> "OE2" Residue "e ARG 80": "NH1" <-> "NH2" Residue "e GLU 90": "OE1" <-> "OE2" Residue "f GLU 7": "OE1" <-> "OE2" Residue "f ARG 14": "NH1" <-> "NH2" Residue "f ARG 39": "NH1" <-> "NH2" Residue "f ARG 55": "NH1" <-> "NH2" Residue "f GLU 61": "OE1" <-> "OE2" Residue "f GLU 65": "OE1" <-> "OE2" Residue "f ARG 86": "NH1" <-> "NH2" Residue "f ARG 108": "NH1" <-> "NH2" Residue "f ARG 141": "NH1" <-> "NH2" Residue "f ARG 142": "NH1" <-> "NH2" Residue "h ARG 21": "NH1" <-> "NH2" Residue "h ARG 87": "NH1" <-> "NH2" Residue "h GLU 96": "OE1" <-> "OE2" Residue "h GLU 111": "OE1" <-> "OE2" Residue "h GLU 113": "OE1" <-> "OE2" Residue "k ARG 118": "NH1" <-> "NH2" Residue "k GLU 120": "OE1" <-> "OE2" Residue "m GLU 66": "OE1" <-> "OE2" Residue "m GLU 71": "OE1" <-> "OE2" Residue "m GLU 97": "OE1" <-> "OE2" Residue "m GLU 125": "OE1" <-> "OE2" Residue "m GLU 126": "OE1" <-> "OE2" Residue "n ARG 13": "NH1" <-> "NH2" Residue "n ARG 40": "NH1" <-> "NH2" Residue "n ARG 44": "NH1" <-> "NH2" Residue "n GLU 52": "OE1" <-> "OE2" Residue "n GLU 60": "OE1" <-> "OE2" Residue "n GLU 62": "OE1" <-> "OE2" Residue "o GLU 252": "OE1" <-> "OE2" Residue "o GLU 257": "OE1" <-> "OE2" Residue "o ARG 295": "NH1" <-> "NH2" Residue "q GLU 48": "OE1" <-> "OE2" Residue "q GLU 111": "OE1" <-> "OE2" Residue "r ARG 7": "NH1" <-> "NH2" Residue "r ARG 25": "NH1" <-> "NH2" Residue "r ARG 57": "NH1" <-> "NH2" Residue "r ARG 75": "NH1" <-> "NH2" Residue "r GLU 79": "OE1" <-> "OE2" Residue "r ARG 88": "NH1" <-> "NH2" Residue "r ARG 89": "NH1" <-> "NH2" Residue "r GLU 94": "OE1" <-> "OE2" Residue "r GLU 99": "OE1" <-> "OE2" Residue "r ARG 113": "NH1" <-> "NH2" Residue "r GLU 128": "OE1" <-> "OE2" Residue "r ARG 133": "NH1" <-> "NH2" Residue "r ARG 144": "NH1" <-> "NH2" Residue "r ARG 173": "NH1" <-> "NH2" Residue "r ARG 182": "NH1" <-> "NH2" Residue "r ARG 183": "NH1" <-> "NH2" Residue "r ARG 234": "NH1" <-> "NH2" Residue "r ARG 244": "NH1" <-> "NH2" Residue "r ARG 266": "NH1" <-> "NH2" Residue "r GLU 274": "OE1" <-> "OE2" Residue "u ARG 14": "NH1" <-> "NH2" Residue "u ARG 14": "NH1" <-> "NH2" Residue "u ARG 62": "NH1" <-> "NH2" Residue "u ARG 140": "NH1" <-> "NH2" Residue "u ARG 143": "NH1" <-> "NH2" Residue "u ARG 169": "NH1" <-> "NH2" Residue "u ARG 195": "NH1" <-> "NH2" Residue "u ARG 298": "NH1" <-> "NH2" Residue "u ARG 304": "NH1" <-> "NH2" Residue "u GLU 305": "OE1" <-> "OE2" Residue "u ARG 307": "NH1" <-> "NH2" Residue "u ARG 317": "NH1" <-> "NH2" Residue "u ARG 321": "NH1" <-> "NH2" Residue "u GLU 334": "OE1" <-> "OE2" Residue "u ASP 343": "OD1" <-> "OD2" Residue "u ARG 376": "NH1" <-> "NH2" Residue "u GLU 386": "OE1" <-> "OE2" Residue "u ARG 406": "NH1" <-> "NH2" Residue "u ARG 415": "NH1" <-> "NH2" Residue "u ARG 438": "NH1" <-> "NH2" Residue "u GLU 451": "OE1" <-> "OE2" Residue "u ARG 454": "NH1" <-> "NH2" Residue "u GLU 468": "OE1" <-> "OE2" Residue "u ARG 483": "NH1" <-> "NH2" Residue "u ARG 489": "NH1" <-> "NH2" Residue "u ARG 502": "NH1" <-> "NH2" Residue "u GLU 517": "OE1" <-> "OE2" Residue "u GLU 548": "OE1" <-> "OE2" Residue "u ARG 572": "NH1" <-> "NH2" Residue "v TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 26": "NH1" <-> "NH2" Residue "x GLU 77": "OE1" <-> "OE2" Residue "x GLU 293": "OE1" <-> "OE2" Residue "x GLU 297": "OE1" <-> "OE2" Residue "x GLU 315": "OE1" <-> "OE2" Residue "x ARG 329": "NH1" <-> "NH2" Residue "x ARG 362": "NH1" <-> "NH2" Residue "x GLU 376": "OE1" <-> "OE2" Residue "x GLU 398": "OE1" <-> "OE2" Residue "x ARG 462": "NH1" <-> "NH2" Residue "x GLU 475": "OE1" <-> "OE2" Residue "y ARG 56": "NH1" <-> "NH2" Residue "y GLU 58": "OE1" <-> "OE2" Residue "y GLU 59": "OE1" <-> "OE2" Residue "y ARG 74": "NH1" <-> "NH2" Residue "y GLU 84": "OE1" <-> "OE2" Residue "y ARG 104": "NH1" <-> "NH2" Residue "y ARG 108": "NH1" <-> "NH2" Residue "y GLU 119": "OE1" <-> "OE2" Residue "y GLU 122": "OE1" <-> "OE2" Residue "y ARG 142": "NH1" <-> "NH2" Residue "y GLU 153": "OE1" <-> "OE2" Residue "y GLU 468": "OE1" <-> "OE2" Residue "y TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 521": "NH1" <-> "NH2" Residue "y GLU 542": "OE1" <-> "OE2" Residue "y GLU 549": "OE1" <-> "OE2" Residue "y ARG 560": "NH1" <-> "NH2" Residue "y ARG 565": "NH1" <-> "NH2" Residue "y ARG 581": "NH1" <-> "NH2" Residue "y ARG 586": "NH1" <-> "NH2" Residue "y ARG 622": "NH1" <-> "NH2" Residue "y ARG 641": "NH1" <-> "NH2" Residue "y ARG 658": "NH1" <-> "NH2" Residue "y GLU 661": "OE1" <-> "OE2" Residue "y GLU 666": "OE1" <-> "OE2" Residue "y ARG 668": "NH1" <-> "NH2" Residue "y ARG 669": "NH1" <-> "NH2" Residue "y ARG 706": "NH1" <-> "NH2" Residue "y ARG 707": "NH1" <-> "NH2" Residue "y ARG 708": "NH1" <-> "NH2" Residue "y ARG 719": "NH1" <-> "NH2" Residue "y ARG 723": "NH1" <-> "NH2" Residue "y ARG 776": "NH1" <-> "NH2" Residue "y ARG 781": "NH1" <-> "NH2" Residue "y GLU 785": "OE1" <-> "OE2" Residue "y GLU 786": "OE1" <-> "OE2" Residue "y ARG 789": "NH1" <-> "NH2" Residue "y GLU 848": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 108194 Number of models: 1 Model: "" Number of chains: 53 Chain: "1" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 2560 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 307} Link IDs: {'PTRANS': 21, 'TRANS': 425} Chain breaks: 1 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1228 Unresolved non-hydrogen angles: 1582 Unresolved non-hydrogen dihedrals: 1087 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 10, 'TYR:plan': 11, 'ASN:plan1': 10, 'TRP:plan': 15, 'ASP:plan': 21, 'PHE:plan': 20, 'GLU:plan': 18, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 717 Chain: "3" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1057 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 189} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 704 Unresolved non-hydrogen angles: 904 Unresolved non-hydrogen dihedrals: 590 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 4, 'ASP:plan': 14, 'PHE:plan': 11, 'GLU:plan': 17, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 404 Chain: "4" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1272 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 226} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 767 Unresolved non-hydrogen angles: 993 Unresolved non-hydrogen dihedrals: 618 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 8, 'TYR:plan': 11, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 6, 'GLU:plan': 15, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 399 Chain: "5" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 1581 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 289} Link IDs: {'PTRANS': 5, 'TRANS': 313} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1124 Unresolved non-hydrogen angles: 1435 Unresolved non-hydrogen dihedrals: 958 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 10, 'TYR:plan': 21, 'ASN:plan1': 11, 'TRP:plan': 3, 'ASP:plan': 18, 'PHE:plan': 18, 'GLU:plan': 21, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 653 Chain: "6" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 1917 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 263} Link IDs: {'PTRANS': 6, 'TRANS': 343} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 914 Unresolved non-hydrogen angles: 1159 Unresolved non-hydrogen dihedrals: 747 Unresolved non-hydrogen chiralities: 90 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 7, 'TYR:plan': 8, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 20, 'PHE:plan': 10, 'GLU:plan': 27, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 473 Chain: "7" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 441 Classifications: {'RNA': 21} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 9, 'rna3p_pyr': 7} Link IDs: {'rna2p': 5, 'rna3p': 15} Chain: "8" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 1571 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 285} Link IDs: {'PTRANS': 12, 'TRANS': 304} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1046 Unresolved non-hydrogen angles: 1332 Unresolved non-hydrogen dihedrals: 868 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 31, 'ASP:plan': 16, 'TYR:plan': 14, 'ASN:plan1': 14, 'TRP:plan': 2, 'HIS:plan': 10, 'ASN%COO:plan1': 1, 'PHE:plan': 10, 'GLU:plan': 24, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 599 Chain: "9" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 230 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "A" Number of atoms: 36668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1719, 36668 Classifications: {'DNA': 2, 'RNA': 1717} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 152, 'rna2p_pyr': 129, 'rna3p': 18, 'rna3p_pur': 739, 'rna3p_pyr': 669} Link IDs: {'rna2p': 281, 'rna3p': 1437} Chain breaks: 6 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {' U:plan': 1, ' C:plan': 2, ' C:plan2': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1166 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain breaks: 1 Chain: "C" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2035 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 14, 'TRANS': 241} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1477 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "E" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1087 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "F" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 378 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain breaks: 1 Chain: "G" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1430 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain breaks: 2 Chain: "H" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 631 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "I" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1208 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "J" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "K" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 617 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "L" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1707 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 12, 'TRANS': 207} Chain: "M" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1015 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "N" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1633 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 12, 'TRANS': 194} Chain: "O" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1715 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 5, 'TRANS': 205} Chain: "P" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 997 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 127} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Q" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 792 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain: "R" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1627 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "S" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1862 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "T" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1015 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "V" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1461 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain breaks: 1 Chain: "Y" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1124 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Z" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 11, 'TRANS': 215} Chain: "a" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 834 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 8, 'TRANS': 90} Chain: "b" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 913 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "c" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "d" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1105 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 4, 'TRANS': 137} Chain: "e" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "f" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1176 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 3, 'TRANS': 138} Chain: "h" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 817 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "i" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 419 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "k" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 435 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain breaks: 1 Chain: "m" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "n" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 498 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "o" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "q" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 782 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 99} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "r" Number of atoms: 2215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2215 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 9, 'TRANS': 265} Chain: "t" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 1750 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 298} Link IDs: {'PTRANS': 15, 'TRANS': 340} Chain breaks: 4 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1009 Unresolved non-hydrogen angles: 1285 Unresolved non-hydrogen dihedrals: 814 Unresolved non-hydrogen chiralities: 125 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 9, 'TYR:plan': 6, 'ASN:plan1': 12, 'TRP:plan': 2, 'HIS:plan': 9, 'PHE:plan': 8, 'GLU:plan': 23, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 445 Chain: "u" Number of atoms: 5383 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 706, 5375 Classifications: {'peptide': 706} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 25, 'TRANS': 680} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 493 Unresolved non-hydrogen angles: 600 Unresolved non-hydrogen dihedrals: 398 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 34, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 304 Conformer: "B" Number of residues, atoms: 706, 5375 Classifications: {'peptide': 706} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 25, 'TRANS': 680} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 493 Unresolved non-hydrogen angles: 600 Unresolved non-hydrogen dihedrals: 398 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 34, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 304 bond proxies already assigned to first conformer: 5455 Chain: "v" Number of atoms: 2635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2635 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 10, 'TRANS': 373} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 559 Unresolved non-hydrogen angles: 715 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 9, 'TYR:plan': 10, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 7, 'GLU:plan': 13, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 342 Chain: "w" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1604 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 32, 'rna3p_pyr': 29} Link IDs: {'rna2p': 14, 'rna3p': 60} Chain: "x" Number of atoms: 2831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 2831 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 172} Link IDs: {'PTRANS': 16, 'TRANS': 404} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 633 Unresolved non-hydrogen angles: 806 Unresolved non-hydrogen dihedrals: 531 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 8, 'TRP:plan': 3, 'ASP:plan': 17, 'PHE:plan': 9, 'GLU:plan': 13, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 352 Chain: "y" Number of atoms: 5197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5197 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 17, 'TRANS': 624} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 65605 SG CYS Q 23 118.437 170.690 159.105 1.00 27.44 S ATOM 65626 SG CYS Q 26 114.287 170.166 158.705 1.00 25.98 S ATOM 66009 SG CYS Q 74 116.780 169.092 155.977 1.00 32.58 S ATOM 66028 SG CYS Q 77 115.858 172.550 157.689 1.00 43.62 S ATOM 83500 SG CYS k 121 20.930 199.821 91.081 1.00102.58 S ATOM 83536 SG CYS k 126 24.537 200.107 91.005 1.00107.22 S ATOM 83654 SG CYS k 141 22.262 197.758 93.447 1.00 93.99 S ATOM 83673 SG CYS k 144 22.890 201.237 94.344 1.00 97.63 S Residues with excluded nonbonded symmetry interactions: 15 residue: pdb=" P C 7 7 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C 7 7 " occ=0.00 residue: pdb=" P A 7 8 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A 7 8 " occ=0.00 residue: pdb=" P C 7 9 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C 7 9 " occ=0.00 residue: pdb=" P C 7 10 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C 7 10 " occ=0.00 residue: pdb=" P A 7 11 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A 7 11 " occ=0.00 residue: pdb=" P U 7 12 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U 7 12 " occ=0.00 residue: pdb=" P G 7 13 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G 7 13 " occ=0.00 residue: pdb=" P G 7 14 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G 7 14 " occ=0.00 residue: pdb=" P U 7 15 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U 7 15 " occ=0.00 residue: pdb=" P C 7 17 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C 7 17 " occ=0.00 residue: pdb=" P U 7 21 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U 7 21 " occ=0.00 residue: pdb=" N ALA t 51 " occ=0.32 ... (3 atoms not shown) pdb=" CB ALA t 51 " occ=0.32 ... (remaining 3 not shown) Time building chain proxies: 42.02, per 1000 atoms: 0.39 Number of scatterers: 108194 At special positions: 0 Unit cell: (303.92, 286.52, 240.12, 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) Zn 2 29.99 S 284 16.00 P 1812 15.00 O 25339 8.00 N 19996 7.00 C 60761 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 40.17 Conformation dependent library (CDL) restraints added in 11.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Q 201 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 26 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 77 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 23 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 74 " pdb=" ZN k 201 " pdb="ZN ZN k 201 " - pdb=" SG CYS k 141 " pdb="ZN ZN k 201 " - pdb=" SG CYS k 126 " pdb="ZN ZN k 201 " - pdb=" SG CYS k 121 " pdb="ZN ZN k 201 " - pdb=" SG CYS k 144 " Number of angles added : 12 18970 Ramachandran restraints generated. 