Starting phenix.real_space_refine on Fri Dec 8 08:06:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp6_14113/12_2023/7qp6_14113_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp6_14113/12_2023/7qp6_14113.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp6_14113/12_2023/7qp6_14113_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp6_14113/12_2023/7qp6_14113_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp6_14113/12_2023/7qp6_14113_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp6_14113/12_2023/7qp6_14113.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp6_14113/12_2023/7qp6_14113.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp6_14113/12_2023/7qp6_14113_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp6_14113/12_2023/7qp6_14113_updated.pdb" } resolution = 4.7 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1812 5.49 5 Mg 2 5.21 5 S 295 5.16 5 C 61862 2.51 5 N 20272 2.21 5 O 25655 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 TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 35": "NH1" <-> "NH2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B ARG 97": "NH1" <-> "NH2" 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 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 17": "NH1" <-> "NH2" 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 29": "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 15": "OE1" <-> "OE2" Residue "H GLU 75": "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 18": "OE1" <-> "OE2" Residue "J GLU 49": "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 ARG 3": "NH1" <-> "NH2" Residue "M ARG 5": "NH1" <-> "NH2" 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 "M ARG 132": "NH1" <-> "NH2" Residue "N GLU 13": "OE1" <-> "OE2" 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 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 GLU 51": "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 GLU 114": "OE1" <-> "OE2" Residue "R GLU 133": "OE1" <-> "OE2" Residue "R GLU 135": "OE1" <-> "OE2" Residue "R GLU 151": "OE1" <-> "OE2" Residue "R GLU 164": "OE1" <-> "OE2" 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 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 "V ARG 198": "NH1" <-> "NH2" 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 38": "OE1" <-> "OE2" Residue "Z GLU 61": "OE1" <-> "OE2" Residue "Z GLU 81": "OE1" <-> "OE2" Residue "Z ARG 94": "NH1" <-> "NH2" Residue "Z ARG 143": "NH1" <-> "NH2" Residue "Z GLU 216": "OE1" <-> "OE2" Residue "a GLU 60": "OE1" <-> "OE2" Residue "a ARG 65": "NH1" <-> "NH2" Residue "a GLU 74": "OE1" <-> "OE2" Residue "a GLU 88": "OE1" <-> "OE2" Residue "b GLU 31": "OE1" <-> "OE2" Residue "b ARG 61": "NH1" <-> "NH2" 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 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 "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 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 125": "OE1" <-> "OE2" Residue "m ASP 57": "OD1" <-> "OD2" Residue "m GLU 66": "OE1" <-> "OE2" Residue "m GLU 71": "OE1" <-> "OE2" Residue "m GLU 97": "OE1" <-> "OE2" Residue "m ARG 101": "NH1" <-> "NH2" 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 "p ARG 38": "NH1" <-> "NH2" Residue "p GLU 81": "OE1" <-> "OE2" Residue "q GLU 22": "OE1" <-> "OE2" Residue "q ARG 24": "NH1" <-> "NH2" Residue "q GLU 34": "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 ASP 77": "OD1" <-> "OD2" Residue "r GLU 79": "OE1" <-> "OE2" Residue "r ARG 88": "NH1" <-> "NH2" Residue "r ARG 89": "NH1" <-> "NH2" 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 GLU 221": "OE1" <-> "OE2" Residue "r ARG 234": "NH1" <-> "NH2" Residue "r ARG 244": "NH1" <-> "NH2" Residue "r ARG 266": "NH1" <-> "NH2" Residue "s ARG 188": "NH1" <-> "NH2" Residue "s ARG 200": "NH1" <-> "NH2" Residue "s ARG 211": "NH1" <-> "NH2" Residue "s GLU 243": "OE1" <-> "OE2" Residue "s ARG 261": "NH1" <-> "NH2" Residue "s GLU 268": "OE1" <-> "OE2" Residue "s GLU 277": "OE1" <-> "OE2" Residue "s ARG 285": "NH1" <-> "NH2" Residue "s ARG 296": "NH1" <-> "NH2" Residue "s ARG 308": "NH1" <-> "NH2" Residue "u GLU 9": "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 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 "x ARG 26": "NH1" <-> "NH2" 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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 109900 Number of models: 1 Model: "" Number of chains: 57 Chain: "1" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 2445 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 284} Link IDs: {'PTRANS': 21, 'TRANS': 402} Chain breaks: 1 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1141 Unresolved non-hydrogen angles: 1478 Unresolved non-hydrogen dihedrals: 1012 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 10, 'TYR:plan': 10, 'ASN:plan1': 10, 'TRP:plan': 15, 'ASP:plan': 20, 'PHE:plan': 19, 'GLU:plan': 16, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 677 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: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 240 Classifications: {'RNA': 20} Modifications used: {'rna3p_pur': 20} Link IDs: {'rna3p': 19} Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {' A%rna3p_pur:plan2': 20, ' A%rna3p_pur:plan': 20} Unresolved non-hydrogen planarities: 240 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': 153, 'rna2p_pyr': 127, 'rna3p': 18, 'rna3p_pur': 738, 'rna3p_pyr': 671} Link IDs: {'rna2p': 280, 'rna3p': 1438} 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: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 330 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} 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: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1064 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} 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: "p" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 691 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "q" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Link IDs: {'TRANS': 87} 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: "s" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1123 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} 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': 13, 'rna3p': 61} 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: 5470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5470 Classifications: {'peptide': 697} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 19, 'TRANS': 677} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 120 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: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 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 65311 SG CYS Q 26 115.866 169.894 161.574 1.00 25.98 S ATOM 65694 SG CYS Q 74 118.248 168.836 158.170 1.00 32.58 S ATOM 83185 SG CYS k 121 23.446 213.870 95.342 1.00102.58 S ATOM 83221 SG CYS k 126 25.121 212.099 95.158 1.00107.22 S ATOM 83339 SG CYS k 141 21.723 211.758 97.739 1.00 93.99 S ATOM 83358 SG CYS k 144 24.731 210.189 96.598 1.00 97.63 S Residues with excluded nonbonded symmetry interactions: 22 residue: pdb=" P A 7 10 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 10 " occ=0.00 residue: pdb=" P A 7 11 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 11 " occ=0.00 residue: pdb=" P A 7 12 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 12 " occ=0.00 residue: pdb=" P A 7 13 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 13 " occ=0.00 residue: pdb=" P A 7 14 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 14 " occ=0.00 residue: pdb=" P A 7 15 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 15 " occ=0.00 residue: pdb=" P A 7 16 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 16 " occ=0.00 residue: pdb=" P A 7 17 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 17 " occ=0.00 residue: pdb=" P A 7 18 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 18 " occ=0.00 residue: pdb=" P A 7 19 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 19 " occ=0.00 residue: pdb=" P A 7 20 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 20 " occ=0.00 residue: pdb=" P A 7 21 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 21 " occ=0.00 ... (remaining 10 not shown) Time building chain proxies: 42.66, per 1000 atoms: 0.39 Number of scatterers: 109900 At special positions: 0 Unit cell: (307.4, 291.16, 238.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 295 16.00 P 1812 15.00 Mg 2 11.99 O 25655 8.00 N 20272 7.00 C 61862 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: 39.10 Conformation dependent library (CDL) restraints added in 11.0 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 74 " pdb=" ZN k 201 " pdb="ZN ZN k 201 " - pdb=" SG CYS k 126 " pdb="ZN ZN k 201 " - pdb=" SG CYS k 141 " pdb="ZN ZN k 201 " - pdb=" SG CYS k 121 " pdb="ZN ZN k 201 " - pdb=" SG CYS k 144 " Number of angles added : 6 19448 Ramachandran restraints generated. 9724 Oldfield, 0 Emsley, 9724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18628 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: 343 helices and 93 sheets defined 47.4% alpha, 13.6% beta 487 base pairs and 942 stacking pairs defined. Time for finding SS restraints: 58.98 Creating SS restraints... Processing helix chain '1' and resid 286 through 300 removed outlier: 4.651A pdb=" N LEU 1 293 " --> pdb=" O ASP 1 289 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARG 1 294 " --> pdb=" O LEU 1 290 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR 1 295 " --> pdb=" O GLY 1 291 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N TRP 1 296 " --> pdb=" O ASN 1 292 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU 1 297 " --> pdb=" O LEU 1 293 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ALA 1 300 " --> pdb=" O TRP 1 296 " (cutoff:3.500A) Processing helix chain '1' and resid 332 through 337 removed outlier: 4.655A pdb=" N THR 1 336 " --> pdb=" O ARG 1 332 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N GLU 1 337 " --> pdb=" O ALA 1 333 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 332 through 337' Processing helix chain '1' and resid 459 through 464 removed outlier: 4.051A pdb=" N LYS 1 463 " --> pdb=" O LYS 1 459 " (cutoff:3.500A) removed outlier: 3.793A 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 '3' and resid 2 through 18 removed outlier: 3.516A pdb=" N ALA 3 9 " --> pdb=" O GLU 3 5 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN 3 10 " --> pdb=" O GLN 3 6 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY 3 17 " --> pdb=" O LYS 3 13 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE 3 18 " --> pdb=" O LEU 3 14 " (cutoff:3.500A) Processing helix chain '3' and resid 22 through 39 removed outlier: 4.394A pdb=" N LEU 3 26 " --> pdb=" O ASN 3 22 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ALA 3 27 " --> pdb=" O PRO 3 23 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N THR 3 28 " --> pdb=" O GLU 3 24 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU 3 29 " --> pdb=" O ASN 3 25 " (cutoff:3.500A) Processing helix chain '3' and resid 43 through 57 removed outlier: 4.008A pdb=" N ASN 3 47 " --> pdb=" O ASP 3 43 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU 3 48 " --> pdb=" O LEU 3 44 " (cutoff:3.500A) Processing helix chain '3' and resid 62 through 75 removed outlier: 3.698A pdb=" N THR 3 66 " --> pdb=" O GLN 3 62 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS 3 72 " --> pdb=" O GLN 3 68 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR 3 75 " --> pdb=" O LEU 3 71 " (cutoff:3.500A) Processing helix chain '3' and resid 80 through 90 removed outlier: 5.394A pdb=" N ASP 3 90 " --> pdb=" O LYS 3 86 " (cutoff:3.500A) Processing helix chain '3' and resid 91 through 96 removed outlier: 4.062A pdb=" N GLU 3 95 " --> pdb=" O GLN 3 91 " (cutoff:3.500A) removed outlier: 4.332A 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: 3.776A pdb=" N LEU 3 105 " --> pdb=" O GLN 3 101 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY 3 106 " --> pdb=" O ILE 3 102 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU 3 108 " --> pdb=" O TYR 3 104 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU 3 109 " --> pdb=" O LEU 3 105 " (cutoff:3.500A) Processing helix chain '3' and resid 113 through 121 removed outlier: 3.560A pdb=" N GLN 3 119 " --> pdb=" O GLN 3 115 " (cutoff:3.500A) Processing helix chain '3' and resid 125 through 132 removed outlier: 3.741A pdb=" N GLY 3 130 " --> pdb=" O ASP 3 126 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE 3 131 " --> pdb=" O LEU 3 127 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR 3 132 " --> pdb=" O LEU 3 128 " (cutoff:3.500A) Processing helix chain '3' and resid 133 through 149 removed outlier: 3.913A pdb=" N VAL 3 138 " --> pdb=" O PHE 3 134 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ARG 3 139 " --> pdb=" O GLU 3 135 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS 3 140 " --> pdb=" O ASP 3 136 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS 3 144 " --> pdb=" O LYS 3 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY 3 147 " --> pdb=" O CYS 3 143 " (cutoff:3.500A) removed outlier: 3.993A 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: 4.014A 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: 3.533A pdb=" N LEU 4 99 " --> pdb=" O HIS 4 95 " (cutoff:3.500A) removed outlier: 3.956A 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: 3.994A pdb=" N GLU 4 193 " --> pdb=" O TYR 4 189 " (cutoff:3.500A) Processing helix chain '4' and resid 244 through 257 removed outlier: 4.850A pdb=" N PHE 4 257 " --> pdb=" O MET 4 253 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 294 removed outlier: 4.716A pdb=" N GLU 4 291 " --> pdb=" O LEU 4 287 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASP 4 292 " --> pdb=" O GLN 4 288 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL 4 293 " --> pdb=" O TYR 4 289 " (cutoff:3.500A) Processing helix chain '4' and resid 301 through 315 removed outlier: 5.140A pdb=" N PHE 4 307 " --> pdb=" O THR 4 303 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU 4 308 " --> pdb=" O VAL 4 304 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET 4 309 " --> pdb=" O GLY 4 305 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL 4 315 " --> pdb=" O LEU 4 311 " (cutoff:3.500A) Processing helix chain '4' and resid 319 through 357 removed outlier: 4.123A pdb=" N LEU 4 354 " --> pdb=" O LEU 4 350 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL 4 355 " --> pdb=" O ASN 4 351 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU 4 357 " --> pdb=" O LYS 4 353 " (cutoff:3.500A) Processing helix chain '5' and resid 183 through 205 removed outlier: 3.725A pdb=" N ILE 5 187 " --> pdb=" O LEU 5 183 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS 5 202 " --> pdb=" O SER 5 198 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS 5 203 " --> pdb=" O GLN 5 199 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR 5 204 " --> pdb=" O TYR 5 200 " (cutoff:3.500A) Processing helix chain '5' and resid 208 through 217 removed outlier: 3.528A 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: 3.879A pdb=" N SER 5 226 " --> pdb=" O TRP 5 222 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS 5 237 " --> pdb=" O SER 5 233 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG 5 242 " --> pdb=" O SER 5 238 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL 5 246 " --> pdb=" O ARG 5 242 " (cutoff:3.500A) Processing helix chain '5' and resid 253 through 260 Processing helix chain '5' and resid 261 through 268 removed outlier: 3.633A pdb=" N MET 5 268 " --> pdb=" O SER 5 264 " (cutoff:3.500A) Processing helix chain '5' and resid 274 through 291 removed outlier: 3.707A pdb=" N ARG 5 279 " --> pdb=" O VAL 5 275 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU 5 283 " --> pdb=" O ARG 5 279 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU 5 284 " --> pdb=" O LEU 5 280 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ILE 5 291 " --> pdb=" O TYR 5 287 " (cutoff:3.500A) Processing helix chain '5' and resid 297 through 304 removed outlier: 5.139A pdb=" N MET 5 304 " --> pdb=" O ASN 5 300 " (cutoff:3.500A) Processing helix chain '5' and resid 311 through 327 removed outlier: 3.816A pdb=" N TYR 5 317 " --> pdb=" O VAL 5 313 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL 5 319 " --> pdb=" O THR 5 315 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY 5 320 " --> pdb=" O TYR 5 316 " (cutoff:3.500A) Processing helix chain '5' and resid 328 through 342 removed outlier: 3.736A pdb=" N ILE 5 333 " --> pdb=" O TYR 5 329 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG 5 334 " --> pdb=" O GLN 5 330 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE 5 336 " --> pdb=" O ALA 5 332 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA 5 337 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASN 5 338 " --> pdb=" O ARG 5 334 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE 5 339 " --> pdb=" O VAL 5 335 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU 5 340 " --> pdb=" O PHE 5 336 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR 5 342 " --> pdb=" O ASN 5 338 " (cutoff:3.500A) Processing helix chain '5' and resid 357 through 375 removed outlier: 3.585A pdb=" N ASN 5 361 " --> pdb=" O TYR 5 357 " (cutoff:3.500A) Processing helix chain '5' and resid 388 through 403 removed outlier: 4.085A pdb=" N LYS 5 393 " --> pdb=" O GLN 5 389 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LYS 5 403 " --> pdb=" O LEU 5 399 " (cutoff:3.500A) Processing helix chain '5' and resid 405 through 417 removed outlier: 4.121A pdb=" N TYR 5 409 " --> pdb=" O ASP 5 405 " (cutoff:3.500A) Processing helix chain '5' and resid 438 through 463 removed outlier: 3.800A pdb=" N ILE 5 460 " --> pdb=" O GLN 5 456 " (cutoff:3.500A) removed outlier: 4.475A 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: 4.746A pdb=" N ASN 5 499 " --> pdb=" O HIS 5 495 " (cutoff:3.500A) Processing helix chain '5' and resid 526 through 549 removed outlier: 3.672A pdb=" N ALA 5 531 " --> pdb=" O MET 5 527 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE 5 547 " --> pdb=" O PHE 5 543 " (cutoff:3.500A) Processing helix chain '6' and resid 15 through 27 removed outlier: 5.226A pdb=" N ARG 6 19 " --> pdb=" O ALA 6 15 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA 6 20 " --> pdb=" O ALA 6 16 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA 6 27 " --> pdb=" O LYS 6 23 " (cutoff:3.500A) Processing helix chain '6' and resid 29 through 40 removed outlier: 4.933A pdb=" N ASN 6 33 " --> pdb=" O ILE 6 29 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY 6 36 " --> pdb=" O GLU 6 32 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY 6 37 " --> pdb=" O ASN 6 33 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU 6 38 " --> pdb=" O SER 6 34 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL 6 40 " --> pdb=" O GLY 6 36 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 54 removed outlier: 3.832A pdb=" N GLU 6 47 " --> pdb=" O ALA 6 43 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA 6 48 " --> pdb=" O GLN 6 44 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL 6 51 " --> pdb=" O GLU 6 47 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N CYS 6 52 " --> pdb=" O ALA 6 48 " (cutoff:3.500A) Processing helix chain '6' and resid 60 through 78 removed outlier: 4.202A pdb=" N ASN 6 65 " --> pdb=" O GLU 6 61 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL 6 68 " --> pdb=" O MET 6 64 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER 6 69 " --> pdb=" O ASN 6 65 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU 6 72 " --> pdb=" O VAL 6 68 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ILE 6 73 " --> pdb=" O SER 6 69 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU 6 74 " --> pdb=" O LEU 6 70 " (cutoff:3.500A) removed outlier: 3.985A 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: 4.730A pdb=" N ILE 6 83 " --> pdb=" O GLN 6 79 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLU 6 84 " --> pdb=" O GLU 6 80 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N SER 6 85 " --> pdb=" O ALA 6 81 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LEU 6 86 " --> pdb=" O LEU 6 82 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS 6 87 " --> pdb=" O ILE 6 83 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N GLU 6 88 " --> pdb=" O GLU 6 84 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS 6 89 " --> pdb=" O SER 6 85 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU 6 90 " --> pdb=" O LEU 6 86 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N VAL 6 91 " --> pdb=" O CYS 6 87 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE 6 93 " --> pdb=" O LYS 6 89 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG 6 94 " --> pdb=" O LEU 6 90 " (cutoff:3.500A) Processing helix chain '6' and resid 97 through 110 removed outlier: 4.326A pdb=" N LEU 6 101 " --> pdb=" O GLU 6 97 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG 6 102 " --> pdb=" O ARG 6 98 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASN 6 108 " --> pdb=" O GLN 6 104 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU 6 109 " --> pdb=" O LEU 6 105 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N PHE 6 110 " --> pdb=" O LEU 6 106 " (cutoff:3.500A) Processing helix chain '6' and resid 116 through 131 removed outlier: 3.923A pdb=" N LYS 6 129 " --> pdb=" O CYS 6 125 " (cutoff:3.500A) Processing helix chain '6' and resid 133 through 138 removed outlier: 4.752A pdb=" N ILE 6 137 " --> pdb=" O SER 6 133 " (cutoff:3.500A) removed outlier: 3.638A 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: 4.532A pdb=" N GLU 6 170 " --> pdb=" O ARG 6 166 " (cutoff:3.500A) removed outlier: 3.722A 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: 3.778A 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 262 through 267 removed outlier: 3.561A pdb=" N LEU 6 266 " --> pdb=" O PHE 6 262 " (cutoff:3.500A) Processing helix chain '6' and resid 268 through 287 removed outlier: 4.033A pdb=" N LEU 6 279 " --> pdb=" O ALA 6 275 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LEU 6 280 " --> pdb=" O LYS 6 276 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR 6 281 " --> pdb=" O MET 6 277 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N PHE 6 282 " --> pdb=" O ARG 6 278 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N MET 6 283 " --> pdb=" O LEU 6 279 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL 6 287 " --> pdb=" O MET 6 283 " (cutoff:3.500A) Processing helix chain '6' and resid 296 through 302 removed outlier: 3.588A pdb=" N GLN 6 302 " --> pdb=" O GLN 6 298 " (cutoff:3.500A) Processing helix chain '6' and resid 306 through 319 removed outlier: 4.636A pdb=" N ALA 6 310 " --> pdb=" O ASP 6 306 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE 6 313 " --> pdb=" O GLU 6 309 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR 6 318 " --> pdb=" O ASP 6 314 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LYS 6 319 " --> pdb=" O ALA 6 315 " (cutoff:3.500A) Processing helix chain '6' and resid 340 through 348 removed outlier: 4.782A pdb=" N LYS 6 344 " --> pdb=" O ARG 6 340 " (cutoff:3.500A) Processing helix chain '6' and resid 349 through 357 removed outlier: 3.716A pdb=" N ALA 6 356 " --> pdb=" O ASP 6 352 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TRP 6 357 " --> pdb=" O THR 6 353 " (cutoff:3.500A) Processing helix chain '6' and resid 251 through 257 removed outlier: 3.903A pdb=" N TYR 6 256 " --> pdb=" O SER 6 251 " (cutoff:3.500A) Processing helix chain '8' and resid 42 through 55 removed outlier: 3.597A pdb=" N LYS 8 51 " --> pdb=" O LEU 8 47 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS 8 52 " --> pdb=" O LYS 8 48 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN 8 54 " --> pdb=" O ILE 8 50 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU 8 55 " --> pdb=" O LYS 8 51 " (cutoff:3.500A) Processing helix chain '8' and resid 97 through 108 removed outlier: 3.966A pdb=" N MET 8 101 " --> pdb=" O VAL 8 97 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG 8 108 " --> pdb=" O MET 8 104 " (cutoff:3.500A) Processing helix chain '8' and resid 130 through 144 removed outlier: 3.836A pdb=" N LEU 8 134 " --> pdb=" O THR 8 130 " (cutoff:3.500A) Processing helix chain '8' and resid 154 through 159 removed outlier: 5.117A pdb=" N ALA 8 158 " --> pdb=" O PRO 8 154 " (cutoff:3.500A) Processing helix chain '8' and resid 170 through 178 removed outlier: 4.016A pdb=" N LYS 8 178 " --> pdb=" O MET 8 174 " (cutoff:3.500A) Processing helix chain '8' and resid 210 through 225 removed outlier: 4.683A pdb=" N LEU 8 214 " --> pdb=" O LEU 8 210 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL 8 224 " --> pdb=" O LYS 8 220 " (cutoff:3.500A) Processing helix chain '8' and resid 227 through 239 removed outlier: 5.795A pdb=" N LEU 8 231 " --> pdb=" O LYS 8 227 " (cutoff:3.500A) Processing helix chain '8' and resid 247 through 286 removed outlier: 4.204A pdb=" N GLN 8 278 " --> pdb=" O LYS 8 274 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLN 8 279 " --> pdb=" O HIS 8 275 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG 8 281 " --> pdb=" O TYR 8 277 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLN 8 282 " --> pdb=" O GLN 8 278 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN 8 283 " --> pdb=" O GLN 8 279 " (cutoff:3.500A) Processing helix chain '8' and resid 315 through 350 Processing helix chain '8' and resid 186 through 192 removed outlier: 3.540A pdb=" N ILE 8 192 " --> pdb=" O LEU 8 187 " (cutoff:3.500A) Processing helix chain '8' and resid 298 through 303 removed outlier: 3.806A 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 22 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: 3.668A pdb=" N VAL C 61 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 121 removed outlier: 3.569A pdb=" N LYS C 120 " --> pdb=" O PRO C 116 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.823A pdb=" N ILE C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.526A 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: 3.913A 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: 3.981A pdb=" N VAL D 43 " --> pdb=" O ASN D 39 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 5.224A 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: 3.761A pdb=" N ILE D 97 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 4.032A 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: 4.221A pdb=" N PHE D 105 " --> pdb=" O LYS D 101 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 106 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG D 109 " --> pdb=" O PHE D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 118 removed outlier: 3.516A pdb=" N LEU D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 133 removed outlier: 3.700A pdb=" N ARG D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 155 removed outlier: 4.437A pdb=" N LYS D 155 " --> pdb=" O LEU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 178 removed outlier: 3.655A pdb=" N ASN D 177 " --> pdb=" O VAL D 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 25 removed outlier: 4.246A pdb=" N TRP E 22 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N HIS E 23 " --> pdb=" O ASP E 19 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP E 24 " --> pdb=" O GLN E 20 " (cutoff:3.500A) removed outlier: 5.749A 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 removed outlier: 4.136A pdb=" N LYS E 37 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA E 38 " --> pdb=" O THR E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 95 removed outlier: 4.373A pdb=" N PHE E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE E 94 " --> pdb=" O CYS E 90 " (cutoff:3.500A) removed outlier: 5.606A 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 removed outlier: 3.513A pdb=" N GLN F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 116 Processing helix chain 'G' and resid 17 through 34 removed outlier: 3.642A pdb=" N ALA G 26 " --> pdb=" O GLY G 22 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU G 29 " --> pdb=" O GLN G 25 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET G 32 " --> pdb=" O LEU G 28 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN G 33 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N SER G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 77 removed outlier: 4.347A pdb=" N LYS G 70 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N SER G 71 " --> pdb=" O PRO G 67 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYS G 74 " --> pdb=" O LYS G 70 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ILE G 75 " --> pdb=" O SER G 71 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN G 76 " --> pdb=" O PHE G 72 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL G 77 " --> pdb=" O GLN G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 88 removed outlier: 3.705A pdb=" N GLU G 82 " --> pdb=" O ARG G 78 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER G 88 " --> pdb=" O GLU G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 122 removed outlier: 