9485 Oldfield, 0 Emsley, 9485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18178 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 340 helices and 89 sheets defined 47.9% alpha, 13.7% beta 495 base pairs and 927 stacking pairs defined. Time for finding SS restraints: 60.50 Creating SS restraints... Processing helix chain '1' and resid 284 through 300 removed outlier: 4.796A pdb=" N LYS 1 288 " --> pdb=" O LYS 1 284 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP 1 289 " --> pdb=" O GLN 1 285 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU 1 293 " --> pdb=" O ASP 1 289 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG 1 294 " --> pdb=" O LEU 1 290 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR 1 295 " --> pdb=" O GLY 1 291 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TRP 1 296 " --> pdb=" O ASN 1 292 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU 1 297 " --> pdb=" O LEU 1 293 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ALA 1 300 " --> pdb=" O TRP 1 296 " (cutoff:3.500A) Processing helix chain '1' and resid 459 through 464 removed outlier: 4.048A pdb=" N LYS 1 463 " --> pdb=" O LYS 1 459 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE 1 464 " --> pdb=" O LYS 1 460 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 459 through 464' Processing helix chain '1' and resid 713 through 718 Processing helix chain '3' and resid 2 through 18 removed outlier: 3.527A pdb=" N ALA 3 9 " --> pdb=" O GLU 3 5 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN 3 10 " --> pdb=" O GLN 3 6 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY 3 17 " --> pdb=" O LYS 3 13 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE 3 18 " --> pdb=" O LEU 3 14 " (cutoff:3.500A) Processing helix chain '3' and resid 22 through 39 removed outlier: 4.334A pdb=" N LEU 3 26 " --> pdb=" O ASN 3 22 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ALA 3 27 " --> pdb=" O PRO 3 23 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N THR 3 28 " --> pdb=" O GLU 3 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU 3 29 " --> pdb=" O ASN 3 25 " (cutoff:3.500A) Processing helix chain '3' and resid 43 through 57 removed outlier: 4.020A pdb=" N ASN 3 47 " --> pdb=" O ASP 3 43 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU 3 48 " --> pdb=" O LEU 3 44 " (cutoff:3.500A) Processing helix chain '3' and resid 62 through 76 removed outlier: 3.708A pdb=" N THR 3 66 " --> pdb=" O GLN 3 62 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE 3 69 " --> pdb=" O VAL 3 65 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS 3 72 " --> pdb=" O GLN 3 68 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR 3 75 " --> pdb=" O LEU 3 71 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASN 3 76 " --> pdb=" O LYS 3 72 " (cutoff:3.500A) Processing helix chain '3' and resid 80 through 90 removed outlier: 5.385A pdb=" N ASP 3 90 " --> pdb=" O LYS 3 86 " (cutoff:3.500A) Processing helix chain '3' and resid 91 through 96 removed outlier: 4.091A pdb=" N GLU 3 95 " --> pdb=" O GLN 3 91 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU 3 96 " --> pdb=" O ALA 3 92 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 91 through 96' Processing helix chain '3' and resid 97 through 112 removed outlier: 3.829A pdb=" N LEU 3 105 " --> pdb=" O GLN 3 101 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY 3 106 " --> pdb=" O ILE 3 102 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU 3 108 " --> pdb=" O TYR 3 104 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU 3 109 " --> pdb=" O LEU 3 105 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS 3 112 " --> pdb=" O LEU 3 108 " (cutoff:3.500A) Processing helix chain '3' and resid 113 through 121 removed outlier: 3.555A pdb=" N GLN 3 119 " --> pdb=" O GLN 3 115 " (cutoff:3.500A) Processing helix chain '3' and resid 125 through 132 removed outlier: 3.808A pdb=" N GLY 3 130 " --> pdb=" O ASP 3 126 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE 3 131 " --> pdb=" O LEU 3 127 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR 3 132 " --> pdb=" O LEU 3 128 " (cutoff:3.500A) Processing helix chain '3' and resid 133 through 149 removed outlier: 4.008A pdb=" N VAL 3 138 " --> pdb=" O PHE 3 134 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ARG 3 139 " --> pdb=" O GLU 3 135 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS 3 140 " --> pdb=" O ASP 3 136 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS 3 144 " --> pdb=" O LYS 3 140 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY 3 147 " --> pdb=" O CYS 3 143 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE 3 148 " --> pdb=" O HIS 3 144 " (cutoff:3.500A) Processing helix chain '3' and resid 154 through 163 Processing helix chain '3' and resid 166 through 178 Processing helix chain '3' and resid 191 through 196 removed outlier: 3.997A pdb=" N ILE 3 196 " --> pdb=" O GLN 3 192 " (cutoff:3.500A) Processing helix chain '3' and resid 206 through 216 Processing helix chain '4' and resid 95 through 109 removed outlier: 3.565A pdb=" N LEU 4 99 " --> pdb=" O HIS 4 95 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG 4 108 " --> pdb=" O ASP 4 104 " (cutoff:3.500A) Processing helix chain '4' and resid 149 through 165 Proline residue: 4 165 - end of helix Processing helix chain '4' and resid 180 through 194 removed outlier: 3.980A pdb=" N GLU 4 193 " --> pdb=" O TYR 4 189 " (cutoff:3.500A) Processing helix chain '4' and resid 244 through 257 removed outlier: 4.788A pdb=" N PHE 4 257 " --> pdb=" O MET 4 253 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 294 removed outlier: 4.735A pdb=" N GLU 4 291 " --> pdb=" O LEU 4 287 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASP 4 292 " --> pdb=" O GLN 4 288 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL 4 293 " --> pdb=" O TYR 4 289 " (cutoff:3.500A) Processing helix chain '4' and resid 295 through 306 removed outlier: 3.870A pdb=" N SER 4 299 " --> pdb=" O SER 4 295 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA 4 300 " --> pdb=" O GLY 4 296 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP 4 301 " --> pdb=" O LYS 4 297 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ASN 4 302 " --> pdb=" O VAL 4 298 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR 4 303 " --> pdb=" O SER 4 299 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL 4 304 " --> pdb=" O ALA 4 300 " (cutoff:3.500A) Processing helix chain '4' and resid 307 through 315 removed outlier: 3.595A pdb=" N VAL 4 315 " --> pdb=" O LEU 4 311 " (cutoff:3.500A) Processing helix chain '4' and resid 319 through 357 removed outlier: 4.203A pdb=" N LEU 4 354 " --> pdb=" O LEU 4 350 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL 4 355 " --> pdb=" O ASN 4 351 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU 4 357 " --> pdb=" O LYS 4 353 " (cutoff:3.500A) Processing helix chain '5' and resid 183 through 206 removed outlier: 3.740A pdb=" N ILE 5 187 " --> pdb=" O LEU 5 183 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS 5 202 " --> pdb=" O SER 5 198 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS 5 203 " --> pdb=" O GLN 5 199 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR 5 204 " --> pdb=" O TYR 5 200 " (cutoff:3.500A) Processing helix chain '5' and resid 208 through 217 removed outlier: 3.552A pdb=" N LEU 5 215 " --> pdb=" O GLU 5 211 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG 5 216 " --> pdb=" O ILE 5 212 " (cutoff:3.500A) Processing helix chain '5' and resid 222 through 248 removed outlier: 3.900A pdb=" N SER 5 226 " --> pdb=" O TRP 5 222 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS 5 237 " --> pdb=" O SER 5 233 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG 5 242 " --> pdb=" O SER 5 238 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL 5 246 " --> pdb=" O ARG 5 242 " (cutoff:3.500A) Processing helix chain '5' and resid 253 through 268 removed outlier: 3.619A pdb=" N ARG 5 262 " --> pdb=" O GLY 5 258 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N HIS 5 263 " --> pdb=" O GLU 5 259 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET 5 268 " --> pdb=" O SER 5 264 " (cutoff:3.500A) Processing helix chain '5' and resid 274 through 291 removed outlier: 3.521A pdb=" N LEU 5 278 " --> pdb=" O LEU 5 274 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG 5 279 " --> pdb=" O VAL 5 275 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU 5 283 " --> pdb=" O ARG 5 279 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU 5 284 " --> pdb=" O LEU 5 280 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE 5 291 " --> pdb=" O TYR 5 287 " (cutoff:3.500A) Processing helix chain '5' and resid 297 through 304 removed outlier: 5.132A pdb=" N MET 5 304 " --> pdb=" O ASN 5 300 " (cutoff:3.500A) Processing helix chain '5' and resid 311 through 327 removed outlier: 3.516A pdb=" N VAL 5 319 " --> pdb=" O THR 5 315 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY 5 320 " --> pdb=" O TYR 5 316 " (cutoff:3.500A) Processing helix chain '5' and resid 328 through 342 removed outlier: 3.757A pdb=" N ILE 5 333 " --> pdb=" O TYR 5 329 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG 5 334 " --> pdb=" O GLN 5 330 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE 5 336 " --> pdb=" O ALA 5 332 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ALA 5 337 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASN 5 338 " --> pdb=" O ARG 5 334 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE 5 339 " --> pdb=" O VAL 5 335 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU 5 340 " --> pdb=" O PHE 5 336 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR 5 342 " --> pdb=" O ASN 5 338 " (cutoff:3.500A) Processing helix chain '5' and resid 357 through 375 removed outlier: 3.612A pdb=" N ASN 5 361 " --> pdb=" O TYR 5 357 " (cutoff:3.500A) Processing helix chain '5' and resid 388 through 403 removed outlier: 4.110A pdb=" N LYS 5 393 " --> pdb=" O GLN 5 389 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYS 5 403 " --> pdb=" O LEU 5 399 " (cutoff:3.500A) Processing helix chain '5' and resid 405 through 417 removed outlier: 4.098A pdb=" N TYR 5 409 " --> pdb=" O ASP 5 405 " (cutoff:3.500A) Processing helix chain '5' and resid 438 through 463 removed outlier: 3.566A pdb=" N GLU 5 450 " --> pdb=" O VAL 5 446 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE 5 460 " --> pdb=" O GLN 5 456 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE 5 463 " --> pdb=" O THR 5 459 " (cutoff:3.500A) Processing helix chain '5' and resid 471 through 481 Processing helix chain '5' and resid 490 through 499 removed outlier: 4.767A pdb=" N ASN 5 499 " --> pdb=" O HIS 5 495 " (cutoff:3.500A) Processing helix chain '5' and resid 526 through 549 removed outlier: 3.637A pdb=" N ALA 5 531 " --> pdb=" O MET 5 527 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE 5 547 " --> pdb=" O PHE 5 543 " (cutoff:3.500A) Processing helix chain '6' and resid 15 through 27 removed outlier: 5.222A pdb=" N ARG 6 19 " --> pdb=" O ALA 6 15 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ALA 6 20 " --> pdb=" O ALA 6 16 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA 6 27 " --> pdb=" O LYS 6 23 " (cutoff:3.500A) Processing helix chain '6' and resid 29 through 40 removed outlier: 4.960A pdb=" N ASN 6 33 " --> pdb=" O ILE 6 29 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY 6 36 " --> pdb=" O GLU 6 32 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY 6 37 " --> pdb=" O ASN 6 33 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU 6 38 " --> pdb=" O SER 6 34 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL 6 40 " --> pdb=" O GLY 6 36 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 54 removed outlier: 3.861A pdb=" N GLU 6 47 " --> pdb=" O ALA 6 43 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA 6 48 " --> pdb=" O GLN 6 44 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL 6 51 " --> pdb=" O GLU 6 47 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N CYS 6 52 " --> pdb=" O ALA 6 48 " (cutoff:3.500A) Processing helix chain '6' and resid 60 through 78 removed outlier: 4.247A pdb=" N ASN 6 65 " --> pdb=" O GLU 6 61 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL 6 68 " --> pdb=" O MET 6 64 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N SER 6 69 " --> pdb=" O ASN 6 65 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU 6 72 " --> pdb=" O VAL 6 68 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ILE 6 73 " --> pdb=" O SER 6 69 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU 6 74 " --> pdb=" O LEU 6 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU 6 75 " --> pdb=" O LEU 6 71 " (cutoff:3.500A) Proline residue: 6 76 - end of helix Processing helix chain '6' and resid 79 through 94 removed outlier: 4.752A pdb=" N ILE 6 83 " --> pdb=" O GLN 6 79 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLU 6 84 " --> pdb=" O GLU 6 80 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N SER 6 85 " --> pdb=" O ALA 6 81 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU 6 86 " --> pdb=" O LEU 6 82 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS 6 87 " --> pdb=" O ILE 6 83 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLU 6 88 " --> pdb=" O GLU 6 84 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS 6 89 " --> pdb=" O SER 6 85 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LEU 6 90 " --> pdb=" O LEU 6 86 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N VAL 6 91 " --> pdb=" O CYS 6 87 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE 6 93 " --> pdb=" O LYS 6 89 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG 6 94 " --> pdb=" O LEU 6 90 " (cutoff:3.500A) Processing helix chain '6' and resid 97 through 106 removed outlier: 4.306A pdb=" N LEU 6 101 " --> pdb=" O GLU 6 97 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG 6 102 " --> pdb=" O ARG 6 98 " (cutoff:3.500A) Processing helix chain '6' and resid 116 through 131 removed outlier: 4.037A pdb=" N LYS 6 129 " --> pdb=" O CYS 6 125 " (cutoff:3.500A) Processing helix chain '6' and resid 133 through 138 removed outlier: 4.849A pdb=" N ILE 6 137 " --> pdb=" O SER 6 133 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN 6 138 " --> pdb=" O CYS 6 134 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 133 through 138' Processing helix chain '6' and resid 154 through 172 removed outlier: 4.554A pdb=" N GLU 6 170 " --> pdb=" O ARG 6 166 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA 6 171 " --> pdb=" O LEU 6 167 " (cutoff:3.500A) Processing helix chain '6' and resid 174 through 193 Processing helix chain '6' and resid 198 through 212 removed outlier: 3.784A pdb=" N VAL 6 202 " --> pdb=" O SER 6 198 " (cutoff:3.500A) Processing helix chain '6' and resid 239 through 244 Processing helix chain '6' and resid 254 through 259 removed outlier: 4.318A pdb=" N ASN 6 258 " --> pdb=" O LYS 6 254 " (cutoff:3.500A) Processing helix chain '6' and resid 262 through 267 removed outlier: 3.576A pdb=" N LEU 6 266 " --> pdb=" O PHE 6 262 " (cutoff:3.500A) Processing helix chain '6' and resid 268 through 287 removed outlier: 4.097A pdb=" N LEU 6 279 " --> pdb=" O ALA 6 275 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU 6 280 " --> pdb=" O LYS 6 276 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR 6 281 " --> pdb=" O MET 6 277 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N PHE 6 282 " --> pdb=" O ARG 6 278 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N MET 6 283 " --> pdb=" O LEU 6 279 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL 6 287 " --> pdb=" O MET 6 283 " (cutoff:3.500A) Processing helix chain '6' and resid 295 through 302 removed outlier: 3.936A pdb=" N GLN 6 299 " --> pdb=" O ASP 6 295 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN 6 302 " --> pdb=" O GLN 6 298 " (cutoff:3.500A) Processing helix chain '6' and resid 306 through 319 removed outlier: 4.596A pdb=" N ALA 6 310 " --> pdb=" O ASP 6 306 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE 6 313 " --> pdb=" O GLU 6 309 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR 6 318 " --> pdb=" O ASP 6 314 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LYS 6 319 " --> pdb=" O ALA 6 315 " (cutoff:3.500A) Processing helix chain '6' and resid 340 through 348 removed outlier: 4.813A pdb=" N LYS 6 344 " --> pdb=" O ARG 6 340 " (cutoff:3.500A) Processing helix chain '6' and resid 349 through 357 removed outlier: 3.724A pdb=" N ALA 6 356 " --> pdb=" O ASP 6 352 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TRP 6 357 " --> pdb=" O THR 6 353 " (cutoff:3.500A) Processing helix chain '6' and resid 110 through 115 removed outlier: 6.488A pdb=" N LYS 6 115 " --> pdb=" O PHE 6 110 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 110 through 115' Processing helix chain '8' and resid 42 through 55 removed outlier: 3.628A pdb=" N LYS 8 51 " --> pdb=" O LEU 8 47 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N HIS 8 52 " --> pdb=" O LYS 8 48 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN 8 54 " --> pdb=" O ILE 8 50 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU 8 55 " --> pdb=" O LYS 8 51 " (cutoff:3.500A) Processing helix chain '8' and resid 97 through 108 removed outlier: 3.951A pdb=" N MET 8 101 " --> pdb=" O VAL 8 97 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG 8 108 " --> pdb=" O MET 8 104 " (cutoff:3.500A) Processing helix chain '8' and resid 130 through 144 removed outlier: 3.859A pdb=" N LEU 8 134 " --> pdb=" O THR 8 130 " (cutoff:3.500A) Processing helix chain '8' and resid 154 through 159 removed outlier: 5.093A pdb=" N ALA 8 158 " --> pdb=" O PRO 8 154 " (cutoff:3.500A) Processing helix chain '8' and resid 170 through 178 removed outlier: 4.014A pdb=" N LYS 8 178 " --> pdb=" O MET 8 174 " (cutoff:3.500A) Processing helix chain '8' and resid 211 through 225 removed outlier: 3.800A pdb=" N VAL 8 224 " --> pdb=" O LYS 8 220 " (cutoff:3.500A) Processing helix chain '8' and resid 228 through 239 Processing helix chain '8' and resid 247 through 285 removed outlier: 3.865A pdb=" N GLN 8 278 " --> pdb=" O LYS 8 274 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLN 8 279 " --> pdb=" O HIS 8 275 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG 8 281 " --> pdb=" O TYR 8 277 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLN 8 282 " --> pdb=" O GLN 8 278 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLN 8 283 " --> pdb=" O GLN 8 279 " (cutoff:3.500A) Processing helix chain '8' and resid 315 through 351 removed outlier: 3.755A pdb=" N ASN 8 351 " --> pdb=" O LEU 8 347 " (cutoff:3.500A) Processing helix chain '8' and resid 186 through 192 removed outlier: 3.549A pdb=" N ILE 8 192 " --> pdb=" O LEU 8 187 " (cutoff:3.500A) Processing helix chain '8' and resid 298 through 303 removed outlier: 3.811A pdb=" N LYS 8 303 " --> pdb=" O GLU 8 298 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 298 through 303' Processing helix chain '9' and resid 2 through 23 Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 57 through 68 removed outlier: 4.085A pdb=" N ARG C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 removed outlier: 4.454A pdb=" N LYS C 120 " --> pdb=" O PRO C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.659A pdb=" N ILE C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N PHE C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 247 through 257 removed outlier: 4.531A pdb=" N ALA C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 36 Processing helix chain 'D' and resid 39 through 64 removed outlier: 3.891A pdb=" N VAL D 43 " --> pdb=" O ASN D 39 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 85 Processing helix chain 'D' and resid 93 through 100 removed outlier: 4.047A pdb=" N ILE D 97 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU D 100 " --> pdb=" O TYR D 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 100' Processing helix chain 'D' and resid 101 through 109 removed outlier: 3.636A pdb=" N PHE D 105 " --> pdb=" O LYS D 101 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG D 109 " --> pdb=" O PHE D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 118 Processing helix chain 'D' and resid 122 through 133 Processing helix chain 'D' and resid 150 through 157 removed outlier: 4.029A pdb=" N LYS D 155 " --> pdb=" O LEU D 151 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 178 Processing helix chain 'E' and resid 9 through 25 removed outlier: 3.923A pdb=" N TRP E 22 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N HIS E 23 " --> pdb=" O ASP E 19 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASP E 24 " --> pdb=" O GLN E 20 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LYS E 25 " --> pdb=" O LYS E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 32 Processing helix chain 'E' and resid 33 through 39 Processing helix chain 'E' and resid 89 through 95 removed outlier: 4.172A pdb=" N PHE E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE E 94 " --> pdb=" O CYS E 90 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLU E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 89 through 95' Processing helix chain 'E' and resid 129 through 136 Processing helix chain 'F' and resid 84 through 90 Processing helix chain 'F' and resid 104 through 116 Processing helix chain 'G' and resid 17 through 34 removed outlier: 3.857A pdb=" N GLN G 25 " --> pdb=" O SER G 21 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N SER G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 41 removed outlier: 4.213A pdb=" N GLN G 39 " --> pdb=" O ASP G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 77 removed outlier: 4.832A pdb=" N LYS G 70 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N SER G 71 " --> pdb=" O PRO G 67 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE G 75 " --> pdb=" O SER G 71 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL G 77 " --> pdb=" O GLN G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 88 removed outlier: 4.787A pdb=" N SER G 88 " --> pdb=" O GLU G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 135 removed outlier: 3.836A pdb=" N VAL G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE G 135 " --> pdb=" O GLU G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 164 removed outlier: 4.393A pdb=" N GLN G 163 " --> pdb=" O ASP G 159 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASN G 164 " --> pdb=" O LYS G 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 159 through 164' Processing helix chain 'G' and resid 169 through 181 Processing helix chain 'H' and resid 11 through 19 removed outlier: 5.645A pdb=" N HIS H 19 " --> pdb=" O GLU H 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 44 removed outlier: 3.697A pdb=" N LYS I 34 " --> pdb=" O SER I 30 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 57 Processing helix chain 'I' and resid 62 through 68 Processing helix chain 'I' and resid 70 through 79 Processing helix chain 'I' and resid 85 through 106 Processing helix chain 'I' and resid 108 through 133 removed outlier: 3.991A pdb=" N LYS I 112 " --> pdb=" O ASP I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 151 removed outlier: 3.652A pdb=" N LEU I 149 " --> pdb=" O THR I 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 21 Processing helix chain 'J' and resid 31 through 45 removed outlier: 3.719A pdb=" N HIS J 44 " --> pdb=" O VAL J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 94 removed outlier: 3.523A pdb=" N LEU J 86 " --> pdb=" O GLN J 82 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU J 87 " --> pdb=" O LEU J 83 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LYS J 88 " --> pdb=" O LYS J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 120 Processing helix chain 'K' and resid 56 through 63 Processing helix chain 'K' and resid 64 through 77 removed outlier: 3.570A pdb=" N SER K 68 " --> pdb=" O GLU K 64 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 73 Processing helix chain 'L' and resid 77 through 85 removed outlier: 3.534A pdb=" N ILE L 81 " --> pdb=" O SER L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 98 removed outlier: 4.599A pdb=" N ILE L 94 " --> pdb=" O GLU L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 162 Processing helix chain 'L' and resid 207 through 218 Processing helix chain 'L' and resid 232 through 250 removed outlier: 4.966A pdb=" N TYR L 248 " --> pdb=" O ILE L 244 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER L 249 " --> pdb=" O SER L 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 257 removed outlier: 3.552A pdb=" N TRP L 256 " --> pdb=" O THR L 252 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LYS L 257 " --> pdb=" O PRO L 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 252 through 257' Processing helix chain 'L' and resid 264 through 270 Processing helix chain 'L' and resid 271 through 276 Processing helix chain 'M' and resid 8 through 20 removed outlier: 4.193A pdb=" N TYR M 20 " --> pdb=" O ILE M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 39 Processing helix chain 'M' and resid 43 through 64 removed outlier: 3.680A pdb=" N GLY M 64 " --> pdb=" O ARG M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 84 Processing helix chain 'M' and resid 99 through 110 removed outlier: 3.721A pdb=" N GLU M 104 " --> pdb=" O PRO M 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 10 removed outlier: 6.422A pdb=" N GLN N 9 " --> pdb=" O LEU N 5 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET N 10 " --> pdb=" O ASP N 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 5 through 10' Processing helix chain 'N' and resid 11 through 22 Processing helix chain 'N' and resid 31 through 39 removed outlier: 4.214A pdb=" N GLU N 35 " --> pdb=" O ASP N 31 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLN N 36 " --> pdb=" O PHE N 32 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N TYR N 37 " --> pdb=" O GLN N 33 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE N 38 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N TYR N 39 " --> pdb=" O GLU N 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 31 through 39' Processing helix chain 'N' and resid 50 through 69 removed outlier: 5.609A pdb=" N GLU N 69 " --> pdb=" O ILE N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 95 removed outlier: 4.259A pdb=" N ARG N 85 " --> pdb=" O ASN N 81 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ALA N 86 " --> pdb=" O THR N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 131 removed outlier: 3.522A pdb=" N HIS N 131 " --> pdb=" O PRO N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 132 through 141 removed outlier: 3.927A pdb=" N TYR N 139 " --> pdb=" O THR N 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 187 Processing helix chain 'N' and resid 198 through 204 removed outlier: 4.480A pdb=" N TYR N 202 " --> pdb=" O MET N 198 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE N 203 " --> pdb=" O PRO N 199 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TYR N 204 " --> pdb=" O ASP N 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 198 through 204' Processing helix chain 'N' and resid 70 through 75 removed outlier: 3.763A pdb=" N VAL N 74 " --> pdb=" O PRO N 71 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER N 75 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 29 removed outlier: 3.525A pdb=" N LYS O 28 " --> pdb=" O PRO O 24 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ASP O 29 " --> pdb=" O PHE O 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 24 through 29' Processing helix chain 'O' and resid 57 through 64 removed outlier: 4.690A pdb=" N GLY O 61 " --> pdb=" O ILE O 57 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU O 62 " --> pdb=" O ALA O 58 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLY O 64 " --> pdb=" O ASP O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 76 removed outlier: 3.733A pdb=" N LEU O 74 " --> pdb=" O SER O 70 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN O 76 " --> pdb=" O ALA O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 115 removed outlier: 5.573A pdb=" N LYS O 115 " --> pdb=" O CYS O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 157 through 179 removed outlier: 3.912A pdb=" N ARG O 162 " --> pdb=" O HIS O 158 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS O 166 " --> pdb=" O ARG O 162 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR O 173 " --> pdb=" O MET O 169 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL O 176 " --> pdb=" O MET O 172 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N THR O 178 " --> pdb=" O ARG O 174 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN O 179 " --> pdb=" O GLU O 175 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 191 Proline residue: O 190 - end of helix Processing helix chain 'O' and resid 192 through 203 removed outlier: 3.573A pdb=" N LYS O 199 " --> pdb=" O LYS O 195 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN O 202 " --> pdb=" O GLU O 198 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N SER O 203 " --> pdb=" O LYS O 199 " (cutoff:3.500A) Processing helix chain 'O' and resid 224 through 233 removed outlier: 3.701A pdb=" N LEU O 228 " --> pdb=" O GLU O 224 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET O 229 " --> pdb=" O LEU O 225 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY O 233 " --> pdb=" O MET O 229 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 62 removed outlier: 3.619A pdb=" N LYS P 61 " --> pdb=" O THR P 57 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL P 62 " --> pdb=" O GLY P 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 57 through 62' Processing helix chain 'P' and resid 65 through 71 removed outlier: 4.815A pdb=" N SER P 69 " --> pdb=" O ASP P 65 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SER P 70 " --> pdb=" O ARG P 66 " (cutoff:3.500A) Proline residue: P 71 - end of helix No H-bonds generated for 'chain 'P' and resid 65 through 71' Processing helix chain 'P' and resid 72 through 89 Processing helix chain 'P' and resid 111 through 123 Processing helix chain 'Q' and resid 31 through 36 removed outlier: 5.788A pdb=" N ILE Q 36 " --> pdb=" O LYS Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 57 removed outlier: 4.404A pdb=" N ARG Q 51 " --> pdb=" O ALA Q 47 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASP Q 52 " --> pdb=" O ALA Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 82 Processing helix chain 'R' and resid 87 through 94 removed outlier: 4.120A pdb=" N VAL R 91 " --> pdb=" O ASN R 87 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG R 92 " --> pdb=" O ASN R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 117 Processing helix chain 'R' and resid 133 through 138 Processing helix chain 'R' and resid 145 through 157 removed outlier: 4.292A pdb=" N TYR R 149 " --> pdb=" O ILE R 145 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS R 157 " --> pdb=" O LYS R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 169 Processing helix chain 'R' and resid 192 through 206 Processing helix chain 'S' and resid 20 through 29 removed outlier: 5.127A pdb=" N THR S 26 " --> pdb=" O ARG S 22 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N PHE S 27 " --> pdb=" O LYS S 23 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU S 29 " --> pdb=" O ARG S 25 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 146 Processing helix chain 'S' and resid 152 through 157 removed outlier: 4.188A pdb=" N TYR S 156 " --> pdb=" O ASP S 152 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 226 Processing helix chain 'T' and resid 36 through 49 Processing helix chain 'T' and resid 51 through 56 removed outlier: 4.124A pdb=" N ILE T 55 " --> pdb=" O THR T 51 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N PHE T 56 " --> pdb=" O PRO T 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 51 through 56' Processing helix chain 'T' and resid 78 through 86 removed outlier: 3.553A pdb=" N LYS T 84 " --> pdb=" O ASP T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 95 Processing helix chain 'T' and resid 103 through 118 removed outlier: 3.676A pdb=" N LYS T 116 " --> pdb=" O ASN T 112 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL T 117 " --> pdb=" O ARG T 113 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ARG T 118 " --> pdb=" O MET T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 119 through 128 removed outlier: 4.945A pdb=" N ALA T 123 " --> pdb=" O GLY T 119 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASN T 124 " --> pdb=" O THR T 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 32 through 39 removed outlier: 3.630A pdb=" N GLN V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP V 37 " --> pdb=" O ILE V 33 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR V 38 " --> pdb=" O SER V 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 61 through 67 removed outlier: 4.491A pdb=" N GLN V 65 " --> pdb=" O PHE V 61 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS V 66 " --> pdb=" O ARG V 62 " (cutoff:3.500A) Proline residue: V 67 - end of helix No H-bonds generated for 'chain 'V' and resid 61 through 67' Processing helix chain 'V' and resid 68 through 77 removed outlier: 3.867A pdb=" N MET V 77 " --> pdb=" O THR V 73 " (cutoff:3.500A) Processing helix chain 'V' and resid 85 through 104 Processing helix chain 'V' and resid 107 through 120 Processing helix chain 'V' and resid 142 through 163 Processing helix chain 'V' and resid 168 through 183 Processing helix chain 'V' and resid 187 through 204 Processing helix chain 'Y' and resid 44 through 59 removed outlier: 3.774A pdb=" N GLN Y 48 " --> pdb=" O PRO Y 44 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N TYR Y 49 " --> pdb=" O ARG Y 45 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LYS Y 50 " --> pdb=" O THR Y 46 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU Y 51 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) Proline residue: Y 54 - end of helix Processing helix chain 'Y' and resid 60 through 65 removed outlier: 4.239A pdb=" N GLY Y 65 " --> pdb=" O GLU Y 61 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 99 Processing helix chain 'Y' and resid 101 through 116 removed outlier: 3.900A pdb=" N LYS Y 105 " --> pdb=" O ASP Y 101 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU Y 107 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) Processing helix chain 'Y' and resid 117 through 122 removed outlier: 5.534A pdb=" N ALA Y 122 " --> pdb=" O ARG Y 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 117 through 122' Processing helix chain 'Z' and resid 6 through 29 Processing helix chain 'Z' and resid 54 through 60 Processing helix chain 'Z' and resid 63 through 78 Processing helix chain 'Z' and resid 97 through 112 removed outlier: 4.701A pdb=" N GLY Z 112 " --> pdb=" O LYS Z 108 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 130 Processing helix chain 'Z' and resid 161 through 168 removed outlier: 4.410A pdb=" N ASN Z 165 " --> pdb=" O GLY Z 161 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR Z 166 " --> pdb=" O ASP Z 162 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 19 Processing helix chain 'a' and resid 41 through 56 Processing helix chain 'a' and resid 72 through 84 Processing helix chain 'a' and resid 91 through 96 removed outlier: 4.623A pdb=" N ARG a 95 " --> pdb=" O PRO a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 33 through 38 removed outlier: 4.468A pdb=" N ASP a 37 " --> pdb=" O GLU a 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 21 through 28 Processing helix chain 'b' and resid 29 through 38 removed outlier: 5.136A pdb=" N SER b 38 " --> pdb=" O MET b 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 39 through 48 removed outlier: 4.613A pdb=" N GLY b 48 " --> pdb=" O ARG b 44 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 67 Processing helix chain 'b' and resid 115 through 121 removed outlier: 4.211A pdb=" N PHE b 119 " --> pdb=" O TYR b 115 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER b 120 " --> pdb=" O LEU b 116 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE b 121 " --> pdb=" O GLY b 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 115 through 121' Processing helix chain 'd' and resid 10 through 26 removed outlier: 4.873A pdb=" N GLY d 26 " --> pdb=" O LEU d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 67 removed outlier: 4.336A pdb=" N ARG d 67 " --> pdb=" O HIS d 63 " (cutoff:3.500A) Processing helix chain 'd' and resid 71 through 80 Processing helix chain 'd' and resid 96 through 111 removed outlier: 3.523A pdb=" N ALA d 100 " --> pdb=" O SER d 96 " (cutoff:3.500A) Processing helix chain 'd' and resid 124 through 144 removed outlier: 3.551A pdb=" N LYS d 143 " --> pdb=" O ALA d 139 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS d 144 " --> pdb=" O ALA d 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 31 through 36 removed outlier: 4.091A pdb=" N ASP d 35 " --> pdb=" O GLU d 32 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 65 removed outlier: 3.538A pdb=" N VAL e 62 " --> pdb=" O LEU e 58 " (cutoff:3.500A) Proline residue: e 63 - end of helix Processing helix chain 'e' and resid 69 through 78 removed outlier: 3.789A pdb=" N LYS e 78 " --> pdb=" O SER e 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 80 through 95 Processing helix chain 'f' and resid 25 through 33 removed outlier: 3.888A pdb=" N THR f 31 " --> pdb=" O ALA f 27 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA f 32 " --> pdb=" O PHE f 28 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ILE f 33 " --> pdb=" O ALA f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 49 removed outlier: 4.170A pdb=" N ASP f 49 " --> pdb=" O LEU f 45 " (cutoff:3.500A) Processing helix chain 'f' and resid 55 through 60 removed outlier: 3.606A pdb=" N LEU f 59 " --> pdb=" O ARG f 55 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N THR f 60 " --> pdb=" O ALA f 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 55 through 60' Processing helix chain 'f' and resid 61 through 74 Proline residue: f 74 - end of helix Processing helix chain 'f' and resid 100 through 118 Processing helix chain 'f' and resid 119 through 128 Processing helix chain 'f' and resid 140 through 145 removed outlier: 3.501A pdb=" N ARG f 144 " --> pdb=" O GLY f 140 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N THR f 145 " --> pdb=" O ARG f 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 140 through 145' Processing helix chain 'h' and resid 28 through 47 Processing helix chain 'h' and resid 94 through 104 removed outlier: 3.507A pdb=" N VAL h 98 " --> pdb=" O PRO h 94 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE h 104 " --> pdb=" O GLN h 100 " (cutoff:3.500A) Processing helix chain 'i' and resid 15 through 20 removed outlier: 3.824A pdb=" N ARG i 19 " --> pdb=" O GLY i 15 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER i 20 " --> pdb=" O GLN i 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 15 through 20' Processing helix chain 'i' and resid 39 through 47 removed outlier: 3.592A pdb=" N GLN i 45 " --> pdb=" O GLN i 41 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 29 Processing helix chain 'm' and resid 34 through 45 removed outlier: 4.166A pdb=" N ALA m 38 " --> pdb=" O GLY m 34 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG m 45 " --> pdb=" O ALA m 41 " (cutoff:3.500A) Processing helix chain 'm' and resid 58 through 73 removed outlier: 3.964A pdb=" N VAL m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS m 72 " --> pdb=" O LEU m 68 " (cutoff:3.500A) Processing helix chain 'm' and resid 81 through 90 Processing helix chain 'm' and resid 119 through 132 removed outlier: 4.918A pdb=" N VAL m 123 " --> pdb=" O GLN m 119 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE m 124 " --> pdb=" O ALA m 120 " (cutoff:3.500A) Processing helix chain 'o' and resid 251 through 261 removed outlier: 3.623A pdb=" N LEU o 255 " --> pdb=" O ARG o 251 " (cutoff:3.500A) Proline residue: o 261 - end of helix Processing helix chain 'o' and resid 289 through 300 removed outlier: 3.702A pdb=" N ALA o 294 " --> pdb=" O ARG o 290 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA o 298 " --> pdb=" O ALA o 294 " (cutoff:3.500A) Processing helix chain 'q' and resid 62 through 69 removed outlier: 3.999A pdb=" N ARG q 66 " --> pdb=" O ARG q 62 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS q 67 " --> pdb=" O GLY q 63 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS q 68 " --> pdb=" O LYS q 64 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL q 69 " --> pdb=" O LEU q 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 62 through 69' Processing helix chain 'q' and resid 96 through 107 Processing helix chain 'r' and resid 47 through 52 removed outlier: 5.191A pdb=" N SER r 52 " --> pdb=" O LEU r 48 " (cutoff:3.500A) Processing helix chain 'r' and resid 58 through 64 removed outlier: 4.160A pdb=" N ARG r 64 " --> pdb=" O ASN r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 86 through 91 removed outlier: 3.969A pdb=" N VAL r 90 " --> pdb=" O SER r 86 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N SER r 91 " --> pdb=" O LYS r 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 86 through 91' Processing helix chain 'r' and resid 92 through 118 Processing helix chain 'r' and resid 123 through 143 removed outlier: 3.581A pdb=" N LEU r 127 " --> pdb=" O LYS r 123 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TRP r 136 " --> pdb=" O GLN r 132 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL r 137 " --> pdb=" O ARG r 133 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE r 138 " --> pdb=" O THR r 134 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR r 142 " --> pdb=" O PHE r 138 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS r 143 " --> pdb=" O ASP r 139 " (cutoff:3.500A) Processing helix chain 'r' and resid 146 through 159 Processing helix chain 'r' and resid 160 through 167 removed outlier: 3.945A pdb=" N SER r 165 " --> pdb=" O SER r 161 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU r 166 " --> pdb=" O ILE r 162 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ASP r 167 " --> pdb=" O LEU r 163 " (cutoff:3.500A) Processing helix chain 'r' and resid 169 through 185 Processing helix chain 'r' and resid 203 through 214 removed outlier: 4.402A pdb=" N ALA r 207 " --> pdb=" O GLU r 203 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL r 208 " --> pdb=" O GLY r 204 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS r 209 " --> pdb=" O ILE r 205 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA r 211 " --> pdb=" O ALA r 207 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU r 212 " --> pdb=" O VAL r 208 " (cutoff:3.500A) Processing helix chain 'r' and resid 245 through 266 removed outlier: 4.021A pdb=" N SER r 249 " --> pdb=" O THR r 245 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL r 250 " --> pdb=" O GLU r 246 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER r 252 " --> pdb=" O LEU r 248 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN r 253 " --> pdb=" O SER r 249 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL r 257 " --> pdb=" O GLN r 253 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU r 260 " --> pdb=" O ALA r 256 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE r 262 " --> pdb=" O ILE r 258 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU r 263 " --> pdb=" O LYS r 259 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU r 264 " --> pdb=" O GLU r 260 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS r 265 " --> pdb=" O LYS r 261 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG r 266 " --> pdb=" O ILE r 262 " (cutoff:3.500A) Processing helix chain 't' and resid 53 through 63 Processing helix chain 't' and resid 69 through 76 Processing helix chain 't' and resid 141 through 153 removed outlier: 3.703A pdb=" N MET t 145 " --> pdb=" O LEU t 141 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN t 147 " --> pdb=" O ALA t 143 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA t 150 " --> pdb=" O LEU t 146 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL t 151 " --> pdb=" O ASN t 147 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASP t 153 " --> pdb=" O ALA t 149 " (cutoff:3.500A) Processing helix chain 't' and resid 168 through 181 Processing helix chain 't' and resid 191 through 196 removed outlier: 5.076A pdb=" N LYS t 196 " --> pdb=" O ILE t 192 " (cutoff:3.500A) Processing helix chain 't' and resid 197 through 211 Processing helix chain 't' and resid 231 through 243 Processing helix chain 't' and resid 344 through 349 Processing helix chain 'u' and resid 7 through 22 removed outlier: 4.153A pdb=" N ALA u 11 " --> pdb=" O ARG u 7 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU u 12 " --> pdb=" O PRO u 8 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS u 13 " --> pdb=" O GLU u 9 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU u 17 " --> pdb=" O LYS u 13 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU u 19 " --> pdb=" O ALA u 15 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU u 20 " --> pdb=" O ASN u 16 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL u 21 " --> pdb=" O GLU u 17 " (cutoff:3.500A) Processing helix chain 'u' and resid 23 through 37 removed outlier: 3.776A pdb=" N LEU u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER u 37 " --> pdb=" O ASP u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 44 through 62 removed outlier: 4.793A pdb=" N GLU u 48 " --> pdb=" O GLN u 44 " (cutoff:3.500A) Proline residue: u 49 - end of helix removed outlier: 4.895A pdb=" N ARG u 62 " --> pdb=" O CYS u 58 " (cutoff:3.500A) Processing helix chain 'u' and resid 63 through 79 removed outlier: 4.789A pdb=" N ALA u 67 " --> pdb=" O LYS u 63 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN u 79 " --> pdb=" O LYS u 75 " (cutoff:3.500A) Processing helix chain 'u' and resid 82 through 117 removed outlier: 4.204A pdb=" N LEU u 86 " --> pdb=" O ASN u 82 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA u 104 " --> pdb=" O LYS u 100 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU u 106 " --> pdb=" O GLU u 102 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLU u 107 " --> pdb=" O ALA u 103 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASP u 117 " --> pdb=" O LEU u 113 " (cutoff:3.500A) Processing helix chain 'u' and resid 123 through 133 removed outlier: 4.574A pdb=" N LEU u 128 " --> pdb=" O PRO u 124 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU u 129 " --> pdb=" O GLU u 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA u 131 " --> pdb=" O VAL u 127 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL u 132 " --> pdb=" O LEU u 128 " (cutoff:3.500A) Processing helix chain 'u' and resid 136 through 146 removed outlier: 3.811A pdb=" N ARG u 143 " --> pdb=" O ASP u 139 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU u 145 " --> pdb=" O THR u 141 " (cutoff:3.500A) Processing helix chain 'u' and resid 147 through 165 removed outlier: 3.549A pdb=" N LEU u 161 " --> pdb=" O TYR u 157 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU u 164 " --> pdb=" O CYS u 160 " (cutoff:3.500A) Processing helix chain 'u' and resid 170 through 189 removed outlier: 3.504A pdb=" N GLN u 187 " --> pdb=" O LYS u 183 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR u 189 " --> pdb=" O CYS u 185 " (cutoff:3.500A) Processing helix chain 'u' and resid 190 through 211 removed outlier: 3.984A pdb=" N PHE u 194 " --> pdb=" O ARG u 190 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG u 195 " --> pdb=" O LYS u 191 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS u 196 " --> pdb=" O ALA u 192 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU u 205 " --> pdb=" O LEU u 201 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE u 208 " --> pdb=" O HIS u 204 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLN u 209 " --> pdb=" O LEU u 205 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG u 210 " --> pdb=" O SER u 206 " (cutoff:3.500A) Processing helix chain 'u' and resid 222 through 244 removed outlier: 3.522A pdb=" N GLU u 231 " --> pdb=" O SER u 227 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR u 232 " --> pdb=" O MET u 228 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG u 233 " --> pdb=" O HIS u 229 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER u 242 " --> pdb=" O ASP u 238 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET u 243 " --> pdb=" O SER u 239 " (cutoff:3.500A) Processing helix chain 'u' and resid 245 through 262 removed outlier: 3.985A pdb=" N PHE u 250 " --> pdb=" O TRP u 246 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER u 261 " --> pdb=" O HIS u 257 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU u 262 " --> pdb=" O GLY u 258 " (cutoff:3.500A) Processing helix chain 'u' and resid 268 through 287 removed outlier: 3.531A pdb=" N MET u 272 " --> pdb=" O LYS u 268 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ALA u 273 " --> pdb=" O PRO u 269 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN u 274 " --> pdb=" O GLN u 270 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN u 277 " --> pdb=" O ALA u 273 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SER u 280 " --> pdb=" O TYR u 276 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TRP u 284 " --> pdb=" O SER u 280 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS u 285 " --> pdb=" O THR u 281 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY u 287 " --> pdb=" O PHE u 283 " (cutoff:3.500A) Processing helix chain 'u' and resid 288 through 307 removed outlier: 4.052A pdb=" N HIS u 292 " --> pdb=" O ASN u 288 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU u 305 " --> pdb=" O HIS u 301 " (cutoff:3.500A) Processing helix chain 'u' and resid 311 through 329 removed outlier: 3.749A pdb=" N SER u 328 " --> pdb=" O LEU u 324 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE u 329 " --> pdb=" O ALA u 325 " (cutoff:3.500A) Processing helix chain 'u' and resid 338 through 345 removed outlier: 5.092A pdb=" N MET u 344 " --> pdb=" O ARG u 340 " (cutoff:3.500A) Processing helix chain 'u' and resid 350 through 360 removed outlier: 4.523A pdb=" N ARG u 354 " --> pdb=" O GLU u 350 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU u 359 " --> pdb=" O LEU u 355 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLY u 360 " --> pdb=" O ALA u 356 " (cutoff:3.500A) Processing helix chain 'u' and resid 369 through 377 removed outlier: 4.299A pdb=" N ASP u 373 " --> pdb=" O GLY u 369 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET u 374 " --> pdb=" O LEU u 370 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE u 377 " --> pdb=" O ASP u 373 " (cutoff:3.500A) Processing helix chain 'u' and resid 378 through 384 removed outlier: 4.377A pdb=" N TYR u 382 " --> pdb=" O ASN u 378 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL u 384 " --> pdb=" O LEU u 380 " (cutoff:3.500A) Processing helix chain 'u' and resid 389 through 395 removed outlier: 3.502A pdb=" N TRP u 393 " --> pdb=" O ASP u 389 " (cutoff:3.500A) Processing helix chain 'u' and resid 402 through 417 removed outlier: 4.401A pdb=" N VAL u 410 " --> pdb=" O ARG u 406 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN u 417 " --> pdb=" O TRP u 413 " (cutoff:3.500A) Processing helix chain 'u' and resid 421 through 447 removed outlier: 4.139A pdb=" N GLN u 425 " --> pdb=" O GLU u 421 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN u 426 " --> pdb=" O PRO u 422 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TYR u 427 " --> pdb=" O GLU u 423 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL u 428 " --> pdb=" O LEU u 424 " (cutoff:3.500A) Proline residue: u 429 - end of helix removed outlier: 4.383A pdb=" N GLN u 445 " --> pdb=" O GLN u 441 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE u 446 " --> pdb=" O GLN u 442 " (cutoff:3.500A) Processing helix chain 'u' and resid 451 through 460 removed outlier: 3.666A pdb=" N LEU u 455 " --> pdb=" O GLU u 451 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER u 457 " --> pdb=" O SER u 453 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL u 459 " --> pdb=" O LEU u 455 " (cutoff:3.500A) Proline residue: u 460 - end of helix Processing helix chain 'u' and resid 463 through 478 removed outlier: 4.561A pdb=" N HIS u 477 " --> pdb=" O ASP u 473 " (cutoff:3.500A) Processing helix chain 'u' and resid 516 through 526 removed outlier: 5.877A pdb=" N ARG u 520 " --> pdb=" O SER u 516 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASN u 521 " --> pdb=" O GLU u 517 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN u 522 " --> pdb=" O GLN u 518 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA u 525 " --> pdb=" O ASN u 521 " (cutoff:3.500A) Processing helix chain 'u' and resid 527 through 540 removed outlier: 4.106A pdb=" N ILE u 537 " --> pdb=" O ALA u 533 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS u 538 " --> pdb=" O LEU u 534 " (cutoff:3.500A) Proline residue: u 539 - end of helix Processing helix chain 'u' and resid 541 through 563 removed outlier: 3.679A pdb=" N GLU u 545 " --> pdb=" O HIS u 541 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS u 546 " --> pdb=" O ILE u 542 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS u 550 " --> pdb=" O LYS u 546 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS u 563 " --> pdb=" O LYS u 559 " (cutoff:3.500A) Processing helix chain 'u' and resid 569 through 574 removed outlier: 4.177A pdb=" N GLN u 573 " --> pdb=" O LEU u 569 " (cutoff:3.500A) Processing helix chain 'u' and resid 580 through 640 removed outlier: 3.556A pdb=" N GLU u 610 " --> pdb=" O LYS u 606 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG u 611 " --> pdb=" O ALA u 607 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU u 640 " --> pdb=" O VAL u 636 " (cutoff:3.500A) Processing helix chain 'u' and resid 652 through 696 removed outlier: 6.036A pdb=" N ILE u 656 " --> pdb=" O ALA u 652 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP u 657 " --> pdb=" O PHE u 653 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU u 659 " --> pdb=" O ASP u 655 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP u 660 " --> pdb=" O ILE u 656 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU u 661 " --> pdb=" O ASP u 657 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU u 662 " --> pdb=" O ILE u 658 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU u 663 " --> pdb=" O GLU u 659 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU u 664 " --> pdb=" O ASP u 660 " (cutoff:3.500A) Proline residue: u 666 - end of helix removed outlier: 3.553A pdb=" N LYS u 682 " --> pdb=" O GLU u 678 " (cutoff:3.500A) Processing helix chain 'v' and resid 48 