3.786A pdb=" N THR G 121 " --> pdb=" O PRO G 117 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU G 122 " --> pdb=" O ARG G 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 117 through 122' Processing helix chain 'G' and resid 123 through 135 removed outlier: 3.568A pdb=" N LEU G 130 " --> pdb=" O HIS G 126 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP G 132 " --> pdb=" O ALA G 128 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N PHE G 135 " --> pdb=" O GLU G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 167 removed outlier: 3.944A pdb=" N VAL G 166 " --> pdb=" O GLN G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 181 removed outlier: 3.953A pdb=" N SER G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY G 175 " --> pdb=" O GLU G 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 19 removed outlier: 4.223A pdb=" N ARG H 17 " --> pdb=" O GLU H 13 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N HIS H 19 " --> pdb=" O GLU H 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 44 removed outlier: 4.031A pdb=" N LYS I 34 " --> pdb=" O SER I 30 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS I 42 " --> pdb=" O TYR I 38 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY I 44 " --> pdb=" O LEU I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 57 removed outlier: 4.094A pdb=" N GLY I 51 " --> pdb=" O PRO I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 67 removed outlier: 3.576A pdb=" N VAL I 66 " --> pdb=" O GLN I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 79 removed outlier: 4.213A pdb=" N SER I 77 " --> pdb=" O ARG I 73 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS I 78 " --> pdb=" O ILE I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 106 removed outlier: 4.614A pdb=" N LEU I 91 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL I 96 " --> pdb=" O ILE I 92 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL I 98 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG I 99 " --> pdb=" O ALA I 95 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG I 104 " --> pdb=" O LYS I 100 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG I 106 " --> pdb=" O LEU I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 133 removed outlier: 4.378A pdb=" N PHE I 113 " --> pdb=" O LYS I 109 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE I 116 " --> pdb=" O LYS I 112 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG I 121 " --> pdb=" O LEU I 117 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N HIS I 123 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG I 124 " --> pdb=" O SER I 120 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR I 131 " --> pdb=" O ARG I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 151 removed outlier: 4.247A pdb=" N LEU I 149 " --> pdb=" O THR I 145 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL I 150 " --> pdb=" O ALA I 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 21 removed outlier: 3.514A pdb=" N ASP J 9 " --> pdb=" O ASN J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 45 removed outlier: 3.821A pdb=" N HIS J 44 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY J 45 " --> pdb=" O MET J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 93 removed outlier: 4.778A pdb=" N GLU J 87 " --> pdb=" O LEU J 83 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LYS J 88 " --> pdb=" O LYS J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 120 removed outlier: 4.073A pdb=" N ARG J 117 " --> pdb=" O HIS J 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS J 120 " --> pdb=" O ALA J 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 63 Processing helix chain 'K' and resid 64 through 77 removed outlier: 4.519A pdb=" N SER K 68 " --> pdb=" O GLU K 64 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLY K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 73 removed outlier: 3.710A pdb=" N LEU L 69 " --> pdb=" O LYS L 65 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET L 73 " --> pdb=" O LEU L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 85 removed outlier: 4.048A pdb=" N ILE L 81 " --> pdb=" O SER L 77 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE L 84 " --> pdb=" O GLU L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 98 removed outlier: 4.736A pdb=" N ILE L 94 " --> pdb=" O GLU L 90 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASP L 95 " --> pdb=" O SER L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 162 removed outlier: 3.652A pdb=" N ILE L 151 " --> pdb=" O VAL L 147 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG L 152 " --> pdb=" O ALA L 148 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU L 160 " --> pdb=" O ILE L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 208 through 218 removed outlier: 3.550A pdb=" N LYS L 212 " --> pdb=" O PRO L 208 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU L 213 " --> pdb=" O VAL L 209 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET L 216 " --> pdb=" O LYS L 212 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA L 217 " --> pdb=" O LEU L 213 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY L 218 " --> pdb=" O LEU L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 250 removed outlier: 3.599A pdb=" N ALA L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR L 240 " --> pdb=" O PHE L 236 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE L 244 " --> pdb=" O THR L 240 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR L 247 " --> pdb=" O ALA L 243 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TYR L 248 " --> pdb=" O ILE L 244 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER L 249 " --> pdb=" O SER L 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 257 removed outlier: 4.120A pdb=" N TRP L 256 " --> pdb=" O THR L 252 " (cutoff:3.500A) removed outlier: 5.140A 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 removed outlier: 3.524A pdb=" N PHE L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N THR L 270 " --> pdb=" O TYR L 266 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 276 removed outlier: 4.772A pdb=" N LYS L 275 " --> pdb=" O ASP L 271 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 21 removed outlier: 3.534A pdb=" N GLU M 18 " --> pdb=" O ARG M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 39 Processing helix chain 'M' and resid 43 through 64 removed outlier: 3.590A pdb=" N GLY M 64 " --> pdb=" O ARG M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 80 removed outlier: 4.282A pdb=" N GLU M 75 " --> pdb=" O ILE M 71 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU M 79 " --> pdb=" O GLU M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 110 removed outlier: 4.503A pdb=" N MET M 105 " --> pdb=" O ASP M 101 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU M 106 " --> pdb=" O THR M 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 11 through 22 removed outlier: 3.682A pdb=" N ALA N 20 " --> pdb=" O LEU N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 39 removed outlier: 5.326A pdb=" N ILE N 38 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N TYR N 39 " --> pdb=" O GLU N 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 34 through 39' Processing helix chain 'N' and resid 50 through 68 removed outlier: 3.540A pdb=" N TRP N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU N 58 " --> pdb=" O THR N 54 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU N 60 " --> pdb=" O GLU N 56 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE N 68 " --> pdb=" O ALA N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 94 removed outlier: 4.350A pdb=" N GLN N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ARG N 85 " --> pdb=" O ASN N 81 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ALA N 86 " --> pdb=" O THR N 82 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU N 88 " --> pdb=" O GLN N 84 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA N 91 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA N 93 " --> pdb=" O LYS N 89 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 131 removed outlier: 3.770A pdb=" N HIS N 131 " --> pdb=" O PRO N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 132 through 141 removed outlier: 4.066A pdb=" N TYR N 139 " --> pdb=" O THR N 135 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL N 140 " --> pdb=" O GLU N 136 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN N 141 " --> pdb=" O ALA N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 187 removed outlier: 3.729A pdb=" N VAL N 171 " --> pdb=" O GLY N 167 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY N 172 " --> pdb=" O ALA N 168 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET N 174 " --> pdb=" O SER N 170 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU N 183 " --> pdb=" O ALA N 179 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET N 185 " --> pdb=" O GLU N 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 204 removed outlier: 4.244A pdb=" N TYR N 202 " --> pdb=" O MET N 198 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE N 203 " --> pdb=" O PRO N 199 " (cutoff:3.500A) removed outlier: 5.535A 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: 3.793A pdb=" N VAL N 74 " --> pdb=" O PRO N 71 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N SER N 75 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 29 removed outlier: 3.528A pdb=" N LYS O 28 " --> pdb=" O PRO O 24 " (cutoff:3.500A) removed outlier: 5.843A 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: 4.649A pdb=" N GLY O 61 " --> pdb=" O ILE O 57 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU O 62 " --> pdb=" O ALA O 58 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLY O 64 " --> pdb=" O ASP O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 76 removed outlier: 3.720A pdb=" N LEU O 74 " --> pdb=" O SER O 70 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN O 76 " --> pdb=" O ALA O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 115 removed outlier: 4.610A pdb=" N VAL O 114 " --> pdb=" O MET O 110 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LYS O 115 " --> pdb=" O CYS O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 157 through 179 removed outlier: 3.885A pdb=" N ARG O 162 " --> pdb=" O HIS O 158 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS O 166 " --> pdb=" O ARG O 162 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR O 173 " --> pdb=" O MET O 169 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL O 176 " --> pdb=" O MET O 172 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR O 178 " --> pdb=" O ARG O 174 " (cutoff:3.500A) removed outlier: 4.209A 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: 3.542A pdb=" N LYS O 199 " --> pdb=" O LYS O 195 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN O 202 " --> pdb=" O GLU O 198 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N SER O 203 " --> pdb=" O LYS O 199 " (cutoff:3.500A) Processing helix chain 'O' and resid 224 through 233 removed outlier: 3.681A pdb=" N LEU O 228 " --> pdb=" O GLU O 224 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET O 229 " --> pdb=" O LEU O 225 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY O 233 " --> pdb=" O MET O 229 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 63 removed outlier: 4.228A pdb=" N LYS P 61 " --> pdb=" O THR P 57 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL P 62 " --> pdb=" O GLY P 58 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS P 63 " --> pdb=" O GLY P 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 57 through 63' Processing helix chain 'P' and resid 64 through 69 removed outlier: 5.910A pdb=" N GLU P 68 " --> pdb=" O ALA P 64 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N SER P 69 " --> pdb=" O ASP P 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 64 through 69' Processing helix chain 'P' and resid 70 through 89 removed outlier: 4.286A pdb=" N ASP P 80 " --> pdb=" O LEU P 76 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL P 81 " --> pdb=" O ALA P 77 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN P 83 " --> pdb=" O GLN P 79 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ARG P 84 " --> pdb=" O ASP P 80 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU P 87 " --> pdb=" O GLN P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 109 through 123 removed outlier: 4.796A pdb=" N GLN P 113 " --> pdb=" O GLY P 109 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER P 114 " --> pdb=" O PRO P 110 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU P 116 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG P 117 " --> pdb=" O GLN P 113 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLY P 123 " --> pdb=" O LEU P 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 57 removed outlier: 3.775A pdb=" N SER Q 57 " --> pdb=" O ILE Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 82 removed outlier: 4.548A pdb=" N ILE Q 79 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS Q 80 " --> pdb=" O SER Q 76 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS Q 82 " --> pdb=" O ALA Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 88 through 95 removed outlier: 3.836A pdb=" N LYS Q 93 " --> pdb=" O ARG Q 89 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP Q 94 " --> pdb=" O GLU Q 90 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ARG Q 95 " --> pdb=" O ALA Q 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 94 removed outlier: 4.174A pdb=" N VAL R 91 " --> pdb=" O ASN R 87 " (cutoff:3.500A) removed outlier: 3.753A 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 145 through 156 removed outlier: 3.561A pdb=" N ARG R 152 " --> pdb=" O LYS R 148 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN R 155 " --> pdb=" O GLU R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 169 Processing helix chain 'R' and resid 192 through 207 removed outlier: 4.785A pdb=" N GLY R 207 " --> pdb=" O LYS R 203 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 28 removed outlier: 4.972A pdb=" N LEU S 24 " --> pdb=" O ASP S 20 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N THR S 26 " --> pdb=" O ARG S 22 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE S 27 " --> pdb=" O LYS S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 146 Processing helix chain 'S' and resid 152 through 157 removed outlier: 4.208A pdb=" N TYR S 156 " --> pdb=" O ASP S 152 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 229 Processing helix chain 'S' and resid 121 through 126 removed outlier: 3.831A pdb=" N ASP S 126 " --> pdb=" O ILE S 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 121 through 126' Processing helix chain 'T' and resid 36 through 49 removed outlier: 3.615A pdb=" N LYS T 46 " --> pdb=" O GLU T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 56 removed outlier: 4.218A pdb=" N ILE T 55 " --> pdb=" O THR T 51 " (cutoff:3.500A) removed outlier: 5.816A 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 Processing helix chain 'T' and resid 87 through 95 removed outlier: 3.737A pdb=" N HIS T 94 " --> pdb=" O ARG T 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 103 through 118 removed outlier: 4.426A pdb=" N LYS T 116 " --> pdb=" O ASN T 112 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL T 117 " --> pdb=" O ARG T 113 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ARG T 118 " --> pdb=" O MET T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 119 through 128 removed outlier: 4.817A pdb=" N ALA T 123 " --> pdb=" O GLY T 119 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN T 124 " --> pdb=" O THR T 120 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY T 128 " --> pdb=" O ASN T 124 " (cutoff:3.500A) Processing helix chain 'V' and resid 35 through 40 removed outlier: 5.599A pdb=" N ALA V 40 " --> pdb=" O GLN V 36 " (cutoff:3.500A) Processing helix chain 'V' and resid 61 through 66 removed outlier: 4.292A pdb=" N GLN V 65 " --> pdb=" O PHE V 61 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N CYS V 66 " --> pdb=" O ARG V 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 61 through 66' Processing helix chain 'V' and resid 67 through 77 removed outlier: 3.846A pdb=" N MET V 77 " --> pdb=" O THR V 73 " (cutoff:3.500A) Processing helix chain 'V' and resid 85 through 104 removed outlier: 3.760A pdb=" N THR V 89 " --> pdb=" O LYS V 85 " (cutoff:3.500A) Processing helix chain 'V' and resid 107 through 120 Processing helix chain 'V' and resid 142 through 163 removed outlier: 3.958A pdb=" N PHE V 163 " --> pdb=" O ARG V 159 " (cutoff:3.500A) Processing helix chain 'V' and resid 168 through 183 Processing helix chain 'V' and resid 187 through 204 removed outlier: 3.772A pdb=" N LYS V 191 " --> pdb=" O SER V 187 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG V 204 " --> pdb=" O ALA V 200 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 59 removed outlier: 4.500A pdb=" N TYR Y 49 " --> pdb=" O ARG Y 45 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS Y 50 " --> pdb=" O THR Y 46 " (cutoff:3.500A) removed outlier: 3.505A 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 66 removed outlier: 3.869A pdb=" N GLY Y 65 " --> pdb=" O GLU Y 61 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL Y 66 " --> pdb=" O ARG Y 62 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 99 Processing helix chain 'Y' and resid 101 through 116 Processing helix chain 'Z' and resid 6 through 30 Processing helix chain 'Z' and resid 54 through 60 Processing helix chain 'Z' and resid 63 through 78 Processing helix chain 'Z' and resid 93 through 98 removed outlier: 4.574A pdb=" N CYS Z 97 " --> pdb=" O THR Z 93 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ALA Z 98 " --> pdb=" O ARG Z 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 93 through 98' Processing helix chain 'Z' and resid 99 through 112 removed outlier: 4.642A pdb=" N GLY Z 112 " --> pdb=" O LYS Z 108 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 130 removed outlier: 3.852A pdb=" N GLY Z 130 " --> pdb=" O ILE Z 126 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 167 removed outlier: 4.652A pdb=" N ASN Z 165 " --> pdb=" O GLY Z 161 " (cutoff:3.500A) removed outlier: 3.954A 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 83 Processing helix chain 'a' and resid 91 through 96 removed outlier: 4.693A pdb=" N ARG a 95 " --> pdb=" O PRO a 91 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG a 96 " --> pdb=" O ALA a 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 91 through 96' Processing helix chain 'b' and resid 21 through 29 removed outlier: 5.999A pdb=" N SER b 29 " --> pdb=" O LEU b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 38 removed outlier: 3.981A pdb=" N GLN b 35 " --> pdb=" O GLU b 31 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU b 36 " --> pdb=" O GLN b 32 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR b 37 " --> pdb=" O LEU b 33 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N SER b 38 " --> pdb=" O MET b 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 39 through 48 removed outlier: 4.920A pdb=" N GLY b 48 " --> pdb=" O ARG b 44 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 67 removed outlier: 3.705A pdb=" N ALA b 67 " --> pdb=" O ALA b 63 " (cutoff:3.500A) Processing helix chain 'b' and resid 115 through 121 removed outlier: 4.933A pdb=" N PHE b 119 " --> pdb=" O TYR b 115 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER b 120 " --> pdb=" O LEU b 116 " (cutoff:3.500A) removed outlier: 5.227A 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: 3.612A pdb=" N ARG d 16 " --> pdb=" O GLN d 12 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLY d 26 " --> pdb=" O LEU d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 67 removed outlier: 4.837A 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: 4.050A pdb=" N ALA d 100 " --> pdb=" O SER d 96 " (cutoff:3.500A) Processing helix chain 'd' and resid 124 through 144 removed outlier: 3.502A pdb=" N LYS d 143 " --> pdb=" O ALA d 139 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYS d 144 " --> pdb=" O ALA d 140 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 61 Processing helix chain 'e' and resid 69 through 78 removed outlier: 3.514A pdb=" N VAL e 73 " --> pdb=" O THR e 69 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER e 74 " --> pdb=" O PRO e 70 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU e 75 " --> pdb=" O ALA e 71 " (cutoff:3.500A) removed outlier: 4.846A 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: 3.609A pdb=" N ILE f 30 " --> pdb=" O ILE f 26 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR f 31 " --> pdb=" O ALA f 27 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA f 32 " --> pdb=" O PHE f 28 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE f 33 " --> pdb=" O ALA f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 49 removed outlier: 4.711A pdb=" N ASP f 49 " --> pdb=" O LEU f 45 " (cutoff:3.500A) Processing helix chain 'f' and resid 60 through 74 Proline residue: f 74 - end of helix Processing helix chain 'f' and resid 99 through 118 removed outlier: 4.460A pdb=" N ASP f 104 " --> pdb=" O ALA f 100 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG f 118 " --> pdb=" O LEU f 114 " (cutoff:3.500A) Processing helix chain 'f' and resid 119 through 128 Processing helix chain 'f' and resid 140 through 145 removed outlier: 3.938A pdb=" N ARG f 144 " --> pdb=" O GLY f 140 " (cutoff:3.500A) removed outlier: 4.992A 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 removed outlier: 3.671A pdb=" N LEU h 32 " --> pdb=" O ASN h 28 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS h 46 " --> pdb=" O GLY h 42 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN h 47 " --> pdb=" O ALA h 43 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 103 removed outlier: 3.656A pdb=" N VAL h 98 " --> pdb=" O PRO h 94 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN h 100 " --> pdb=" O GLU h 96 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N SER h 103 " --> pdb=" O LYS h 99 " (cutoff:3.500A) Processing helix chain 'i' and resid 39 through 47 Processing helix chain 'm' and resid 13 through 29 Processing helix chain 'm' and resid 34 through 45 removed outlier: 4.261A pdb=" N LEU m 42 " --> pdb=" O ALA m 38 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG m 45 " --> pdb=" O ALA m 41 " (cutoff:3.500A) Processing helix chain 'm' and resid 58 through 73 removed outlier: 3.846A pdb=" N VAL m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL m 65 " --> pdb=" O TYR m 61 " (cutoff:3.500A) removed outlier: 3.544A 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: 4.724A pdb=" N VAL m 123 " --> pdb=" O GLN m 119 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE m 124 " --> pdb=" O ALA m 120 " (cutoff:3.500A) Processing helix chain 'o' and resid 251 through 261 removed outlier: 3.616A 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 301 removed outlier: 3.694A pdb=" N ALA o 294 " --> pdb=" O ARG o 290 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA o 298 " --> pdb=" O ALA o 294 " (cutoff:3.500A) Processing helix chain 'p' and resid 55 through 68 removed outlier: 3.633A pdb=" N LEU p 59 " --> pdb=" O ASP p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 89 through 101 removed outlier: 3.577A pdb=" N CYS p 94 " --> pdb=" O ARG p 90 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN p 95 " --> pdb=" O LYS p 91 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLU p 99 " --> pdb=" O GLN p 95 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE p 100 " --> pdb=" O PHE p 96 " (cutoff:3.500A) Processing helix chain 'p' and resid 104 through 109 removed outlier: 6.030A pdb=" N LYS p 109 " --> pdb=" O ASP p 105 " (cutoff:3.500A) Processing helix chain 'q' and resid 97 through 107 removed outlier: 3.648A pdb=" N SER q 102 " --> pdb=" O ASP q 98 " (cutoff:3.500A) Processing helix chain 'r' and resid 47 through 52 removed outlier: 5.021A pdb=" N SER r 52 " --> pdb=" O LEU r 48 " (cutoff:3.500A) Processing helix chain 'r' and resid 58 through 63 removed outlier: 3.663A pdb=" N LEU r 62 " --> pdb=" O SER r 58 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE r 63 " --> pdb=" O ILE r 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 58 through 63' Processing helix chain 'r' and resid 91 through 120 removed outlier: 3.516A pdb=" N ALA r 95 " --> pdb=" O SER r 91 " (cutoff:3.500A) Processing helix chain 'r' and resid 123 through 143 removed outlier: 3.530A pdb=" N GLU r 128 " --> pdb=" O ASP r 124 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR r 134 " --> pdb=" O LEU r 130 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TRP r 136 " --> pdb=" O GLN r 132 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL r 137 " --> pdb=" O ARG r 133 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE r 138 " --> pdb=" O THR r 134 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR r 142 " --> pdb=" O PHE r 138 " (cutoff:3.500A) Processing helix chain 'r' and resid 146 through 159 removed outlier: 4.373A pdb=" N SER r 158 " --> pdb=" O LYS r 154 " (cutoff:3.500A) Processing helix chain 'r' and resid 160 through 166 removed outlier: 3.686A pdb=" N SER r 165 " --> pdb=" O SER r 161 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU r 166 " --> pdb=" O ILE r 162 " (cutoff:3.500A) Processing helix chain 'r' and resid 169 through 185 removed outlier: 3.906A pdb=" N ARG r 173 " --> pdb=" O ASN r 169 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU r 174 " --> pdb=" O GLU r 170 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL r 175 " --> pdb=" O ASP r 171 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN r 181 " --> pdb=" O ILE r 177 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ARG r 182 " --> pdb=" O ASN r 178 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ARG r 183 " --> pdb=" O ASN r 179 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LEU r 184 " --> pdb=" O ILE r 180 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR r 185 " --> pdb=" O ASN r 181 " (cutoff:3.500A) Processing helix chain 'r' and resid 203 through 219 removed outlier: 5.217A pdb=" N SER r 219 " --> pdb=" O GLY r 215 " (cutoff:3.500A) Processing helix chain 'r' and resid 243 through 265 removed outlier: 3.641A pdb=" N GLY r 247 " --> pdb=" O GLU r 243 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER r 249 " --> pdb=" O THR r 245 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU r 264 " --> pdb=" O GLU r 260 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LYS r 265 " --> pdb=" O LYS r 261 " (cutoff:3.500A) Processing helix chain 's' and resid 176 through 186 removed outlier: 3.619A pdb=" N ASN s 181 " --> pdb=" O GLU s 177 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN s 185 " --> pdb=" O ASN s 181 " (cutoff:3.500A) Processing helix chain 's' and resid 221 through 228 removed outlier: 3.728A pdb=" N ILE s 225 " --> pdb=" O ASN s 221 " (cutoff:3.500A) Processing helix chain 's' and resid 232 through 245 removed outlier: 3.994A pdb=" N LEU s 236 " --> pdb=" O GLN s 232 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU s 237 " --> pdb=" O PRO s 233 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA s 238 " --> pdb=" O LYS s 234 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE s 239 " --> pdb=" O HIS s 235 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU s 244 " --> pdb=" O LEU s 240 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY s 245 " --> pdb=" O LEU s 241 " (cutoff:3.500A) Processing helix chain 's' and resid 263 through 278 removed outlier: 3.861A pdb=" N ILE s 267 " --> pdb=" O GLN s 263 " (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 152 removed outlier: 3.696A pdb=" N MET t 145 " --> pdb=" O LEU t 141 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN t 147 " --> pdb=" O ALA t 143 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA t 150 " --> pdb=" O LEU t 146 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL t 151 " --> pdb=" O ASN t 147 " (cutoff:3.500A) Processing helix chain 't' and resid 168 through 181 Processing helix chain 't' and resid 191 through 196 removed outlier: 5.089A 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 215 through 220 removed outlier: 4.654A pdb=" N ALA t 219 " --> pdb=" O VAL t 215 " (cutoff:3.500A) Proline residue: t 220 - end of helix No H-bonds generated for 'chain 't' and resid 215 through 220' 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: 4.520A pdb=" N ALA u 11 " --> pdb=" O ARG u 7 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU u 12 " --> pdb=" O PRO u 8 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS u 13 " --> pdb=" O GLU u 9 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU u 17 " --> pdb=" O LYS u 13 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU u 19 " --> pdb=" O ALA u 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU u 20 " --> pdb=" O ASN u 16 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL u 21 " --> pdb=" O GLU u 17 " (cutoff:3.500A) Processing helix chain 'u' and resid 23 through 