through 56 removed outlier: 3.579A pdb=" N ASP v 52 " --> pdb=" O THR v 48 " (cutoff:3.500A) Processing helix chain 'v' and resid 61 through 71 removed outlier: 3.769A pdb=" N ASP v 65 " --> pdb=" O LEU v 61 " (cutoff:3.500A) Proline residue: v 67 - end of helix removed outlier: 4.201A pdb=" N ARG v 71 " --> pdb=" O PRO v 67 " (cutoff:3.500A) Processing helix chain 'v' and resid 76 through 85 removed outlier: 3.545A pdb=" N LEU v 84 " --> pdb=" O GLN v 80 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLN v 85 " --> pdb=" O LEU v 81 " (cutoff:3.500A) Processing helix chain 'v' and resid 92 through 113 removed outlier: 4.747A pdb=" N GLU v 96 " --> pdb=" O VAL v 92 " (cutoff:3.500A) Proline residue: v 98 - end of helix removed outlier: 4.179A pdb=" N THR v 107 " --> pdb=" O GLN v 103 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ARG v 108 " --> pdb=" O MET v 104 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASP v 109 " --> pdb=" O GLN v 105 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLY v 110 " --> pdb=" O SER v 106 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG v 111 " --> pdb=" O THR v 107 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET v 112 " --> pdb=" O ARG v 108 " (cutoff:3.500A) Processing helix chain 'v' and resid 128 through 139 removed outlier: 4.208A pdb=" N LYS v 136 " --> pdb=" O TYR v 132 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE v 137 " --> pdb=" O ARG v 133 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR v 139 " --> pdb=" O ALA v 135 " (cutoff:3.500A) Processing helix chain 'v' and resid 146 through 151 Processing helix chain 'v' and resid 164 through 180 removed outlier: 4.411A pdb=" N TRP v 170 " --> pdb=" O LEU v 166 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER v 175 " --> pdb=" O GLY v 171 " (cutoff:3.500A) Processing helix chain 'v' and resid 181 through 197 removed outlier: 3.688A pdb=" N ILE v 196 " --> pdb=" O LEU v 192 " (cutoff:3.500A) Processing helix chain 'v' and resid 203 through 219 removed outlier: 4.915A pdb=" N LEU v 219 " --> pdb=" O ILE v 215 " (cutoff:3.500A) Processing helix chain 'v' and resid 224 through 234 removed outlier: 3.718A pdb=" N GLY v 228 " --> pdb=" O ASN v 224 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ASP v 230 " --> pdb=" O PRO v 226 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ASN v 231 " --> pdb=" O LYS v 227 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE v 232 " --> pdb=" O GLY v 228 " (cutoff:3.500A) Processing helix chain 'v' and resid 236 through 246 Proline residue: v 240 - end of helix removed outlier: 3.716A pdb=" N ILE v 246 " --> pdb=" O TYR v 242 " (cutoff:3.500A) Processing helix chain 'v' and resid 250 through 263 removed outlier: 3.592A pdb=" N ILE v 262 " --> pdb=" O THR v 258 " (cutoff:3.500A) Processing helix chain 'v' and resid 272 through 282 removed outlier: 4.624A pdb=" N ASP v 276 " --> pdb=" O GLN v 272 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL v 278 " --> pdb=" O LEU v 274 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS v 279 " --> pdb=" O LYS v 275 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE v 281 " --> pdb=" O LEU v 277 " (cutoff:3.500A) Processing helix chain 'v' and resid 286 through 291 removed outlier: 3.972A pdb=" N ASP v 290 " --> pdb=" O TYR v 286 " (cutoff:3.500A) Proline residue: v 291 - end of helix No H-bonds generated for 'chain 'v' and resid 286 through 291' Processing helix chain 'v' and resid 292 through 302 removed outlier: 4.525A pdb=" N VAL v 296 " --> pdb=" O ILE v 292 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU v 299 " --> pdb=" O PHE v 295 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TYR v 300 " --> pdb=" O VAL v 296 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL v 301 " --> pdb=" O GLU v 297 " (cutoff:3.500A) Processing helix chain 'v' and resid 305 through 322 removed outlier: 5.758A pdb=" N GLN v 309 " --> pdb=" O PHE v 305 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS v 310 " --> pdb=" O ASP v 306 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LYS v 311 " --> pdb=" O GLY v 307 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU v 312 " --> pdb=" O ALA v 308 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG v 313 " --> pdb=" O GLN v 309 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU v 314 " --> pdb=" O LYS v 310 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER v 317 " --> pdb=" O ARG v 313 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL v 318 " --> pdb=" O GLU v 314 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN v 321 " --> pdb=" O SER v 317 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP v 322 " --> pdb=" O VAL v 318 " (cutoff:3.500A) Processing helix chain 'v' and resid 324 through 348 removed outlier: 5.420A pdb=" N CYS v 328 " --> pdb=" O PHE v 324 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU v 329 " --> pdb=" O LEU v 325 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU v 330 " --> pdb=" O VAL v 326 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASP v 331 " --> pdb=" O ALA v 327 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE v 332 " --> pdb=" O CYS v 328 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE v 341 " --> pdb=" O ARG v 337 " (cutoff:3.500A) Processing helix chain 'v' and resid 352 through 358 removed outlier: 3.606A pdb=" N ALA v 357 " --> pdb=" O ILE v 353 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ASP v 358 " --> pdb=" O ASN v 354 " (cutoff:3.500A) Processing helix chain 'v' and resid 363 through 379 removed outlier: 3.650A pdb=" N GLU v 368 " --> pdb=" O PRO v 364 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG v 369 " --> pdb=" O GLU v 365 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ALA v 378 " --> pdb=" O LEU v 374 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ARG v 379 " --> pdb=" O ILE v 375 " (cutoff:3.500A) Processing helix chain 'v' and resid 402 through 420 removed outlier: 3.923A pdb=" N MET v 420 " --> pdb=" O GLN v 416 " (cutoff:3.500A) Processing helix chain 'v' and resid 37 through 42 removed outlier: 3.933A pdb=" N GLY v 40 " --> pdb=" O LEU v 37 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS v 41 " --> pdb=" O LEU v 38 " (cutoff:3.500A) Processing helix chain 'x' and resid 175 through 182 removed outlier: 3.756A pdb=" N LYS x 181 " --> pdb=" O PRO x 177 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET x 182 " --> pdb=" O GLN x 178 " (cutoff:3.500A) Processing helix chain 'x' and resid 203 through 209 Processing helix chain 'x' and resid 228 through 233 Proline residue: x 233 - end of helix Processing helix chain 'x' and resid 234 through 242 removed outlier: 3.562A pdb=" N LEU x 238 " --> pdb=" O VAL x 234 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LYS x 240 " --> pdb=" O ARG x 236 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N THR x 241 " --> pdb=" O LYS x 237 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN x 242 " --> pdb=" O LEU x 238 " (cutoff:3.500A) Processing helix chain 'x' and resid 250 through 257 removed outlier: 5.343A pdb=" N THR x 254 " --> pdb=" O ALA x 250 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU x 255 " --> pdb=" O ILE x 251 " (cutoff:3.500A) Processing helix chain 'x' and resid 308 through 327 removed outlier: 4.147A pdb=" N SER x 324 " --> pdb=" O ASN x 320 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN x 325 " --> pdb=" O HIS x 321 " (cutoff:3.500A) Processing helix chain 'x' and resid 408 through 413 removed outlier: 3.516A pdb=" N LYS x 412 " --> pdb=" O ASP x 408 " (cutoff:3.500A) Processing helix chain 'x' and resid 416 through 428 removed outlier: 3.580A pdb=" N VAL x 420 " --> pdb=" O GLN x 416 " (cutoff:3.500A) Processing helix chain 'x' and resid 429 through 443 removed outlier: 3.934A pdb=" N CYS x 438 " --> pdb=" O ARG x 434 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY x 443 " --> pdb=" O ALA x 439 " (cutoff:3.500A) Processing helix chain 'x' and resid 472 through 481 removed outlier: 4.191A pdb=" N ASN x 481 " --> pdb=" O ALA x 477 " (cutoff:3.500A) Processing helix chain 'x' and resid 483 through 501 removed outlier: 3.972A pdb=" N LYS x 500 " --> pdb=" O ASP x 496 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU x 501 " --> pdb=" O ILE x 497 " (cutoff:3.500A) Processing helix chain 'y' and resid 51 through 74 Processing helix chain 'y' and resid 75 through 98 removed outlier: 4.803A pdb=" N SER y 95 " --> pdb=" O GLY y 91 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ILE y 96 " --> pdb=" O LYS y 92 " (cutoff:3.500A) Processing helix chain 'y' and resid 103 through 122 removed outlier: 4.838A pdb=" N GLU y 122 " --> pdb=" O ASN y 118 " (cutoff:3.500A) Processing helix chain 'y' and resid 123 through 128 Processing helix chain 'y' and resid 133 through 149 Processing helix chain 'y' and resid 152 through 160 Processing helix chain 'y' and resid 327 through 341 removed outlier: 4.246A pdb=" N LYS y 331 " --> pdb=" O ALA y 327 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA y 339 " --> pdb=" O GLU y 335 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG y 340 " --> pdb=" O ILE y 336 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY y 341 " --> pdb=" O LEU y 337 " (cutoff:3.500A) Processing helix chain 'y' and resid 346 through 365 removed outlier: 3.666A pdb=" N ILE y 351 " --> pdb=" O ARG y 347 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU y 352 " --> pdb=" O ALA y 348 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN y 365 " --> pdb=" O ALA y 361 " (cutoff:3.500A) Processing helix chain 'y' and resid 367 through 386 removed outlier: 4.092A pdb=" N ILE y 371 " --> pdb=" O GLY y 367 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE y 379 " --> pdb=" O LYS y 375 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASN y 386 " --> pdb=" O LEU y 382 " (cutoff:3.500A) Processing helix chain 'y' and resid 394 through 416 Proline residue: y 416 - end of helix Processing helix chain 'y' and resid 443 through 463 removed outlier: 6.405A pdb=" N ASP y 463 " --> pdb=" O MET y 459 " (cutoff:3.500A) Processing helix chain 'y' and resid 466 through 493 removed outlier: 4.063A pdb=" N VAL y 470 " --> pdb=" O SER y 466 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASP y 475 " --> pdb=" O GLU y 471 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLU y 476 " --> pdb=" O HIS y 472 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ALA y 477 " --> pdb=" O LEU y 473 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLN y 478 " --> pdb=" O LYS y 474 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL y 479 " --> pdb=" O ASP y 475 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU y 491 " --> pdb=" O GLN y 487 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU y 492 " --> pdb=" O ARG y 488 " (cutoff:3.500A) Processing helix chain 'y' and resid 496 through 511 removed outlier: 3.584A pdb=" N CYS y 500 " --> pdb=" O THR y 496 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ARG y 501 " --> pdb=" O GLU y 497 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS y 509 " --> pdb=" O LEU y 505 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR y 510 " --> pdb=" O ARG y 506 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR y 511 " --> pdb=" O ILE y 507 " (cutoff:3.500A) Processing helix chain 'y' and resid 515 through 522 removed outlier: 4.272A pdb=" N HIS y 519 " --> pdb=" O ASP y 515 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ARG y 521 " --> pdb=" O LYS y 517 " (cutoff:3.500A) Processing helix chain 'y' and resid 543 through 558 removed outlier: 3.513A pdb=" N LEU y 547 " --> pdb=" O ASP y 543 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET y 548 " --> pdb=" O SER y 544 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU y 549 " --> pdb=" O ALA y 545 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE y 555 " --> pdb=" O LEU y 551 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA y 557 " --> pdb=" O LYS y 553 " (cutoff:3.500A) Processing helix chain 'y' and resid 561 through 580 removed outlier: 4.243A pdb=" N ARG y 565 " --> pdb=" O THR y 561 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR y 566 " --> pdb=" O ASP y 562 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS y 579 " --> pdb=" O HIS y 575 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER y 580 " --> pdb=" O HIS y 576 " (cutoff:3.500A) Processing helix chain 'y' and resid 581 through 593 removed outlier: 4.091A pdb=" N ALA y 585 " --> pdb=" O ARG y 581 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP y 587 " --> pdb=" O TYR y 583 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU y 588 " --> pdb=" O GLN y 584 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER y 592 " --> pdb=" O LEU y 588 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N HIS y 593 " --> pdb=" O MET y 589 " (cutoff:3.500A) Processing helix chain 'y' and resid 594 through 602 removed outlier: 5.703A pdb=" N GLN y 599 " --> pdb=" O GLN y 595 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N HIS y 600 " --> pdb=" O ASP y 596 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA y 601 " --> pdb=" O ASN y 597 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ASP y 602 " --> pdb=" O ILE y 598 " (cutoff:3.500A) Processing helix chain 'y' and resid 603 through 624 removed outlier: 4.515A pdb=" N LEU y 608 " --> pdb=" O PRO y 604 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY y 624 " --> pdb=" O ALA y 620 " (cutoff:3.500A) Processing helix chain 'y' and resid 625 through 640 removed outlier: 4.559A pdb=" N ALA y 629 " --> pdb=" O LEU y 625 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASP y 635 " --> pdb=" O ASN y 631 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE y 636 " --> pdb=" O ALA y 632 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER y 639 " --> pdb=" O ASP y 635 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY y 640 " --> pdb=" O ILE y 636 " (cutoff:3.500A) Processing helix chain 'y' and resid 641 through 647 removed outlier: 4.047A pdb=" N GLY y 647 " --> pdb=" O LYS y 643 " (cutoff:3.500A) Processing helix chain 'y' and resid 650 through 655 removed outlier: 7.181A pdb=" N SER y 654 " --> pdb=" O LEU y 650 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU y 655 " --> pdb=" O LEU y 651 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 650 through 655' Processing helix chain 'y' and resid 660 through 669 removed outlier: 5.049A pdb=" N ARG y 669 " --> pdb=" O VAL y 665 " (cutoff:3.500A) Processing helix chain 'y' and resid 678 through 700 Proline residue: y 696 - end of helix Processing helix chain 'y' and resid 711 through 724 removed outlier: 4.169A pdb=" N HIS y 715 " --> pdb=" O SER y 711 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN y 724 " --> pdb=" O VAL y 720 " (cutoff:3.500A) Processing helix chain 'y' and resid 732 through 747 removed outlier: 3.596A pdb=" N LYS y 745 " --> pdb=" O SER y 741 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET y 746 " --> pdb=" O LYS y 742 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY y 747 " --> pdb=" O ALA y 743 " (cutoff:3.500A) Processing helix chain 'y' and resid 748 through 758 removed outlier: 4.984A pdb=" N CYS y 752 " --> pdb=" O ASP y 748 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN y 758 " --> pdb=" O SER y 754 " (cutoff:3.500A) Processing helix chain 'y' and resid 759 through 765 Processing helix chain 'y' and resid 771 through 800 removed outlier: 4.444A pdb=" N VAL y 775 " --> pdb=" O GLU y 771 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N SER y 797 " --> pdb=" O PHE y 793 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL y 798 " --> pdb=" O THR y 794 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASP y 800 " --> pdb=" O SER y 796 " (cutoff:3.500A) Processing helix chain 'y' and resid 803 through 811 removed outlier: 3.829A pdb=" N LEU y 807 " --> pdb=" O SER y 803 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER y 808 " --> pdb=" O MET y 804 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP y 809 " --> pdb=" O GLU y 805 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE y 811 " --> pdb=" O LEU y 807 " (cutoff:3.500A) Processing helix chain 'y' and resid 814 through 829 removed outlier: 3.613A pdb=" N MET y 825 " --> pdb=" O ILE y 821 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE y 826 " --> pdb=" O ILE y 822 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE y 827 " --> pdb=" O SER y 823 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASN y 828 " --> pdb=" O LYS y 824 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU y 829 " --> pdb=" O MET y 825 " (cutoff:3.500A) Processing helix chain 'y' and resid 851 through 862 removed outlier: 3.629A pdb=" N GLU y 861 " --> pdb=" O LEU y 857 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LYS y 862 " --> pdb=" O GLN y 858 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '1' and resid 315 through 319 Processing sheet with id= 2, first strand: chain '1' and resid 340 through 343 removed outlier: 5.504A pdb=" N TYR 1 348 " --> pdb=" O SER 1 343 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '1' and resid 377 through 382 removed outlier: 5.641A pdb=" N TYR 1 387 " --> pdb=" O SER 1 382 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ARG 1 386 " --> pdb=" O ILE 1 409 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE 1 406 " --> pdb=" O LYS 1 415 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS 1 413 " --> pdb=" O ASP 1 408 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '1' and resid 429 through 432 removed outlier: 5.999A pdb=" N PHE 1 437 " --> pdb=" O SER 1 432 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LYS 1 436 " --> pdb=" O THR 1 451 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE 1 448 " --> pdb=" O LEU 1 457 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY 1 455 " --> pdb=" O GLU 1 450 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '1' and resid 469 through 473 removed outlier: 4.978A pdb=" N ILE 1 478 " --> pdb=" O SER 1 473 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARG 1 505 " --> pdb=" O LEU 1 495 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '1' and resid 513 through 520 removed outlier: 4.204A pdb=" N ASP 1 514 " --> pdb=" O ASP 1 531 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS 1 516 " --> pdb=" O LYS 1 529 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N TYR 1 525 " --> pdb=" O GLN 1 520 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU 1 526 " --> pdb=" O PHE 1 547 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL 1 541 " --> pdb=" O ARG 1 532 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR 1 542 " --> pdb=" O MET 1 561 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '1' and resid 566 through 571 removed outlier: 5.516A pdb=" N LYS 1 576 " --> pdb=" O GLU 1 571 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N SER 1 575 " --> pdb=" O VAL 1 594 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE 1 591 " --> pdb=" O ILE 1 603 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '1' and resid 614 through 617 removed outlier: 3.599A pdb=" N PHE 1 615 " --> pdb=" O VAL 1 624 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N PHE 1 622 " --> pdb=" O SER 1 617 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLN 1 621 " --> pdb=" O THR 1 640 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA 1 636 " --> pdb=" O LEU 1 625 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN 1 647 " --> pdb=" O PHE 1 637 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '1' and resid 655 through 660 removed outlier: 5.496A pdb=" N TYR 1 665 " --> pdb=" O ASP 1 660 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP 1 684 " --> pdb=" O VAL 1 666 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA 1 680 " --> pdb=" O VAL 1 670 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASN 1 679 " --> pdb=" O LYS 1 696 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN 1 692 " --> pdb=" O LEU 1 683 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '1' and resid 588 through 591 Processing sheet with id= 11, first strand: chain '4' and resid 91 through 94 removed outlier: 3.672A pdb=" N VAL 4 129 " --> pdb=" O VAL 4 91 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '4' and resid 133 through 136 removed outlier: 4.134A pdb=" N VAL 4 116 " --> pdb=" O THR 4 175 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR 4 175 " --> pdb=" O VAL 4 116 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE 4 198 " --> pdb=" O LEU 4 170 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL 4 202 " --> pdb=" O ALA 4 174 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '5' and resid 504 through 507 removed outlier: 3.833A pdb=" N SER 5 507 " --> pdb=" O GLU 5 512 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU 5 512 " --> pdb=" O SER 5 507 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '8' and resid 38 through 41 removed outlier: 3.804A pdb=" N ILE 8 78 " --> pdb=" O GLN 8 40 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '8' and resid 65 through 68 removed outlier: 3.738A pdb=" N GLY 8 65 " --> pdb=" O TYR 8 120 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '8' and resid 148 through 153 removed outlier: 4.992A pdb=" N VAL 8 149 " --> pdb=" O TYR 8 167 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP 8 153 " --> pdb=" O SER 8 163 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER 8 163 " --> pdb=" O ASP 8 153 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'B' and resid 71 through 76 removed outlier: 5.781A pdb=" N ARG B 71 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR B 127 " --> pdb=" O LEU B 143 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 85 through 97 removed outlier: 6.273A pdb=" N THR B 85 " --> pdb=" O HIS B 112 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N HIS B 112 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 87 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N SER B 110 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG B 89 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN B 108 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASP B 91 " --> pdb=" O HIS B 106 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N HIS B 106 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU B 93 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS B 104 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR B 95 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE B 102 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG B 97 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'B' and resid 124 through 127 Processing sheet with id= 20, first strand: chain 'C' and resid 87 through 92 removed outlier: 4.334A pdb=" N ASP C 88 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN C 98 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N HIS C 112 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE C 102 " --> pdb=" O ALA C 110 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA C 110 " --> pdb=" O ILE C 102 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'C' and resid 121 through 127 removed outlier: 4.138A pdb=" N ASP C 158 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP C 171 " --> pdb=" O GLN C 161 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'C' and resid 128 through 132 removed outlier: 3.565A pdb=" N ILE C 136 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG C 145 " --> pdb=" O THR C 141 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'C' and resid 197 through 200 Processing sheet with id= 24, first strand: chain 'E' and resid 46 through 49 removed outlier: 6.361A pdb=" N LEU E 101 " --> pdb=" O VAL E 123 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'E' and resid 53 through 59 removed outlier: 3.577A pdb=" N GLU E 53 " --> pdb=" O ARG E 71 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA E 59 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ALA E 65 " --> pdb=" O ALA E 59 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'G' and resid 47 through 52 removed outlier: 3.922A pdb=" N ALA G 47 " --> pdb=" O PHE G 63 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE G 95 " --> pdb=" O ILE G 62 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'G' and resid 141 through 147 removed outlier: 3.534A pdb=" N LYS G 155 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER G 151 " --> pdb=" O LYS G 147 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASP G 184 " --> pdb=" O ARG G 152 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN G 186 " --> pdb=" O ILE G 154 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'H' and resid 43 through 48 removed outlier: 7.050A pdb=" N TYR H 31 " --> pdb=" O SER H 48 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE H 32 " --> pdb=" O LYS H 82 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'J' and resid 23 through 28 removed outlier: 5.592A pdb=" N ARG J 23 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLU J 49 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'J' and resid 102 through 105 removed outlier: 6.569A pdb=" N VAL J 103 " --> pdb=" O LEU J 126 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'K' and resid 15 through 18 removed outlier: 4.554A pdb=" N ARG K 15 " --> pdb=" O ILE K 24 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG K 22 " --> pdb=" O CYS K 17 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'K' and resid 32 through 38 removed outlier: 4.434A pdb=" N VAL K 36 " --> pdb=" O LYS K 51 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN K 49 " --> pdb=" O GLU K 38 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'L' and resid 103 through 107 removed outlier: 3.525A pdb=" N GLY L 131 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE L 127 " --> pdb=" O LEU L 107 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'L' and resid 182 through 187 removed outlier: 8.131A pdb=" N CYS L 182 " --> pdb=" O PRO L 197 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL L 184 " --> pdb=" O LEU L 195 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ALA L 198 " --> pdb=" O ASP L 221 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASP L 221 " --> pdb=" O ALA L 198 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'L' and resid 124 through 131 removed outlier: 4.298A pdb=" N GLY L 138 " --> pdb=" O ILE L 130 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'M' and resid 95 through 98 removed outlier: 3.520A pdb=" N ILE M 96 " --> pdb=" O ASN M 116 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'N' and resid 121 through 125 removed outlier: 3.528A pdb=" N ILE N 161 " --> pdb=" O ALA N 146 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'O' and resid 45 through 48 removed outlier: 3.910A pdb=" N GLY O 45 " --> pdb=" O VAL O 33 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N THR O 98 " --> pdb=" O LYS O 34 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR O 88 " --> pdb=" O ARG O 65 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ARG O 65 " --> pdb=" O THR O 88 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'O' and resid 119 through 128 removed outlier: 5.392A pdb=" N THR O 119 " --> pdb=" O THR O 143 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR O 143 " --> pdb=" O THR O 119 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU O 134 " --> pdb=" O LEU O 218 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS O 214 " --> pdb=" O PHE O 138 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'O' and resid 101 through 105 removed outlier: 8.218A pdb=" N HIS O 101 " --> pdb=" O MET O 217 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N MET O 217 " --> pdb=" O HIS O 101 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL O 215 " --> pdb=" O MET O 103 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N ARG O 213 " --> pdb=" O LEU O 105 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'P' and resid 40 through 46 removed outlier: 5.234A pdb=" N ILE P 95 " --> pdb=" O GLY P 127 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'Q' and resid 37 through 43 Processing sheet with id= 43, first strand: chain 'R' and resid 42 through 48 removed outlier: 6.266A pdb=" N ARG R 42 " --> pdb=" O LEU R 58 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ARG R 56 " --> pdb=" O HIS R 44 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN R 52 " --> pdb=" O VAL R 48 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'R' and resid 72 through 76 removed outlier: 3.589A pdb=" N ASN R 64 " --> pdb=" O ALA R 185 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASP R 186 " --> pdb=" O ALA R 176 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N CYS R 100 " --> pdb=" O ILE R 175 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'S' and resid 13 through 17 removed outlier: 5.773A pdb=" N ASN S 110 " --> pdb=" O SER S 53 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL S 49 " --> pdb=" O VAL S 114 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR S 34 " --> pdb=" O ILE S 52 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'S' and resid 72 through 76 Processing sheet with id= 47, first strand: chain 'T' and resid 5 through 10 removed outlier: 4.030A pdb=" N LEU T 28 " --> pdb=" O THR T 6 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL T 24 " --> pdb=" O LYS T 11 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS T 11 " --> pdb=" O VAL T 24 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'T' and resid 58 through 63 removed outlier: 4.961A pdb=" N GLY T 59 " --> pdb=" O PHE T 72 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N PHE T 72 " --> pdb=" O GLY T 59 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LYS T 68 " --> pdb=" O HIS T 63 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'T' and resid 20 through 29 removed outlier: 4.085A pdb=" N GLY T 67 " --> pdb=" O HIS T 29 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'V' and resid 123 through 128 removed outlier: 5.182A pdb=" N ARG V 135 " --> pdb=" O ILE V 128 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'Y' and resid 9 through 15 removed outlier: 7.288A pdb=" N THR Y 18 " --> pdb=" O GLY Y 75 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY Y 75 " --> pdb=" O THR Y 18 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU Y 31 " --> pdb=" O VAL Y 66 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'Z' and resid 36 through 41 removed outlier: 3.514A pdb=" N GLY Z 36 " --> pdb=" O LEU Z 51 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR Z 87 " --> pdb=" O ILE Z 48 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'Z' and resid 148 through 155 removed outlier: 3.910A pdb=" N GLY Z 133 " --> pdb=" O MET Z 189 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'a' and resid 20 through 24 Processing sheet with id= 55, first strand: chain 'b' and resid 75 through 78 removed outlier: 4.675A pdb=" N SER b 92 " --> pdb=" O ILE b 107 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'c' and resid 3 through 8 removed outlier: 5.070A pdb=" N GLN c 4 " --> pdb=" O THR c 313 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N THR c 313 " --> pdb=" O GLN c 4 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL c 309 " --> pdb=" O ARG c 8 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY c 9 " --> pdb=" O VAL c 309 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'c' and resid 19 through 23 removed outlier: 4.076A pdb=" N GLN c 20 " --> pdb=" O ALA c 34 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP c 29 " --> pdb=" O LEU c 45 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE c 31 " --> pdb=" O TRP c 43 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N MET c 42 " --> pdb=" O GLN c 56 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR c 52 " --> pdb=" O THR c 46 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'c' and resid 67 through 72 removed outlier: 5.849A pdb=" N PHE c 77 " --> pdb=" O SER c 72 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLN c 76 " --> pdb=" O LEU c 92 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU c 89 " --> pdb=" O THR c 98 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'c' and resid 110 through 114 removed outlier: 5.595A pdb=" N GLN c 119 " --> pdb=" O SER c 114 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR c 128 " --> pdb=" O SER c 124 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'c' and resid 152 through 157 removed outlier: 4.036A pdb=" N CYS c 153 " --> pdb=" O CYS c 168 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE c 164 " --> pdb=" O SER c 157 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY c 169 " --> pdb=" O LEU c 173 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU c 173 " --> pdb=" O GLY c 169 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'c' and resid 197 through 201 removed outlier: 3.632A pdb=" N THR c 197 " --> pdb=" O GLY c 210 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU c 206 " --> pdb=" O SER c 201 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER c 209 " --> pdb=" O MET c 217 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET c 217 " --> pdb=" O SER c 209 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY c 214 " --> pdb=" O GLY c 232 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU c 230 " --> pdb=" O ALA c 216 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR c 228 " --> pdb=" O LEU c 218 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'c' and resid 238 through 241 removed outlier: 4.044A pdb=" N ALA c 238 " --> pdb=" O ALA c 251 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N TYR c 246 " --> pdb=" O LEU c 261 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE c 258 " --> pdb=" O VAL c 267 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'c' and resid 288 through 292 removed outlier: 3.746A pdb=" N SER c 288 " --> pdb=" O GLY c 301 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N THR c 297 " --> pdb=" O SER c 292 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'c' and resid 39 through 42 Processing sheet with id= 65, first strand: chain 'c' and resid 86 through 89 removed outlier: 4.046A pdb=" N ARG c 99 " --> pdb=" O LEU c 89 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'c' and resid 296 through 302 removed outlier: 5.195A pdb=" N GLN c 296 " --> pdb=" O VAL c 312 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR c 302 " --> pdb=" O LEU c 306 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU c 306 " --> pdb=" O TYR c 302 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'd' and resid 81 through 85 removed outlier: 4.656A pdb=" N ASN d 85 " --> pdb=" O PRO d 89 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'd' and resid 113 through 116 removed outlier: 4.226A pdb=" N GLY d 120 " --> pdb=" O ASP d 116 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'h' and resid 53 through 56 removed outlier: 4.527A pdb=" N LYS h 86 " --> pdb=" O MET h 56 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'k' and resid 138 through 142 Processing sheet with id= 71, first strand: chain 'm' and resid 30 through 33 removed outlier: 7.075A pdb=" N GLY m 30 " --> pdb=" O LYS m 112 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL m 110 " --> pdb=" O ALA m 32 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASN m 75 " --> pdb=" O HIS m 48 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU m 52 " --> pdb=" O ILE m 77 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL m 79 " --> pdb=" O LEU m 52 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N SER m 54 " --> pdb=" O VAL m 79 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'n' and resid 9 through 14 removed outlier: 4.593A pdb=" N ASP n 54 " --> pdb=" O VAL n 14 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'n' and resid 15 through 18 removed outlier: 3.726A pdb=" N LYS n 16 " --> pdb=" O ARG n 31 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN n 29 " --> pdb=" O LEU n 18 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY n 19 " --> pdb=" O GLN n 29 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'n' and resid 29 through 33 Processing sheet with id= 75, first strand: chain 'o' and resid 267 through 271 removed outlier: 5.162A pdb=" N PHE o 282 " --> pdb=" O ALA o 271 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ALA o 239 " --> pdb=" O PHE o 287 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'q' and resid 33 through 37 removed outlier: 6.547A pdb=" N LEU q 78 " --> pdb=" O ILE q 92 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASP q 90 " --> pdb=" O GLY q 80 