37 removed outlier: 3.750A pdb=" N LEU u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER u 37 " --> pdb=" O ASP u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 44 through 62 removed outlier: 4.772A pdb=" N GLU u 48 " --> pdb=" O GLN u 44 " (cutoff:3.500A) Proline residue: u 49 - end of helix removed outlier: 4.914A pdb=" N ARG u 62 " --> pdb=" O CYS u 58 " (cutoff:3.500A) Processing helix chain 'u' and resid 63 through 79 removed outlier: 4.771A pdb=" N ALA u 67 " --> pdb=" O LYS u 63 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN u 79 " --> pdb=" O LYS u 75 " (cutoff:3.500A) Processing helix chain 'u' and resid 82 through 117 removed outlier: 4.167A pdb=" N LEU u 86 " --> pdb=" O ASN u 82 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA u 104 " --> pdb=" O LYS u 100 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU u 106 " --> pdb=" O GLU u 102 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLU u 107 " --> pdb=" O ALA u 103 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASP u 117 " --> pdb=" O LEU u 113 " (cutoff:3.500A) Processing helix chain 'u' and resid 123 through 133 removed outlier: 4.564A pdb=" N LEU u 128 " --> pdb=" O PRO u 124 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU u 129 " --> pdb=" O GLU u 125 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA u 131 " --> pdb=" O VAL u 127 " (cutoff:3.500A) Processing helix chain 'u' and resid 136 through 146 removed outlier: 3.800A pdb=" N ARG u 143 " --> pdb=" O ASP u 139 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU u 145 " --> pdb=" O THR u 141 " (cutoff:3.500A) Processing helix chain 'u' and resid 147 through 165 removed outlier: 3.541A pdb=" N LEU u 161 " --> pdb=" O TYR u 157 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU u 164 " --> pdb=" O CYS u 160 " (cutoff:3.500A) Processing helix chain 'u' and resid 170 through 189 removed outlier: 4.822A pdb=" N THR u 189 " --> pdb=" O CYS u 185 " (cutoff:3.500A) Processing helix chain 'u' and resid 190 through 211 removed outlier: 3.969A pdb=" N PHE u 194 " --> pdb=" O ARG u 190 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG u 195 " --> pdb=" O LYS u 191 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS u 196 " --> pdb=" O ALA u 192 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU u 205 " --> pdb=" O LEU u 201 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE u 208 " --> pdb=" O HIS u 204 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLN u 209 " --> pdb=" O LEU u 205 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG u 210 " --> pdb=" O SER u 206 " (cutoff:3.500A) Processing helix chain 'u' and resid 222 through 244 removed outlier: 3.505A pdb=" N GLU u 231 " --> pdb=" O SER u 227 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR u 232 " --> pdb=" O MET u 228 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG u 233 " --> pdb=" O HIS u 229 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER u 242 " --> pdb=" O ASP u 238 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET u 243 " --> pdb=" O SER u 239 " (cutoff:3.500A) Processing helix chain 'u' and resid 245 through 262 removed outlier: 3.957A pdb=" N PHE u 250 " --> pdb=" O TRP u 246 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER u 261 " --> pdb=" O HIS u 257 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU u 262 " --> pdb=" O GLY u 258 " (cutoff:3.500A) Processing helix chain 'u' and resid 268 through 287 removed outlier: 3.527A pdb=" N MET u 272 " --> pdb=" O LYS u 268 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ALA u 273 " --> pdb=" O PRO u 269 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN u 274 " --> pdb=" O GLN u 270 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN u 277 " --> pdb=" O ALA u 273 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N SER u 280 " --> pdb=" O TYR u 276 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TRP u 284 " --> pdb=" O SER u 280 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS u 285 " --> pdb=" O THR u 281 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY u 287 " --> pdb=" O PHE u 283 " (cutoff:3.500A) Processing helix chain 'u' and resid 288 through 307 removed outlier: 4.030A pdb=" N HIS u 292 " --> pdb=" O ASN u 288 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU u 305 " --> pdb=" O HIS u 301 " (cutoff:3.500A) Processing helix chain 'u' and resid 311 through 329 removed outlier: 3.740A pdb=" N SER u 328 " --> pdb=" O LEU u 324 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE u 329 " --> pdb=" O ALA u 325 " (cutoff:3.500A) Processing helix chain 'u' and resid 338 through 345 removed outlier: 5.049A pdb=" N MET u 344 " --> pdb=" O ARG u 340 " (cutoff:3.500A) Processing helix chain 'u' and resid 350 through 360 removed outlier: 4.555A pdb=" N ARG u 354 " --> pdb=" O GLU u 350 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU u 359 " --> pdb=" O LEU u 355 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY u 360 " --> pdb=" O ALA u 356 " (cutoff:3.500A) Processing helix chain 'u' and resid 369 through 377 removed outlier: 4.295A pdb=" N ASP u 373 " --> pdb=" O GLY u 369 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET u 374 " --> pdb=" O LEU u 370 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE u 377 " --> pdb=" O ASP u 373 " (cutoff:3.500A) Processing helix chain 'u' and resid 378 through 384 removed outlier: 4.375A pdb=" N TYR u 382 " --> pdb=" O ASN u 378 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL u 384 " --> pdb=" O LEU u 380 " (cutoff:3.500A) Processing helix chain 'u' and resid 389 through 395 Processing helix chain 'u' and resid 402 through 417 removed outlier: 4.377A pdb=" N VAL u 410 " --> pdb=" O ARG u 406 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN u 417 " --> pdb=" O TRP u 413 " (cutoff:3.500A) Processing helix chain 'u' and resid 421 through 447 removed outlier: 4.126A pdb=" N GLN u 425 " --> pdb=" O GLU u 421 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN u 426 " --> pdb=" O PRO u 422 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR u 427 " --> pdb=" O GLU u 423 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL u 428 " --> pdb=" O LEU u 424 " (cutoff:3.500A) Proline residue: u 429 - end of helix removed outlier: 4.364A pdb=" N GLN u 445 " --> pdb=" O GLN u 441 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE u 446 " --> pdb=" O GLN u 442 " (cutoff:3.500A) Processing helix chain 'u' and resid 451 through 460 removed outlier: 3.650A pdb=" N LEU u 455 " --> pdb=" O GLU u 451 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER u 457 " --> pdb=" O SER u 453 " (cutoff:3.500A) removed outlier: 3.664A 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: 4.492A pdb=" N HIS u 477 " --> pdb=" O ASP u 473 " (cutoff:3.500A) Processing helix chain 'u' and resid 516 through 526 removed outlier: 5.893A pdb=" N ARG u 520 " --> pdb=" O SER u 516 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN u 521 " --> pdb=" O GLU u 517 " (cutoff:3.500A) removed outlier: 3.651A 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: 4.089A pdb=" N ILE u 537 " --> pdb=" O ALA u 533 " (cutoff:3.500A) removed outlier: 3.950A 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: 3.654A pdb=" N GLU u 545 " --> pdb=" O HIS u 541 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS u 546 " --> pdb=" O ILE u 542 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HIS u 550 " --> pdb=" O LYS u 546 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS u 563 " --> pdb=" O LYS u 559 " (cutoff:3.500A) Processing helix chain 'u' and resid 569 through 574 removed outlier: 4.176A pdb=" N GLN u 573 " --> pdb=" O LEU u 569 " (cutoff:3.500A) Processing helix chain 'u' and resid 579 through 639 removed outlier: 3.551A pdb=" N GLU u 610 " --> pdb=" O LYS u 606 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG u 611 " --> pdb=" O ALA u 607 " (cutoff:3.500A) Processing helix chain 'u' and resid 652 through 700 removed outlier: 5.705A pdb=" N ILE u 656 " --> pdb=" O ALA u 652 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP u 657 " --> pdb=" O PHE u 653 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU u 659 " --> pdb=" O ASP u 655 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP u 660 " --> pdb=" O ILE u 656 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU u 661 " --> pdb=" O ASP u 657 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU u 662 " --> pdb=" O ILE u 658 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU u 663 " --> pdb=" O GLU u 659 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU u 664 " --> pdb=" O ASP u 660 " (cutoff:3.500A) Proline residue: u 666 - end of helix Processing helix chain 'v' and resid 48 through 56 removed outlier: 3.593A pdb=" N ASP v 52 " --> pdb=" O THR v 48 " (cutoff:3.500A) Processing helix chain 'v' and resid 61 through 71 removed outlier: 3.777A pdb=" N ASP v 65 " --> pdb=" O LEU v 61 " (cutoff:3.500A) Proline residue: v 67 - end of helix removed outlier: 4.234A pdb=" N ARG v 71 " --> pdb=" O PRO v 67 " (cutoff:3.500A) Processing helix chain 'v' and resid 76 through 85 removed outlier: 3.541A pdb=" N LEU v 84 " --> pdb=" O GLN v 80 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN v 85 " --> pdb=" O LEU v 81 " (cutoff:3.500A) Processing helix chain 'v' and resid 92 through 113 removed outlier: 4.737A pdb=" N GLU v 96 " --> pdb=" O VAL v 92 " (cutoff:3.500A) Proline residue: v 98 - end of helix removed outlier: 4.174A pdb=" N THR v 107 " --> pdb=" O GLN v 103 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ARG v 108 " --> pdb=" O MET v 104 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP v 109 " --> pdb=" O GLN v 105 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLY v 110 " --> pdb=" O SER v 106 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ARG v 111 " --> pdb=" O THR v 107 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET v 112 " --> pdb=" O ARG v 108 " (cutoff:3.500A) Processing helix chain 'v' and resid 128 through 139 removed outlier: 4.233A pdb=" N LYS v 136 " --> pdb=" O TYR v 132 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE v 137 " --> pdb=" O ARG v 133 " (cutoff:3.500A) Processing helix chain 'v' and resid 146 through 151 Processing helix chain 'v' and resid 164 through 180 removed outlier: 4.396A pdb=" N TRP v 170 " --> pdb=" O LEU v 166 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER v 175 " --> pdb=" O GLY v 171 " (cutoff:3.500A) Processing helix chain 'v' and resid 181 through 197 removed outlier: 3.680A pdb=" N ILE v 196 " --> pdb=" O LEU v 192 " (cutoff:3.500A) Processing helix chain 'v' and resid 203 through 219 removed outlier: 4.925A 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: 4.855A pdb=" N ASP v 230 " --> pdb=" O PRO v 226 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASN v 231 " --> pdb=" O LYS v 227 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE v 232 " --> pdb=" O GLY v 228 " (cutoff:3.500A) Processing helix chain 'v' and resid 237 through 246 removed outlier: 3.697A pdb=" N ILE v 246 " --> pdb=" O TYR v 242 " (cutoff:3.500A) Processing helix chain 'v' and resid 250 through 263 removed outlier: 3.581A pdb=" N ILE v 262 " --> pdb=" O THR v 258 " (cutoff:3.500A) Processing helix chain 'v' and resid 272 through 282 removed outlier: 4.627A pdb=" N ASP v 276 " --> pdb=" O GLN v 272 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL v 278 " --> pdb=" O LEU v 274 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS v 279 " --> pdb=" O LYS v 275 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE v 281 " --> pdb=" O LEU v 277 " (cutoff:3.500A) Processing helix chain 'v' and resid 286 through 291 removed outlier: 3.961A 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: 4.520A pdb=" N VAL v 296 " --> pdb=" O ILE v 292 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU v 299 " --> pdb=" O PHE v 295 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N TYR v 300 " --> pdb=" O VAL v 296 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL v 301 " --> pdb=" O GLU v 297 " (cutoff:3.500A) Processing helix chain 'v' and resid 305 through 322 removed outlier: 5.757A pdb=" N GLN v 309 " --> pdb=" O PHE v 305 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS v 310 " --> pdb=" O ASP v 306 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS v 311 " --> pdb=" O GLY v 307 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU v 312 " --> pdb=" O ALA v 308 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ARG v 313 " --> pdb=" O GLN v 309 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU v 314 " --> pdb=" O LYS v 310 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER v 317 " --> pdb=" O ARG v 313 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL v 318 " --> pdb=" O GLU v 314 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN v 321 " --> pdb=" O SER v 317 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP v 322 " --> pdb=" O VAL v 318 " (cutoff:3.500A) Processing helix chain 'v' and resid 324 through 348 removed outlier: 5.403A pdb=" N CYS v 328 " --> pdb=" O PHE v 324 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU v 329 " --> pdb=" O LEU v 325 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLU v 330 " --> pdb=" O VAL v 326 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP v 331 " --> pdb=" O ALA v 327 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N PHE v 332 " --> pdb=" O CYS v 328 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE v 341 " --> pdb=" O ARG v 337 " (cutoff:3.500A) Processing helix chain 'v' and resid 352 through 358 removed outlier: 3.587A pdb=" N ALA v 357 " --> pdb=" O ILE v 353 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASP v 358 " --> pdb=" O ASN v 354 " (cutoff:3.500A) Processing helix chain 'v' and resid 363 through 379 removed outlier: 3.639A pdb=" N GLU v 368 " --> pdb=" O PRO v 364 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG v 369 " --> pdb=" O GLU v 365 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALA v 378 " --> pdb=" O LEU v 374 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ARG v 379 " --> pdb=" O ILE v 375 " (cutoff:3.500A) Processing helix chain 'v' and resid 402 through 420 removed outlier: 3.922A pdb=" N MET v 420 " --> pdb=" O GLN v 416 " (cutoff:3.500A) Processing helix chain 'v' and resid 37 through 42 removed outlier: 3.914A pdb=" N GLY v 40 " --> pdb=" O LEU v 37 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS v 41 " --> pdb=" O LEU v 38 " (cutoff:3.500A) Processing helix chain 'x' and resid 175 through 182 removed outlier: 