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'r' and resid 32 through 36 removed outlier: 3.609A pdb=" N ILE r 42 " --> pdb=" O LEU r 36 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'r' and resid 190 through 194 removed outlier: 3.946A pdb=" N ILE r 191 " --> pdb=" O THR r 239 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR r 239 " --> pdb=" O ILE r 191 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL r 236 " --> pdb=" O ASN r 228 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS r 226 " --> pdb=" O THR r 238 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 't' and resid 81 through 87 removed outlier: 3.675A pdb=" N ILE t 42 " --> pdb=" O HIS t 129 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY t 48 " --> pdb=" O CYS t 135 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 't' and resid 313 through 318 removed outlier: 4.428A pdb=" N GLN t 292 " --> pdb=" O ILE t 318 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL t 357 " --> pdb=" O ARG t 297 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 't' and resid 319 through 322 removed outlier: 4.435A pdb=" N SER t 320 " --> pdb=" O GLY t 340 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 't' and resid 404 through 407 removed outlier: 3.565A pdb=" N GLU t 439 " --> pdb=" O ILE t 459 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'u' and resid 482 through 486 Processing sheet with id= 84, first strand: chain 'x' and resid 190 through 193 removed outlier: 6.463A pdb=" N TYR x 360 " --> pdb=" O ILE x 193 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'x' and resid 390 through 398 removed outlier: 3.544A pdb=" N TYR x 446 " --> pdb=" O PHE x 390 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL x 452 " --> pdb=" O LEU x 396 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG x 454 " --> pdb=" O GLU x 398 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N TYR x 451 " --> pdb=" O LEU x 466 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'x' and resid 516 through 522 removed outlier: 3.773A pdb=" N VAL x 516 " --> pdb=" O ASP x 511 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG x 518 " --> pdb=" O LEU x 509 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS x 505 " --> pdb=" O LEU x 522 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN x 270 " --> pdb=" O PHE x 277 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE x 277 " --> pdb=" O GLN x 270 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR x 248 " --> pdb=" O PHE x 278 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LYS x 280 " --> pdb=" O THR x 248 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'x' and resid 355 through 363 No H-bonds generated for sheet with id= 87 Processing sheet with id= 88, first strand: chain 'x' and resid 447 through 451 Processing sheet with id= 89, first strand: chain 'y' and resid 831 through 836 removed outlier: 5.393A pdb=" N LEU y 831 " --> pdb=" O MET y 844 " (cutoff:3.500A) 3267 hydrogen bonds defined for protein. 9683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1232 hydrogen bonds 1956 hydrogen bond angles 0 basepair planarities 495 basepair parallelities 927 stacking parallelities Total time for adding SS restraints: 67.63 Time building geometry restraints manager: 43.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 14251 1.31 - 1.44: 39982 1.44 - 1.56: 55424 1.56 - 1.69: 3629 1.69 - 1.82: 442 Bond restraints: 113728 Sorted by residual: bond pdb=" C4 5MU A 814 " pdb=" C5 5MU A 814 " ideal model delta sigma weight residual 1.802 1.468 0.334 2.00e-02 2.50e+03 2.79e+02 bond pdb=" N1 5MU A 814 " pdb=" C6 5MU A 814 " ideal model delta sigma weight residual 1.635 1.330 0.305 2.00e-02 2.50e+03 2.32e+02 bond pdb=" C5 5MU A 814 " pdb=" C6 5MU A 814 " ideal model delta sigma weight residual 1.155 1.379 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C2' A2M A 166 " pdb=" C1' A2M A 166 " ideal model delta sigma weight residual 1.305 1.511 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" O4' A2M A 668 " pdb=" C1' A2M A 668 " ideal model delta sigma weight residual 1.615 1.411 0.204 2.00e-02 2.50e+03 1.04e+02 ... (remaining 113723 not shown) Histogram of bond angle deviations from ideal: 77.15 - 89.11: 2 89.11 - 101.07: 719 101.07 - 113.02: 73227 113.02 - 124.98: 80959 124.98 - 136.94: 7838 Bond angle restraints: 162745 Sorted by residual: angle pdb=" N VAL N 7 " pdb=" CA VAL N 7 " pdb=" C VAL N 7 " ideal model delta sigma weight residual 108.95 77.15 31.80 1.65e+00 3.67e-01 3.71e+02 angle pdb=" N GLY B 53 " pdb=" CA GLY B 53 " pdb=" C GLY B 53 " ideal model delta sigma weight residual 112.54 136.07 -23.53 1.28e+00 6.10e-01 3.38e+02 angle pdb=" N ALA f 100 " pdb=" CA ALA f 100 " pdb=" C ALA f 100 " ideal model delta sigma weight residual 111.07 127.32 -16.25 1.07e+00 8.73e-01 2.31e+02 angle pdb=" N GLY q 45 " pdb=" CA GLY q 45 " pdb=" C GLY q 45 " ideal model delta sigma weight residual 112.73 94.82 17.91 1.20e+00 6.94e-01 2.23e+02 angle pdb=" N LEU q 42 " pdb=" CA LEU q 42 " pdb=" C LEU q 42 " ideal model delta sigma weight residual 109.24 86.14 23.10 1.63e+00 3.76e-01 2.01e+02 ... (remaining 162740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 64243 35.99 - 71.99: 4933 71.99 - 107.98: 629 107.98 - 143.98: 22 143.98 - 179.97: 22 Dihedral angle restraints: 69849 sinusoidal: 41895 harmonic: 27954 Sorted by residual: dihedral pdb=" C4' U A 1 " pdb=" C3' U A 1 " pdb=" C2' U A 1 " pdb=" C1' U A 1 " ideal model delta sinusoidal sigma weight residual 36.34 -22.14 58.48 1 3.10e+00 1.04e-01 4.77e+02 dihedral pdb=" CD BARG u 14 " pdb=" NE BARG u 14 " pdb=" CZ BARG u 14 " pdb=" NH1BARG u 14 " ideal model delta sinusoidal sigma weight residual 0.00 -178.91 178.91 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" O4' U A 1 " pdb=" C2' U A 1 " pdb=" C1' U A 1 " pdb=" C3' U A 1 " ideal model delta sinusoidal sigma weight residual -94.41 -34.60 -59.80 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 69846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 18104 0.181 - 0.362: 1799 0.362 - 0.543: 144 0.543 - 0.725: 19 0.725 - 0.906: 3 Chirality restraints: 20069 Sorted by residual: chirality pdb=" CA ARG J 28 " pdb=" N ARG J 28 " pdb=" C ARG J 28 " pdb=" CB ARG J 28 " both_signs ideal model delta sigma weight residual False 2.51 1.60 0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CA SER J 76 " pdb=" N SER J 76 " pdb=" C SER J 76 " pdb=" CB SER J 76 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.03e+01 chirality pdb=" CA ASN y 133 " pdb=" N ASN y 133 " pdb=" C ASN y 133 " pdb=" CB ASN y 133 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.83e+01 ... (remaining 20066 not shown) Planarity restraints: 14279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MU A 814 " 0.047 2.00e-02 2.50e+03 5.81e-01 7.61e+03 pdb=" C4' 5MU A 814 " -0.433 2.00e-02 2.50e+03 pdb=" O4' 5MU A 814 " -0.596 2.00e-02 2.50e+03 pdb=" C3' 5MU A 814 " 0.641 2.00e-02 2.50e+03 pdb=" O3' 5MU A 814 " 0.568 2.00e-02 2.50e+03 pdb=" C2' 5MU A 814 " 0.186 2.00e-02 2.50e+03 pdb=" O2' 5MU A 814 " -0.976 2.00e-02 2.50e+03 pdb=" C1' 5MU A 814 " -0.275 2.00e-02 2.50e+03 pdb=" N1 5MU A 814 " 0.839 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A 509 " -0.056 2.00e-02 2.50e+03 5.80e-01 7.56e+03 pdb=" C4' OMG A 509 " 0.422 2.00e-02 2.50e+03 pdb=" O4' OMG A 509 " 0.683 2.00e-02 2.50e+03 pdb=" C3' OMG A 509 " -0.631 2.00e-02 2.50e+03 pdb=" O3' OMG A 509 " -0.522 2.00e-02 2.50e+03 pdb=" C2' OMG A 509 " -0.202 2.00e-02 2.50e+03 pdb=" O2' OMG A 509 " 0.893 2.00e-02 2.50e+03 pdb=" C1' OMG A 509 " 0.296 2.00e-02 2.50e+03 pdb=" N9 OMG A 509 " -0.883 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A 644 " 0.059 2.00e-02 2.50e+03 5.78e-01 7.53e+03 pdb=" C4' OMG A 644 " -0.458 2.00e-02 2.50e+03 pdb=" O4' OMG A 644 " -0.726 2.00e-02 2.50e+03 pdb=" C3' OMG A 644 " 0.581 2.00e-02 2.50e+03 pdb=" O3' OMG A 644 " 0.498 2.00e-02 2.50e+03 pdb=" C2' OMG A 644 " 0.248 2.00e-02 2.50e+03 pdb=" O2' OMG A 644 " -0.859 2.00e-02 2.50e+03 pdb=" C1' OMG A 644 " -0.250 2.00e-02 2.50e+03 pdb=" N9 OMG A 644 " 0.907 2.00e-02 2.50e+03 ... (remaining 14276 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 153 2.41 - 3.03: 63656 3.03 - 3.65: 185399 3.65 - 4.28: 284709 4.28 - 4.90: 411032 Nonbonded interactions: 944949 Sorted by model distance: nonbonded pdb=" N VAL N 7 " pdb=" O VAL N 7 " model vdw 1.782 2.496 nonbonded pdb=" O2' G A1754 " pdb=" OP1 C A1755 " model vdw 1.852 2.440 nonbonded pdb=" N4 C A1231 " pdb=" O4 U A1232 " model vdw 1.869 2.520 nonbonded pdb=" OP1 G A1255 " pdb=" O2' G A1256 " model vdw 1.888 2.440 nonbonded pdb=" O2' A A 545 " pdb=" O4' G A 546 " model vdw 1.915 2.440 ... (remaining 944944 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 12.390 Check model and map are aligned: 1.050 Set scattering table: 0.680 Process input model: 309.300 Find NCS groups from input model: 2.930 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 331.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 : 0.013 0.334 113728 Z= 0.836 Angle : 1.520 39.001 162745 Z= 1.017 Chirality : 0.112 0.906 20069 Planarity : 0.016 0.581 14279 Dihedral : 21.894 179.970 51671 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.99 % Favored : 95.70 % Rotamer: Outliers : 9.36 % Allowed : 12.69 % Favored : 77.95 % Cbeta Deviations : 0.87 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.08), residues: 9485 helix: 0.86 (0.08), residues: 3649 sheet: -0.04 (0.15), residues: 1208 loop : -0.97 (0.09), residues: 4628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.004 TRP v 213 HIS 0.016 0.002 HIS y 701 PHE 0.041 0.003 PHE u 398 TYR 0.053 0.003 TYR P 72 ARG 0.016 0.001 ARG v 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18970 Ramachandran restraints generated. 9485 Oldfield, 0 Emsley, 9485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18970 Ramachandran restraints generated. 9485 Oldfield, 0 Emsley, 9485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2265 residues out of total 8473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 576 poor density : 1689 time to evaluate : 7.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 576 outliers final: 169 residues processed: 2127 average time/residue: 1.0128 time to fit residues: 3696.1326 Evaluate side-chains 1212 residues out of total 8473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1043 time to evaluate : 6.898 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. outliers start: 169 outliers final: 3 residues processed: 169 average time/residue: 0.8309 time to fit residues: 271.7675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1124 random chunks: chunk 949 optimal weight: 20.0000 chunk 851 optimal weight: 6.9990 chunk 472 optimal weight: 0.9980 chunk 291 optimal weight: 0.7980 chunk 574 optimal weight: 7.9990 chunk 455 optimal weight: 4.9990 chunk 880 optimal weight: 10.0000 chunk 340 optimal weight: 5.9990 chunk 535 optimal weight: 0.8980 chunk 655 optimal weight: 1.9990 chunk 1020 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 327 GLN ** 6 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN C 224 ASN D 75 ASN ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 HIS F 89 GLN F 130 ASN G 33 ASN G 165 ASN ** I 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 HIS ** L 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 48 ASN M 74 GLN M 93 GLN N 36 GLN ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 GLN O 179 ASN O 186 ASN R 84 ASN R 146 GLN R 168 GLN S 70 HIS S 155 GLN S 177 GLN S 187 HIS T 89 HIS T 112 ASN ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 ASN V 165 ASN V 186 ASN Y 35 ASN ** Y 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 145 GLN b 79 HIS c 187 ASN d 12 GLN d 51 ASN d 63 HIS d 128 GLN e 45 ASN h 92 HIS i 26 ASN ** n 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 256 GLN ** q 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 68 ASN r 178 ASN r 270 ASN u 10 ASN ** u 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 270 GLN u 309 ASN u 392 ASN ** u 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 209 GLN v 283 GLN v 402 GLN ** x 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 456 HIS x 481 ASN ** y 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 436 GLN y 597 ASN y 631 ASN ** y 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 852 GLN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 113728 Z= 0.230 Angle : 0.760 18.204 162745 Z= 0.406 Chirality : 0.043 0.680 20069 Planarity : 0.006 0.137 14279 Dihedral : 22.019 179.944 37114 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.10 % Rotamer: Outliers : 3.87 % Allowed : 19.76 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.08), residues: 9485 helix: 0.42 (0.08), residues: 3812 sheet: -0.27 (0.14), residues: 1244 loop : -1.11 (0.09), residues: 4429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP m 88 HIS 0.011 0.001 HIS m 72 PHE 0.029 0.002 PHE L 236 TYR 0.040 0.002 TYR Y 115 ARG 0.010 0.001 ARG u 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18970 Ramachandran restraints generated. 9485 Oldfield, 0 Emsley, 9485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18970 Ramachandran restraints generated. 9485 Oldfield, 0 Emsley, 9485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1459 residues out of total 8473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1221 time to evaluate : 6.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 238 outliers final: 113 residues processed: 1383 average time/residue: 0.9247 time to fit residues: 2247.2691 Evaluate side-chains 1096 residues out of total 8473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 983 time to evaluate : 6.883 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. outliers start: 113 outliers final: 1 residues processed: 113 average time/residue: 0.7712 time to fit residues: 171.3846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1124 random chunks: chunk 567 optimal weight: 3.9990 chunk 316 optimal weight: 10.0000 chunk 849 optimal weight: 7.9990 chunk 695 optimal weight: 0.7980 chunk 281 optimal weight: 10.0000 chunk 1022 optimal weight: 20.0000 chunk 1104 optimal weight: 10.0000 chunk 910 optimal weight: 20.0000 chunk 1014 optimal weight: 8.9990 chunk 348 optimal weight: 10.0000 chunk 820 optimal weight: 8.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 345 GLN B 83 GLN B 100 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN D 75 ASN ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 HIS E 61 GLN F 130 ASN G 73 GLN I 13 GLN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN M 93 GLN ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 113 GLN R 22 HIS T 89 HIS ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 101 HIS Y 8 GLN Y 77 HIS Y 97 GLN ** Y 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 66 HIS c 159 ASN c 244 ASN c 296 GLN d 10 ASN d 126 GLN d 137 GLN h 81 GLN ** n 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 85 GLN ** q 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 44 GLN ** u 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 372 ASN ** u 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 216 HIS v 252 HIS ** x 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 325 GLN ** x 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 479 GLN x 481 ASN y 436 GLN y 659 ASN ** y 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 784 GLN y 852 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 113728 Z= 0.395 Angle : 0.801 18.007 162745 Z= 0.420 Chirality : 0.045 0.435 20069 Planarity : 0.006 0.140 14279 Dihedral : 21.870 179.433 37114 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.07 % Favored : 94.87 % Rotamer: Outliers : 4.44 % Allowed : 21.52 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.08), residues: 9485 helix: 0.37 (0.08), residues: 3791 sheet: -0.65 (0.14), residues: 1304 loop : -1.28 (0.09), residues: 4390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP 1 472 HIS 0.013 0.002 HIS C 209 PHE 0.042 0.003 PHE N 203 TYR 0.032 0.002 TYR P 72 ARG 0.013 0.001 ARG m 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18970 Ramachandran restraints generated. 9485 Oldfield, 0 Emsley, 9485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18970 Ramachandran restraints generated. 9485 Oldfield, 0 Emsley, 9485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1264 residues out of total 8473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 991 time to evaluate : 6.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 273 outliers final: 137 residues processed: 1199 average time/residue: 0.8926 time to fit residues: 1878.1755 Evaluate side-chains 1020 residues out of total 8473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 883 time to evaluate : 6.950 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. outliers start: 137 outliers final: 1 residues processed: 137 average time/residue: 0.7580 time to fit residues: 204.9740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1124 random chunks: chunk 1010 optimal weight: 8.9990 chunk 768 optimal weight: 0.5980 chunk 530 optimal weight: 2.9990 chunk 113 optimal weight: 40.0000 chunk 488 optimal weight: 6.9990 chunk 686 optimal weight: 0.8980 chunk 1026 optimal weight: 50.0000 chunk 1086 optimal weight: 5.9990 chunk 536 optimal weight: 3.9990 chunk 972 optimal weight: 50.0000 chunk 292 optimal weight: 7.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 522 ASN ** 6 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 345 GLN C 179 ASN D 75 ASN F 130 ASN G 91 HIS I 13 GLN I 36 GLN I 58 HIS J 70 ASN K 21 ASN ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 GLN ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 110 ASN ** Y 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 187 ASN c 222 ASN e 89 GLN ** n 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 80 GLN ** u 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 309 ASN ** u 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 396 ASN x 296 ASN x 416 GLN x 479 GLN ** y 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 113728 Z= 0.218 Angle : 0.683 17.767 162745 Z= 0.361 Chirality : 0.040 0.413 20069 Planarity : 0.005 0.131 14279 Dihedral : 21.800 179.790 37114 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.63 % Favored : 95.32 % Rotamer: Outliers : 2.81 % Allowed : 22.77 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.08), residues: 9485 helix: 0.63 (0.08), residues: 3811 sheet: -0.65 (0.14), residues: 1277 loop : -1.24 (0.09), residues: 4397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP c 219 HIS 0.010 0.001 HIS m 72 PHE 0.036 0.002 PHE L 84 TYR 0.019 0.001 TYR S 156 ARG 0.007 0.000 ARG 9 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18970 Ramachandran restraints generated. 9485 Oldfield, 0 Emsley, 9485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18970 Ramachandran restraints generated. 9485 Oldfield, 0 Emsley, 9485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1179 residues out of total 8473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1006 time to evaluate : 6.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 173 outliers final: 78 residues processed: 1124 average time/residue: 0.9419 time to fit residues: 1869.9637 Evaluate side-chains 976 residues out of total 8473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 898 time to evaluate : 6.896 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. outliers start: 78 outliers final: 1 residues processed: 78 average time/residue: 0.7934 time to fit residues: 123.8961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1124 random chunks: chunk 904 optimal weight: 0.8980 chunk 616 optimal weight: 9.9990 chunk 15 optimal weight: 30.0000 chunk 808 optimal weight: 6.9990 chunk 448 optimal weight: 0.3980 chunk 927 optimal weight: 30.0000 chunk 751 optimal weight: 10.0000 chunk 1 optimal weight: 50.0000 chunk 554 optimal weight: 1.9990 chunk 975 optimal weight: 40.0000 chunk 274 optimal weight: 10.0000 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 345 GLN B 83 GLN B 121 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN D 75 ASN I 13 GLN ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 GLN M 127 ASN ** N 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 HIS ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 110 ASN ** Y 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 165 ASN a 66 HIS ** b 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 288 HIS ** q 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 73 HIS x 296 ASN x 325 GLN x 403 HIS ** x 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 481 ASN ** y 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 113728 Z= 0.274 Angle : 0.701 17.619 162745 Z= 0.367 Chirality : 0.041 0.402 20069 Planarity : 0.005 0.135 14279 Dihedral : 21.700 179.725 37114 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.31 % Favored : 94.62 % Rotamer: Outliers : 2.94 % Allowed : 23.66 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.08), residues: 9485 helix: 0.74 (0.08), residues: 3862 sheet: -0.77 (0.14), residues: 1280 loop : -1.29 (0.09), residues: 4343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP x 399 HIS 0.019 0.001 HIS o 288 PHE 0.035 0.002 PHE L 84 TYR 0.023 0.002 TYR B 55 ARG 0.014 0.001 ARG y 563 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18970 Ramachandran restraints generated. 9485 Oldfield, 0 Emsley, 9485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18970 Ramachandran restraints generated. 9485 Oldfield, 0 Emsley, 9485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 8473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 916 time to evaluate : 6.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 181 outliers final: 83 residues processed: 1052 average time/residue: 0.9013 time to fit residues: 1671.2075 Evaluate side-chains 939 residues out of total 8473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 856 time to evaluate : 6.281 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. outliers start: 83 outliers final: 1 residues processed: 83 average time/residue: 0.7626 time to fit residues: 128.7020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1124 random chunks: chunk 365 optimal weight: 5.9990 chunk 978 optimal weight: 50.0000 chunk 214 optimal weight: 10.0000 chunk 637 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 chunk 1087 optimal weight: 6.9990 chunk 902 optimal weight: 50.0000 chunk 503 optimal weight: 1.9990 chunk 90 optimal weight: 70.0000 chunk 359 optimal weight: 8.9990 chunk 570 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 348 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN C 209 HIS D 75 ASN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 ASN I 13 GLN ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 GLN ** N 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 165 ASN a 66 HIS b 104 GLN c 159 ASN c 187 ASN f 76 GLN ** k 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 288 HIS ** q 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 228 ASN ** r 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 399 ASN ** u 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 481 ASN ** y 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 113728 Z= 0.357 Angle : 0.751 17.484 162745 Z= 0.389 Chirality : 0.043 0.392 20069 Planarity : 0.006 0.136 14279 Dihedral : 21.737 179.943 37114 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.54 % Favored : 94.41 % Rotamer: Outliers : 2.26 % Allowed : 24.56 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.09), residues: 9485 helix: 0.73 (0.08), residues: 3856 sheet: -0.88 (0.14), residues: 1278 loop : -1.36 (0.09), residues: 4351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP u 154 HIS 0.023 0.002 HIS o 288 PHE 0.040 0.002 PHE o 303 TYR 0.023 0.002 TYR N 156 ARG 0.012 0.001 ARG Y 146 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18970 Ramachandran restraints generated. 9485 Oldfield, 0 Emsley, 9485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18970 Ramachandran restraints generated. 9485 Oldfield, 0 Emsley, 9485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 8473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 871 time to evaluate : 6.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 139 outliers final: 72 residues processed: 978 average time/residue: 0.9000 time to fit residues: 1552.4176 Evaluate side-chains 899 residues out of total 8473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 827 time to evaluate : 6.240 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. outliers start: 72 outliers final: 1 residues processed: 72 average time/residue: 0.7399 time to fit residues: 107.7423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1124 random chunks: chunk 1048 optimal weight: 10.0000 chunk 122 optimal weight: 50.0000 chunk 619 optimal weight: 9.9990 chunk 794 optimal weight: 4.9990 chunk 615 optimal weight: 30.0000 chunk 915 optimal weight: 20.0000 chunk 607 optimal weight: 20.0000 chunk 1083 optimal weight: 0.6980 chunk 677 optimal weight: 3.9990 chunk 660 optimal weight: 0.7980 chunk 500 optimal weight: 0.7980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN B 121 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN D 75 ASN E 127 ASN F 130 ASN I 13 GLN J 56 HIS J 98 GLN ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 GLN ** N 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 110 ASN ** Y 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 165 ASN c 159 ASN k 139 HIS ** m 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 82 ASN ** n 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 120 ASN v 402 GLN x 481 ASN ** y 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 465 HIS ** y 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 113728 Z= 0.191 Angle : 0.660 17.507 162745 Z= 0.345 Chirality : 0.039 0.399 20069 Planarity : 0.005 0.129 14279 Dihedral : 21.654 179.985 37114 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.03 % Favored : 94.92 % Rotamer: Outliers : 1.35 % Allowed : 25.21 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.09), residues: 9485 helix: 1.00 (0.08), residues: 3854 sheet: -0.78 (0.14), residues: 1267 loop : -1.31 (0.09), residues: 4364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP q 70 HIS 0.012 0.001 HIS u 257 PHE 0.029 0.001 PHE o 303 TYR 0.032 0.001 TYR y 469 ARG 0.006 0.000 ARG 1 505 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18970 Ramachandran restraints generated. 9485 Oldfield, 0 Emsley, 9485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18970 Ramachandran restraints generated. 9485 Oldfield, 0 Emsley, 9485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 8473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 911 time to evaluate : 6.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 26 residues processed: 962 average time/residue: 0.9081 time to fit residues: 1545.9578 Evaluate side-chains 869 residues out of total 8473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 843 time to evaluate : 6.156 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. outliers start: 26 outliers final: 1 residues processed: 26 average time/residue: 0.7190 time to fit residues: 43.6736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1124 random chunks: chunk 670 optimal weight: 10.0000 chunk 432 optimal weight: 5.9990 chunk 647 optimal weight: 10.0000 chunk 326 optimal weight: 10.0000 chunk 212 optimal weight: 20.0000 chunk 209 optimal weight: 40.0000 chunk 688 optimal weight: 1.9990 chunk 738 optimal weight: 9.9990 chunk 535 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 851 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN D 75 ASN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 ASN G 44 ASN ** I 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 GLN ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 ASN M 93 GLN ** N 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 110 ASN S 186 GLN V 95 HIS ** Y 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 165 ASN a 66 HIS c 159 ASN c 187 ASN d 128 GLN f 10 GLN ** m 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 37 GLN ** q 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 361 ASN y 478 GLN ** y 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 113728 Z= 0.413 Angle : 0.785 17.323 162745 Z= 0.404 Chirality : 0.044 0.421 20069 Planarity : 0.006 0.138 14279 Dihedral : 21.695 179.802 37114 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.28 % Favored : 93.67 % Rotamer: Outliers : 1.67 % Allowed : 25.82 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.09), residues: 9485 helix: 0.80 (0.08), residues: 3842 sheet: -0.94 (0.14), residues: 1280 loop : -1.40 (0.09), residues: 4363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP y 749 HIS 0.026 0.002 HIS o 288 PHE 0.035 0.002 PHE L 84 TYR 0.028 0.002 TYR m 61 ARG 0.014 0.001 ARG 9 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18970 Ramachandran restraints generated. 9485 Oldfield, 0 Emsley, 9485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18970 Ramachandran restraints generated. 9485 Oldfield, 0 Emsley, 9485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 8473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 831 time to evaluate : 6.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 64 residues processed: 894 average time/residue: 0.9166 time to fit residues: 1446.7449 Evaluate side-chains 866 residues out of total 8473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 802 time to evaluate : 6.969 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. outliers start: 64 outliers final: 1 residues processed: 64 average time/residue: 0.7925 time to fit residues: 103.8573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1124 random chunks: chunk 985 optimal weight: 50.0000 chunk 1037 optimal weight: 10.0000 chunk 946 optimal weight: 30.0000 chunk 1009 optimal weight: 5.9990 chunk 607 optimal weight: 20.0000 chunk 439 optimal weight: 7.9990 chunk 792 optimal weight: 2.9990 chunk 309 optimal weight: 10.0000 chunk 912 optimal weight: 9.9990 chunk 954 optimal weight: 40.0000 chunk 1006 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN F 130 ASN ** I 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 GLN ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 GLN ** N 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 20 GLN ** Q 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 177 GLN ** Y 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 165 ASN ** a 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 66 HIS c 311 GLN f 10 GLN ** f 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 135 HIS ** k 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 180 GLN ** u 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 206 GLN ** x 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 113728 Z= 0.406 Angle : 0.787 17.716 162745 Z= 0.406 Chirality : 0.044 0.391 20069 Planarity : 0.006 0.136 14279 Dihedral : 21.771 179.971 37114 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.37 % Favored : 93.59 % Rotamer: Outliers : 0.78 % Allowed : 26.64 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.09), residues: 9485 helix: 0.66 (0.08), residues: 3847 sheet: -1.11 (0.14), residues: 1266 loop : -1.49 (0.09), residues: 4372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP y 749 HIS 0.028 0.002 HIS o 288 PHE 0.031 0.002 PHE 1 547 TYR 0.028 0.002 TYR v 238 ARG 0.015 0.001 ARG 9 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18970 Ramachandran restraints generated. 9485 Oldfield, 0 Emsley, 9485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18970 Ramachandran restraints generated. 9485 Oldfield, 0 Emsley, 9485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 8473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 831 time to evaluate : 6.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 21 residues processed: 869 average time/residue: 0.9389 time to fit residues: 1440.7893 Evaluate side-chains 811 residues out of total 8473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 790 time to evaluate : 7.022 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. outliers start: 21 outliers final: 1 residues processed: 21 average time/residue: 0.8940 time to fit residues: 42.7794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1124 random chunks: chunk 662 optimal weight: 1.9990 chunk 1067 optimal weight: 6.9990 chunk 651 optimal weight: 3.9990 chunk 506 optimal weight: 1.9990 chunk 742 optimal weight: 9.9990 chunk 1119 optimal weight: 30.0000 chunk 1030 optimal weight: 50.0000 chunk 891 optimal weight: 40.0000 chunk 92 optimal weight: 0.2980 chunk 688 optimal weight: 5.9990 chunk 546 optimal weight: 0.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 345 GLN 6 349 GLN C 36 HIS F 130 ASN I 5 HIS I 13 GLN ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 GLN ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 ASN R 9 HIS ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 177 GLN ** Y 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 159 ASN c 187 ASN c 311 GLN f 76 GLN k 139 HIS ** m 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 29 GLN ** o 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 113728 Z= 0.187 Angle : 0.679 17.592 162745 Z= 0.353 Chirality : 0.039 0.403 20069 Planarity : 0.005 0.128 14279 Dihedral : 21.640 179.477 37114 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.20 % Favored : 94.76 % Rotamer: Outliers : 0.39 % Allowed : 27.01 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.09), residues: 9485 helix: 1.03 (0.08), residues: 3850 sheet: -0.93 (0.14), residues: 1262 loop : -1.33 (0.09), residues: 4373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP y 749 HIS 0.026 0.001 HIS o 288 PHE 0.033 0.002 PHE y 105 TYR 0.038 0.002 TYR 1 525 ARG 0.008 0.000 ARG 9 6 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18970 Ramachandran restraints generated. 9485 Oldfield, 0 Emsley, 9485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18970 Ramachandran restraints generated. 9485 Oldfield, 0 Emsley, 9485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 8473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 888 time to evaluate : 7.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 902 average time/residue: 0.9461 time to fit residues: 1507.9357 Evaluate side-chains 842 residues out of total 8473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 834 time to evaluate : 7.059 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.8624 time to fit residues: 21.2170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1124 random chunks: chunk 708 optimal weight: 10.0000 chunk 949 optimal weight: 5.9990 chunk 273 optimal weight: 10.0000 chunk 822 optimal weight: 0.5980 chunk 131 optimal weight: 7.9990 chunk 247 optimal weight: 10.0000 chunk 893 optimal weight: 10.0000 chunk 373 optimal weight: 10.0000 chunk 917 optimal weight: 20.0000 chunk 113 optimal weight: 40.0000 chunk 164 optimal weight: 50.0000 overall best weight: 6.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 345 GLN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 ASN G 44 ASN I 13 GLN ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 GLN ** N 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 159 ASN f 135 HIS k 139 HIS ** m 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 425 GLN ** u 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.096885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.069576 restraints weight = 413743.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.069373 restraints weight = 241762.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.069339 restraints weight = 155796.487| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 347 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 347 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 113728 Z= 0.415 Angle : 0.792 17.333 162745 Z= 0.406 Chirality : 0.044 0.386 20069 Planarity : 0.006 0.138 14279 Dihedral : 21.668 179.958 37114 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.46 % Favored : 93.49 % Rotamer: Outliers : 0.57 % Allowed : 27.06 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.09), residues: 9485 helix: 0.83 (0.08), residues: 3853 sheet: -1.01 (0.14), residues: 1239 loop : -1.45 (0.09), residues: 4393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP y 749 HIS 0.029 0.002 HIS o 288 PHE 0.042 0.002 PHE c 65 TYR 0.057 0.002 TYR 1 525 ARG 0.017 0.001 ARG 9 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27232.53 seconds wall clock time: 475 minutes 41.63 seconds (28541.63 seconds total)