3.750A pdb=" N LYS x 181 " --> pdb=" O PRO x 177 " (cutoff:3.500A) removed outlier: 3.562A 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: 3.585A pdb=" N LEU x 238 " --> pdb=" O VAL x 234 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LYS x 240 " --> pdb=" O ARG x 236 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N THR x 241 " --> pdb=" O LYS x 237 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN x 242 " --> pdb=" O LEU x 238 " (cutoff:3.500A) Processing helix chain 'x' and resid 250 through 257 removed outlier: 5.316A pdb=" N THR x 254 " --> pdb=" O ALA x 250 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU x 255 " --> pdb=" O ILE x 251 " (cutoff:3.500A) Processing helix chain 'x' and resid 308 through 327 removed outlier: 4.136A pdb=" N SER x 324 " --> pdb=" O ASN x 320 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN x 325 " --> pdb=" O HIS x 321 " (cutoff:3.500A) Processing helix chain 'x' and resid 408 through 413 removed outlier: 3.507A pdb=" N LYS x 412 " --> pdb=" O ASP x 408 " (cutoff:3.500A) Processing helix chain 'x' and resid 416 through 428 removed outlier: 3.552A pdb=" N VAL x 420 " --> pdb=" O GLN x 416 " (cutoff:3.500A) Processing helix chain 'x' and resid 429 through 443 removed outlier: 3.921A pdb=" N CYS x 438 " --> pdb=" O ARG x 434 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY x 443 " --> pdb=" O ALA x 439 " (cutoff:3.500A) Processing helix chain 'x' and resid 472 through 481 removed outlier: 4.095A pdb=" N ASN x 481 " --> pdb=" O ALA x 477 " (cutoff:3.500A) Processing helix chain 'x' and resid 483 through 501 removed outlier: 3.965A pdb=" N LYS x 500 " --> pdb=" O ASP x 496 " (cutoff:3.500A) removed outlier: 4.693A 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: 4.788A pdb=" N SER y 95 " --> pdb=" O GLY y 91 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ILE y 96 " --> pdb=" O LYS y 92 " (cutoff:3.500A) Processing helix chain 'y' and resid 103 through 122 removed outlier: 4.830A 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 151 removed outlier: 3.574A pdb=" N ARG y 150 " --> pdb=" O ARG y 146 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ASP y 151 " --> pdb=" O LYS y 147 " (cutoff:3.500A) Processing helix chain 'y' and resid 152 through 160 Processing helix chain 'y' and resid 264 through 281 removed outlier: 3.540A pdb=" N LYS y 279 " --> pdb=" O GLU y 275 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS y 280 " --> pdb=" O ASP y 276 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LYS y 281 " --> pdb=" O LYS y 277 " (cutoff:3.500A) Processing helix chain 'y' and resid 287 through 296 removed outlier: 3.853A pdb=" N GLU y 293 " --> pdb=" O LEU y 289 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU y 294 " --> pdb=" O ASP y 290 " (cutoff:3.500A) Processing helix chain 'y' and resid 314 through 319 removed outlier: 5.297A pdb=" N PHE y 318 " --> pdb=" O LYS y 314 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ALA y 319 " --> pdb=" O PRO y 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 314 through 319' Processing helix chain 'y' and resid 327 through 341 removed outlier: 4.225A pdb=" N LYS y 331 " --> pdb=" O ALA y 327 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA y 339 " --> pdb=" O GLU y 335 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG y 340 " --> pdb=" O ILE y 336 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLY y 341 " --> pdb=" O LEU y 337 " (cutoff:3.500A) Processing helix chain 'y' and resid 346 through 365 removed outlier: 3.648A pdb=" N ILE y 351 " --> pdb=" O ARG y 347 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU y 352 " --> pdb=" O ALA y 348 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASN y 365 " --> pdb=" O ALA y 361 " (cutoff:3.500A) Processing helix chain 'y' and resid 367 through 386 removed outlier: 4.083A pdb=" N ILE y 371 " --> pdb=" O GLY y 367 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE y 379 " --> pdb=" O LYS y 375 " (cutoff:3.500A) removed outlier: 4.769A 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 462 Processing helix chain 'y' and resid 466 through 493 removed outlier: 4.037A pdb=" N VAL y 470 " --> pdb=" O SER y 466 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASP y 475 " --> pdb=" O GLU y 471 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLU y 476 " --> pdb=" O HIS y 472 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ALA y 477 " --> pdb=" O LEU y 473 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLN y 478 " --> pdb=" O LYS y 474 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL y 479 " --> pdb=" O ASP y 475 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU y 491 " --> pdb=" O GLN y 487 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU y 492 " --> pdb=" O ARG y 488 " (cutoff:3.500A) Processing helix chain 'y' and resid 496 through 511 removed outlier: 3.558A pdb=" N CYS y 500 " --> pdb=" O THR y 496 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ARG y 501 " --> pdb=" O GLU y 497 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS y 509 " --> pdb=" O LEU y 505 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR y 510 " --> pdb=" O ARG y 506 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR y 511 " --> pdb=" O ILE y 507 " (cutoff:3.500A) Processing helix chain 'y' and resid 515 through 522 removed outlier: 4.253A pdb=" N HIS y 519 " --> pdb=" O ASP y 515 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARG y 521 " --> pdb=" O LYS y 517 " (cutoff:3.500A) Processing helix chain 'y' and resid 543 through 558 removed outlier: 3.500A pdb=" N LEU y 547 " --> pdb=" O ASP y 543 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET y 548 " --> pdb=" O SER y 544 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE y 555 " --> pdb=" O LEU y 551 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA y 557 " --> pdb=" O LYS y 553 " (cutoff:3.500A) Processing helix chain 'y' and resid 561 through 580 removed outlier: 4.227A pdb=" N ARG y 565 " --> pdb=" O THR y 561 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR y 566 " --> pdb=" O ASP y 562 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS y 579 " --> pdb=" O HIS y 575 " (cutoff:3.500A) removed outlier: 3.607A 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: 4.165A pdb=" N ASP y 587 " --> pdb=" O TYR y 583 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU y 588 " --> pdb=" O GLN y 584 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER y 592 " --> pdb=" O LEU y 588 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS y 593 " --> pdb=" O MET y 589 " (cutoff:3.500A) Processing helix chain 'y' and resid 594 through 602 removed outlier: 5.709A pdb=" N GLN y 599 " --> pdb=" O GLN y 595 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N HIS y 600 " --> pdb=" O ASP y 596 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA y 601 " --> pdb=" O ASN y 597 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASP y 602 " --> pdb=" O ILE y 598 " (cutoff:3.500A) Processing helix chain 'y' and resid 603 through 624 removed outlier: 4.505A pdb=" N LEU y 608 " --> pdb=" O PRO y 604 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY y 624 " --> pdb=" O ALA y 620 " (cutoff:3.500A) Processing helix chain 'y' and resid 625 through 640 removed outlier: 4.550A pdb=" N ALA y 629 " --> pdb=" O LEU y 625 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASP y 635 " --> pdb=" O ASN y 631 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILE y 636 " --> pdb=" O ALA y 632 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER y 639 " --> pdb=" O ASP y 635 " (cutoff:3.500A) removed outlier: 3.789A 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: 4.504A 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: 4.162A pdb=" N HIS y 715 " --> pdb=" O SER y 711 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN y 724 " --> pdb=" O VAL y 720 " (cutoff:3.500A) Processing helix chain 'y' and resid 732 through 747 removed outlier: 3.580A pdb=" N LYS y 745 " --> pdb=" O SER y 741 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N MET y 746 " --> pdb=" O LYS y 742 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY y 747 " --> pdb=" O ALA y 743 " (cutoff:3.500A) Processing helix chain 'y' and resid 748 through 758 removed outlier: 4.976A pdb=" N CYS y 752 " --> pdb=" O ASP y 748 " (cutoff:3.500A) removed outlier: 3.626A 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: 4.432A pdb=" N VAL y 775 " --> pdb=" O GLU y 771 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N SER y 797 " --> pdb=" O PHE y 793 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL y 798 " --> pdb=" O THR y 794 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASP y 800 " --> pdb=" O SER y 796 " (cutoff:3.500A) Processing helix chain 'y' and resid 803 through 811 removed outlier: 3.822A pdb=" N LEU y 807 " --> pdb=" O SER y 803 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER y 808 " --> pdb=" O MET y 804 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASP y 809 " --> pdb=" O GLU y 805 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE y 811 " --> pdb=" O LEU y 807 " (cutoff:3.500A) Processing helix chain 'y' and resid 814 through 829 removed outlier: 3.593A pdb=" N MET y 825 " --> pdb=" O ILE y 821 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE y 826 " --> pdb=" O ILE y 822 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE y 827 " --> pdb=" O SER y 823 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASN y 828 " --> pdb=" O LYS y 824 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU y 829 " --> pdb=" O MET y 825 " (cutoff:3.500A) Processing helix chain 'y' and resid 850 through 862 removed outlier: 4.434A pdb=" N ASN y 854 " --> pdb=" O THR y 850 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA y 860 " --> pdb=" O ALA y 856 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU y 861 " --> pdb=" O LEU y 857 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LYS y 862 " --> pdb=" O GLN y 858 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '1' and resid 338 through 343 removed outlier: 4.910A pdb=" N TYR 1 339 " --> pdb=" O PHE 1 352 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N PHE 1 352 " --> pdb=" O TYR 1 339 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TYR 1 348 " --> pdb=" O SER 1 343 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '1' and resid 377 through 382 removed outlier: 5.582A pdb=" N TYR 1 387 " --> pdb=" O SER 1 382 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '1' and resid 429 through 432 removed outlier: 5.871A pdb=" N PHE 1 437 " --> pdb=" O SER 1 432 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '1' and resid 469 through 473 removed outlier: 5.039A pdb=" N ILE 1 478 " --> pdb=" O SER 1 473 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU 1 495 " --> pdb=" O ARG 1 505 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ARG 1 505 " --> pdb=" O LEU 1 495 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '1' and resid 513 through 520 removed outlier: 4.083A pdb=" N ASP 1 514 " --> pdb=" O ASP 1 531 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N TYR 1 525 " --> pdb=" O GLN 1 520 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU 1 526 " --> pdb=" O PHE 1 547 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N VAL 1 541 " --> pdb=" O ARG 1 532 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '1' and resid 566 through 571 removed outlier: 5.608A pdb=" N LYS 1 576 " --> pdb=" O GLU 1 571 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N SER 1 575 " --> pdb=" O VAL 1 594 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS 1 599 " --> pdb=" O LYS 1 595 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '1' and resid 613 through 617 removed outlier: 5.747A pdb=" N PHE 1 622 " --> pdb=" O SER 1 617 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN 1 621 " --> pdb=" O THR 1 640 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA 1 636 " --> pdb=" O LEU 1 625 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '1' and resid 655 through 660 removed outlier: 5.420A pdb=" N TYR 1 665 " --> pdb=" O ASP 1 660 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP 1 684 " --> pdb=" O VAL 1 666 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA 1 680 " --> pdb=" O VAL 1 670 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ASN 1 679 " --> pdb=" O LYS 1 696 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '1' and resid 588 through 592 Processing sheet with id= 10, first strand: chain '4' and resid 91 through 94 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 91 through 94 current: chain '4' and resid 128 through 131 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain '4' and resid 133 through 136 removed outlier: 4.135A pdb=" N VAL 4 116 " --> pdb=" O THR 4 175 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR 4 175 " --> pdb=" O VAL 4 116 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE 4 198 " --> pdb=" O LEU 4 170 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL 4 202 " --> pdb=" O ALA 4 174 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '5' and resid 502 through 507 removed outlier: 5.378A pdb=" N THR 5 503 " --> pdb=" O ALA 5 516 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER 5 507 " --> pdb=" O GLU 5 512 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU 5 512 " --> pdb=" O SER 5 507 " (cutoff:3.500A) Processing sheet with id= 13, 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= 14, first strand: chain '8' and resid 65 through 68 removed outlier: 3.728A pdb=" N GLY 8 65 " --> pdb=" O TYR 8 120 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '8' and resid 148 through 153 removed outlier: 4.988A pdb=" N VAL 8 149 " --> pdb=" O TYR 8 167 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP 8 153 " --> pdb=" O SER 8 163 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER 8 163 " --> pdb=" O ASP 8 153 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'B' and resid 71 through 76 removed outlier: 6.035A pdb=" N ARG B 71 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR B 127 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ARG B 139 " --> pdb=" O CYS B 131 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'B' and resid 85 through 95 No H-bonds generated for sheet with id= 17 Processing sheet with id= 18, first strand: chain 'B' and resid 124 through 127 Processing sheet with id= 19, first strand: chain 'C' and resid 87 through 93 removed outlier: 4.113A pdb=" N ASP C 88 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN C 98 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS C 112 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE C 102 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'C' and resid 122 through 126 removed outlier: 3.507A pdb=" N CYS C 124 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP C 158 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP C 171 " --> pdb=" O GLN C 161 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'C' and resid 128 through 131 removed outlier: 3.818A pdb=" N LYS C 128 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG C 145 " --> pdb=" O THR C 141 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'C' and resid 197 through 200 removed outlier: 3.582A pdb=" N ASN C 197 " --> pdb=" O HIS C 209 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'E' and resid 46 through 49 removed outlier: 6.526A pdb=" N LEU E 101 " --> pdb=" O VAL E 123 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'E' and resid 53 through 59 removed outlier: 3.533A pdb=" N GLU E 53 " --> pdb=" O ARG E 71 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ALA E 65 " --> pdb=" O ALA E 59 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'G' and resid 47 through 52 removed outlier: 4.253A pdb=" N ALA G 47 " --> pdb=" O PHE G 63 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE G 61 " --> pdb=" O LYS G 49 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE G 51 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'G' and resid 141 through 146 removed outlier: 4.566A pdb=" N GLY G 141 " --> pdb=" O HIS G 157 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'H' and resid 43 through 47 removed outlier: 7.104A pdb=" N PHE H 32 " --> pdb=" O LYS H 82 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'J' and resid 23 through 28 removed outlier: 6.098A pdb=" N ARG J 23 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU J 65 " --> pdb=" O ARG J 23 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN J 64 " --> pdb=" O GLU J 49 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLU J 49 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'K' and resid 15 through 18 removed outlier: 4.444A pdb=" N ARG K 15 " --> pdb=" O ILE K 24 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ARG K 22 " --> pdb=" O CYS K 17 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'K' and resid 32 through 38 removed outlier: 4.003A pdb=" N ILE K 55 " --> pdb=" O ILE K 32 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLN K 49 " --> pdb=" O GLU K 38 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'L' and resid 102 through 107 removed outlier: 3.514A pdb=" N GLY L 131 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N PHE L 127 " --> pdb=" O LEU L 107 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'L' and resid 183 through 187 removed outlier: 3.761A pdb=" N VAL L 184 " --> pdb=" O LEU L 195 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER L 225 " --> pdb=" O ARG L 194 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA L 198 " --> pdb=" O ASP L 221 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASP L 221 " --> pdb=" O ALA L 198 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'L' and resid 123 through 127 Processing sheet with id= 34, first strand: chain 'M' and resid 95 through 98 Processing sheet with id= 35, first strand: chain 'N' and resid 121 through 125 Processing sheet with id= 36, first strand: chain 'O' and resid 45 through 48 removed outlier: 3.877A pdb=" N GLY O 45 " --> pdb=" O VAL O 33 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N THR O 98 " --> pdb=" O LYS O 34 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR O 88 " --> pdb=" O ARG O 65 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ARG O 65 " --> pdb=" O THR O 88 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'O' and resid 119 through 128 removed outlier: 5.404A pdb=" N THR O 119 " --> pdb=" O THR O 143 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR O 143 " --> pdb=" O THR O 119 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU O 134 " --> pdb=" O LEU O 218 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LYS O 214 " --> pdb=" O PHE O 138 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'O' and resid 101 through 105 removed outlier: 8.244A pdb=" N HIS O 101 " --> pdb=" O MET O 217 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N MET O 217 " --> pdb=" O HIS O 101 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL O 215 " --> pdb=" O MET O 103 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ARG O 213 " --> pdb=" O LEU O 105 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'P' and resid 40 through 46 removed outlier: 3.572A pdb=" N HIS P 43 " --> pdb=" O HIS P 32 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA P 92 " --> pdb=" O VAL P 27 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE P 95 " --> pdb=" O GLY P 127 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'Q' and resid 36 through 43 Processing sheet with id= 41, first strand: chain 'R' and resid 42 through 47 removed outlier: 6.450A pdb=" N ARG R 42 " --> pdb=" O LEU R 58 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS R 54 " --> pdb=" O VAL R 46 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'R' and resid 71 through 76 removed outlier: 3.642A pdb=" N ASN R 64 " --> pdb=" O ALA R 185 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLY R 68 " --> pdb=" O VAL R 189 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP R 186 " --> pdb=" O ALA R 176 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU R 172 " --> pdb=" O LEU R 190 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE R 175 " --> pdb=" O CYS R 100 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N CYS R 100 " --> pdb=" O ILE R 175 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE R 101 " --> pdb=" O VAL R 82 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP R 80 " --> pdb=" O LEU R 103 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'S' and resid 11 through 17 removed outlier: 6.112A pdb=" N ASN S 110 " --> pdb=" O SER S 53 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL S 49 " --> pdb=" O VAL S 114 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR S 34 " --> pdb=" O ILE S 52 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'S' and resid 73 through 76 Processing sheet with id= 45, first strand: chain 'S' and resid 159 through 163 removed outlier: 4.245A pdb=" N ARG S 170 " --> pdb=" O LEU S 162 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'T' and resid 5 through 10 removed outlier: 4.353A pdb=" N VAL T 24 " --> pdb=" O LYS T 11 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LYS T 11 " --> pdb=" O VAL T 24 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'T' and resid 59 through 63 removed outlier: 5.302A pdb=" N GLY T 59 " --> pdb=" O PHE T 72 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE T 72 " --> pdb=" O GLY T 59 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LYS T 68 " --> pdb=" O HIS T 63 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'T' and resid 20 through 29 removed outlier: 4.057A pdb=" N GLY T 67 " --> pdb=" O HIS T 29 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'V' and resid 122 through 127 removed outlier: 6.613A pdb=" N ARG V 122 " --> pdb=" O VAL V 141 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL V 141 " --> pdb=" O ARG V 122 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'Y' and resid 9 through 15 Processing sheet with id= 51, first strand: chain 'Z' and resid 33 through 38 removed outlier: 6.704A pdb=" N GLY Z 33 " --> pdb=" O THR Z 53 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU Z 51 " --> pdb=" O SER Z 35 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL Z 37 " --> pdb=" O ILE Z 49 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE Z 49 " --> pdb=" O VAL Z 37 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'Z' and resid 148 through 155 removed outlier: 3.519A pdb=" N GLY Z 180 " --> pdb=" O LEU Z 177 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'a' and resid 20 through 24 removed outlier: 3.603A pdb=" N TYR a 68 " --> pdb=" O GLN a 61 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'b' and resid 75 through 78 Processing sheet with id= 55, first strand: chain 'c' and resid 3 through 8 removed outlier: 4.494A pdb=" N GLN c 4 " --> pdb=" O THR c 313 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL c 309 " --> pdb=" O ARG c 8 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL c 307 " --> pdb=" O LEU c 11 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY c 9 " --> pdb=" O VAL c 309 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'c' and resid 19 through 23 removed outlier: 5.867A pdb=" N ASP c 29 " --> pdb=" O LEU c 45 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE c 31 " --> pdb=" O TRP c 43 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N MET c 42 " --> pdb=" O GLN c 56 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR c 52 " --> pdb=" O THR c 46 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'c' and resid 68 through 72 removed outlier: 6.017A pdb=" N PHE c 77 " --> pdb=" O SER c 72 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N GLN c 76 " --> pdb=" O LEU c 92 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU c 89 " --> pdb=" O THR c 98 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'c' and resid 110 through 114 removed outlier: 6.744A pdb=" N GLN c 119 " --> pdb=" O SER c 114 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE c 129 " --> pdb=" O VAL c 142 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR c 140 " --> pdb=" O LEU c 131 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'c' and resid 153 through 157 removed outlier: 4.991A pdb=" N ILE c 164 " --> pdb=" O SER c 157 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL c 176 " --> pdb=" O LYS c 185 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'c' and resid 197 through 201 removed outlier: 5.463A pdb=" N LEU c 206 " --> pdb=" O SER c 201 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N SER c 205 " --> pdb=" O LEU c 221 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU c 218 " --> pdb=" O LEU c 227 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS c 225 " --> pdb=" O ASP c 220 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'c' and resid 238 through 242 removed outlier: 3.616A pdb=" N ALA c 238 " --> pdb=" O ALA c 251 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TRP c 247 " --> pdb=" O SER c 242 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'c' and resid 288 through 292 removed outlier: 4.238A pdb=" N SER c 288 " --> pdb=" O GLY c 301 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N THR c 297 " --> pdb=" O SER c 292 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'c' and resid 39 through 42 No H-bonds generated for sheet with id= 63 Processing sheet with id= 64, first strand: chain 'c' and resid 86 through 89 Processing sheet with id= 65, first strand: chain 'c' and resid 173 through 176 Processing sheet with id= 66, first strand: chain 'c' and resid 214 through 218 removed outlier: 5.651A pdb=" N GLY c 214 " --> pdb=" O GLY c 232 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR c 228 " --> pdb=" O LEU c 218 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'c' and resid 296 through 302 removed outlier: 6.717A pdb=" N GLN c 296 " --> pdb=" O VAL c 312 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU c 306 " --> pdb=" O TYR c 302 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'd' and resid 81 through 84 Processing sheet with id= 69, first strand: chain 'd' and resid 113 through 116 removed outlier: 4.692A pdb=" N GLY d 120 " --> pdb=" O ASP d 116 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'h' and resid 53 through 56 removed outlier: 4.798A pdb=" N LYS h 86 " --> pdb=" O MET h 56 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER h 93 " --> pdb=" O HIS h 18 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'h' and resid 58 through 66 Processing sheet with id= 72, first strand: chain 'm' and resid 30 through 33 removed outlier: 6.167A pdb=" N GLY m 30 " --> pdb=" O LYS m 112 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASN m 75 " --> pdb=" O HIS m 48 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL m 79 " --> pdb=" O LEU m 52 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'n' and resid 9 through 13 Processing sheet with id= 74, first strand: chain 'n' and resid 18 through 22 Processing sheet with id= 75, first strand: chain 'o' and resid 267 through 271 removed outlier: 5.141A pdb=" N PHE o 282 " --> pdb=" O ALA o 271 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ALA o 239 " --> pdb=" O PHE o 287 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'p' and resid 32 through 37 removed outlier: 6.226A pdb=" N HIS p 32 " --> pdb=" O GLN p 48 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ASN p 70 " --> pdb=" O GLN p 86 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'q' and resid 46 through 51 removed outlier: 4.973A pdb=" N VAL q 55 " --> pdb=" O CYS q 51 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'q' and resid 78 through 81 removed outlier: 6.724A pdb=" N LEU q 78 " --> pdb=" O ILE q 92 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'r' and resid 19 through 23 Processing sheet with id= 80, first strand: chain 'r' and resid 32 through 37 Processing sheet with id= 81, first strand: chain 'r' and resid 75 through 78 No H-bonds generated for sheet with id= 81 Processing sheet with id= 82, first strand: chain 'r' and resid 190 through 196 removed outlier: 3.673A pdb=" N MET r 237 " --> pdb=" O ALA r 193 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG r 234 " --> pdb=" O ILE r 230 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN r 228 " --> pdb=" O VAL r 236 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR r 240 " --> pdb=" O PRO r 224 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 't' and resid 81 through 87 removed outlier: 3.661A pdb=" N ILE t 42 " --> pdb=" O HIS t 129 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLY t 48 " --> pdb=" O CYS t 135 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N HIS t 184 " --> pdb=" O ASP t 153 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 't' and resid 292 through 297 removed outlier: 4.385A pdb=" N GLN t 292 " --> pdb=" O ILE t 318 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 't' and resid 319 through 322 removed outlier: 4.396A pdb=" N SER t 320 " --> pdb=" O GLY t 340 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 't' and resid 404 through 407 removed outlier: 3.540A pdb=" N GLU t 439 " --> pdb=" O ILE t 459 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'u' and resid 482 through 486 Processing sheet with id= 88, first strand: chain 'x' and resid 190 through 193 removed outlier: 6.464A pdb=" N TYR x 360 " --> pdb=" O ILE x 193 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'x' and resid 390 through 398 removed outlier: 3.524A pdb=" N TYR x 446 " --> pdb=" O PHE x 390 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL x 452 " --> pdb=" O LEU x 396 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG x 454 " --> pdb=" O GLU x 398 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR x 451 " --> pdb=" O LEU x 466 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'x' and resid 516 through 522 removed outlier: 3.749A pdb=" N VAL x 516 " --> pdb=" O ASP x 511 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG x 518 " --> pdb=" O LEU x 509 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS x 505 " --> pdb=" O LEU x 522 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN x 270 " --> pdb=" O PHE x 277 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE x 277 " --> pdb=" O GLN x 270 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR x 248 " --> pdb=" O PHE x 278 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LYS x 280 " --> pdb=" O THR x 248 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'x' and resid 355 through 363 No H-bonds generated for sheet with id= 91 Processing sheet with id= 92, first strand: chain 'x' and resid 447 through 451 Processing sheet with id= 93, first strand: chain 'y' and resid 831 through 835 removed outlier: 5.415A pdb=" N LEU y 831 " --> pdb=" O MET y 844 " (cutoff:3.500A) 3236 hydrogen bonds defined for protein. 9602 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1197 hydrogen bonds 1838 hydrogen bond angles 0 basepair planarities 487 basepair parallelities 942 stacking parallelities Total time for adding SS restraints: 68.21 Time building geometry restraints manager: 42.47 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: 14799 1.31 - 1.44: 39914 1.44 - 1.57: 56650 1.57 - 1.70: 3608 1.70 - 1.83: 456 Bond restraints: 115427 Sorted by residual: bond pdb=" C4 5MU A 814 " pdb=" C5 5MU A 814 " ideal model delta sigma weight residual 1.802 1.464 0.338 2.00e-02 2.50e+03 2.86e+02 bond pdb=" N1 5MU A 814 " pdb=" C6 5MU A 814 " ideal model delta sigma weight residual 1.635 1.360 0.275 2.00e-02 2.50e+03 1.89e+02 bond pdb=" C2' A2M A 668 " pdb=" C1' A2M A 668 " ideal model delta sigma weight residual 1.305 1.526 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C2' A2M A 484 " pdb=" C1' A2M A 484 " ideal model delta sigma weight residual 1.305 1.524 -0.219 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C2' A2M A 166 " pdb=" C1' A2M A 166 " ideal model delta sigma weight residual 1.305 1.520 -0.215 2.00e-02 2.50e+03 1.15e+02 ... (remaining 115422 not shown) Histogram of bond angle deviations from ideal: 94.22 - 102.65: 3942 102.65 - 111.08: 53531 111.08 - 119.52: 60126 119.52 - 127.95: 44015 127.95 - 136.38: 3355 Bond angle restraints: 164969 Sorted by residual: angle pdb=" O3' U A1304 " pdb=" C3' U A1304 " pdb=" C2' U A1304 " ideal model delta sigma weight residual 113.70 134.87 -21.17 1.50e+00 4.44e-01 1.99e+02 angle pdb=" CA ASP P 138 " pdb=" CB ASP P 138 " pdb=" CG ASP P 138 " ideal model delta sigma weight residual 112.60 126.62 -14.02 1.00e+00 1.00e+00 1.97e+02 angle pdb=" C1' A2M A 27 " pdb=" N9 A2M A 27 " pdb=" C8 A2M A 27 " ideal model delta sigma weight residual 88.50 127.25 -38.75 3.00e+00 1.11e-01 1.67e+02 angle pdb=" C1' A2M A 668 " pdb=" N9 A2M A 668 " pdb=" C8 A2M A 668 " ideal model delta sigma weight residual 88.50 126.91 -38.41 3.00e+00 1.11e-01 1.64e+02 angle pdb=" C1' A2M A 166 " pdb=" N9 A2M A 166 " pdb=" C8 A2M A 166 " ideal model delta sigma weight residual 88.50 126.57 -38.07 3.00e+00 1.11e-01 1.61e+02 ... (remaining 164964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 65692 35.97 - 71.94: 4618 71.94 - 107.91: 611 107.91 - 143.88: 21 143.88 - 179.85: 15 Dihedral angle restraints: 70957 sinusoidal: 42306 harmonic: 28651 Sorted by residual: 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 0.00 179.85 -179.85 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" N ILE 1 648 " pdb=" C ILE 1 648 " pdb=" CA ILE 1 648 " pdb=" CB ILE 1 648 " ideal model delta harmonic sigma weight residual 123.40 156.80 -33.40 0 2.50e+00 1.60e-01 1.79e+02 dihedral pdb=" C ILE 1 648 " pdb=" N ILE 1 648 " pdb=" CA ILE 1 648 " pdb=" CB ILE 1 648 " ideal model delta harmonic sigma weight residual -122.00 -155.25 33.25 0 2.50e+00 1.60e-01 1.77e+02 ... (remaining 70954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.302: 20164 0.302 - 0.604: 140 0.604 - 0.906: 18 0.906 - 1.208: 7 1.208 - 1.510: 8 Chirality restraints: 20337 Sorted by residual: chirality pdb=" C3' A A 392 " pdb=" C4' A A 392 " pdb=" O3' A A 392 " pdb=" C2' A A 392 " both_signs ideal model delta sigma weight residual False -2.48 -0.97 -1.51 2.00e-01 2.50e+01 5.70e+01 chirality pdb=" C3' U A1867 " pdb=" C4' U A1867 " pdb=" O3' U A1867 " pdb=" C2' U A1867 " both_signs ideal model delta sigma weight residual False -2.74 -1.27 -1.48 2.00e-01 2.50e+01 5.46e+01 chirality pdb=" C3' U A 368 " pdb=" C4' U A 368 " pdb=" O3' U A 368 " pdb=" C2' U A 368 " both_signs ideal model delta sigma weight residual False -2.74 -1.27 -1.48 2.00e-01 2.50e+01 5.44e+01 ... (remaining 20334 not shown) Planarity restraints: 14592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG A 683 " 0.094 2.00e-02 2.50e+03 6.13e-01 8.46e+03 pdb=" C4' OMG A 683 " 0.429 2.00e-02 2.50e+03 pdb=" O4' OMG A 683 " 0.591 2.00e-02 2.50e+03 pdb=" C3' OMG A 683 " -0.629 2.00e-02 2.50e+03 pdb=" O3' OMG A 683 " -0.690 2.00e-02 2.50e+03 pdb=" C2' OMG A 683 " -0.152 2.00e-02 2.50e+03 pdb=" O2' OMG A 683 " 1.043 2.00e-02 2.50e+03 pdb=" C1' OMG A 683 " 0.216 2.00e-02 2.50e+03 pdb=" N9 OMG A 683 " -0.902 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU A 814 " -0.072 2.00e-02 2.50e+03 6.00e-01 8.10e+03 pdb=" C4' 5MU A 814 " -0.439 2.00e-02 2.50e+03 pdb=" O4' 5MU A 814 " -0.587 2.00e-02 2.50e+03 pdb=" C3' 5MU A 814 " 0.610 2.00e-02 2.50e+03 pdb=" O3' 5MU A 814 " 0.666 2.00e-02 2.50e+03 pdb=" C2' 5MU A 814 " 0.166 2.00e-02 2.50e+03 pdb=" O2' 5MU A 814 " -1.012 2.00e-02 2.50e+03 pdb=" C1' 5MU A 814 " -0.216 2.00e-02 2.50e+03 pdb=" N1 5MU A 814 " 0.884 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC A 517 " 0.049 2.00e-02 2.50e+03 5.94e-01 7.94e+03 pdb=" C4' OMC A 517 " 0.446 2.00e-02 2.50e+03 pdb=" O4' OMC A 517 " 0.634 2.00e-02 2.50e+03 pdb=" C3' OMC A 517 " -0.605 2.00e-02 2.50e+03 pdb=" O3' OMC A 517 " -0.639 2.00e-02 2.50e+03 pdb=" C2' OMC A 517 " -0.182 2.00e-02 2.50e+03 pdb=" O2' OMC A 517 " 0.967 2.00e-02 2.50e+03 pdb=" C1' OMC A 517 " 0.215 2.00e-02 2.50e+03 pdb=" N1 OMC A 517 " -0.885 2.00e-02 2.50e+03 ... (remaining 14589 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 1902 2.59 - 3.17: 88713 3.17 - 3.75: 203292 3.75 - 4.32: 266086 4.32 - 4.90: 388270 Nonbonded interactions: 948263 Sorted by model distance: nonbonded pdb=" OP1 A A1589 " pdb="MG MG d 201 " model vdw 2.016 2.170 nonbonded pdb=" O2' C A 453 " pdb=" O ARG S 92 " model vdw 2.081 2.440 nonbonded pdb=" NE2 GLN B 5 " pdb=" O GLU B 7 " model vdw 2.095 2.520 nonbonded pdb=" O GLY d 80 " pdb="MG MG d 201 " model vdw 2.123 2.170 nonbonded pdb=" O HIS 3 152 " pdb=" O ILE 5 506 " model vdw 2.147 3.040 ... (remaining 948258 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 13.440 Check model and map are aligned: 1.180 Set scattering table: 0.730 Process input model: 305.200 Find NCS groups from input model: 2.980 Set up NCS constraints: 0.290 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:2.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 327.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 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 : 0.011 0.338 115427 Z= 0.720 Angle : 1.504 38.751 164969 Z= 1.003 Chirality : 0.105 1.510 20337 Planarity : 0.016 0.613 14592 Dihedral : 21.170 179.852 52329 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.40 % Favored : 95.27 % Rotamer: Outliers : 5.29 % Allowed : 13.33 % Favored : 81.38 % Cbeta Deviations : 0.55 % 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: -1.97 (0.08), residues: 9724 helix: -0.59 (0.08), residues: 3613 sheet: -1.14 (0.14), residues: 1198 loop : -1.91 (0.08), residues: 4913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP v 213 HIS 0.018 0.002 HIS q 60 PHE 0.040 0.003 PHE f 28 TYR 0.041 0.004 TYR k 140 ARG 0.025 0.001 ARG M 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19448 Ramachandran restraints generated. 9724 Oldfield, 0 Emsley, 9724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19448 Ramachandran restraints generated. 9724 Oldfield, 0 Emsley, 9724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2660 residues out of total 8689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 2324 time to evaluate : 7.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 336 outliers final: 76 residues processed: 2546 average time/residue: 0.9946 time to fit residues: 4286.3592 Evaluate side-chains 1206 residues out of total 8689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1130 time to evaluate : 6.946 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 1 residues processed: 76 average time/residue: 0.9469 time to fit residues: 133.1663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1147 random chunks: chunk 968 optimal weight: 20.0000 chunk 869 optimal weight: 6.9990 chunk 482 optimal weight: 5.9990 chunk 296 optimal weight: 10.0000 chunk 586 optimal weight: 5.9990 chunk 464 optimal weight: 0.8980 chunk 899 optimal weight: 1.9990 chunk 347 optimal weight: 20.0000 chunk 546 optimal weight: 1.9990 chunk 669 optimal weight: 3.9990 chunk 1041 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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** 6 349 GLN B 11 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN ** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 216 ASN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN H 65 GLN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 HIS J 70 ASN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 ASN J 98 GLN L 113 GLN N 9 GLN Q 43 ASN R 168 GLN ** S 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 112 ASN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 95 HIS ** Y 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 86 GLN Z 101 GLN ** a 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 28 HIS a 39 ASN ** a 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 66 HIS b 41 GLN c 14 HIS c 196 ASN c 272 GLN ** d 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 83 GLN f 105 ASN ** h 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 185 ASN s 230 HIS s 282 HIS ** s 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 211 HIS u 219 ASN u 221 ASN u 312 GLN ** u 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 448 GLN v 216 HIS v 231 ASN v 282 GLN ** x 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 69 ASN ** y 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 615 GLN ** y 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 115427 Z= 0.239 Angle : 0.784 17.973 164969 Z= 0.414 Chirality : 0.043 0.369 20337 Planarity : 0.006 0.134 14592 Dihedral : 21.527 179.528 37300 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.16 % Favored : 95.72 % Rotamer: Outliers : 0.19 % Allowed : 5.08 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.08), residues: 9724 helix: -0.33 (0.08), residues: 3777 sheet: -1.04 (0.14), residues: 1268 loop : -1.80 (0.08), residues: 4679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP a 64 HIS 0.013 0.002 HIS I 5 PHE 0.041 0.002 PHE V 97 TYR 0.049 0.002 TYR k 140 ARG 0.010 0.001 ARG N 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19448 Ramachandran restraints generated. 9724 Oldfield, 0 Emsley, 9724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19448 Ramachandran restraints generated. 9724 Oldfield, 0 Emsley, 9724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1557 residues out of total 8689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1545 time to evaluate : 7.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 12 outliers final: 4 residues processed: 1550 average time/residue: 0.9894 time to fit residues: 2640.1617 Evaluate side-chains 1023 residues out of total 8689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1019 time to evaluate : 6.919 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.8032 time to fit residues: 14.6463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1147 random chunks: chunk 578 optimal weight: 0.0070 chunk 323 optimal weight: 10.0000 chunk 866 optimal weight: 6.9990 chunk 709 optimal weight: 0.5980 chunk 287 optimal weight: 20.0000 chunk 1043 optimal weight: 9.9990 chunk 1127 optimal weight: 3.9990 chunk 929 optimal weight: 4.9990 chunk 1034 optimal weight: 30.0000 chunk 355 optimal weight: 20.0000 chunk 837 optimal weight: 9.9990 overall best weight: 3.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN G 163 GLN H 65 GLN I 5 HIS I 36 GLN J 15 ASN J 113 HIS K 33 GLN L 113 GLN ** M 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN V 79 HIS V 95 HIS V 149 GLN Y 11 GLN Z 57 ASN Z 174 HIS ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 56 GLN ** d 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 26 ASN ** i 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 107 GLN ** r 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 180 GLN u 236 GLN u 316 GLN ** u 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 355 GLN y 423 ASN ** y 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 713 GLN y 753 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 115427 Z= 0.211 Angle : 0.707 18.259 164969 Z= 0.375 Chirality : 0.041 0.383 20337 Planarity : 0.006 0.127 14592 Dihedral : 21.438 177.996 37300 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.00 % Favored : 94.94 % Rotamer: Outliers : 0.19 % Allowed : 4.77 % Favored : 95.04 % 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: -1.42 (0.08), residues: 9724 helix: -0.04 (0.08), residues: 3832 sheet: -0.98 (0.14), residues: 1296 loop : -1.69 (0.09), residues: 4596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP y 766 HIS 0.019 0.001 HIS V 79 PHE 0.043 0.002 PHE p 63 TYR 0.046 0.002 TYR k 140 ARG 0.015 0.001 ARG c 308 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19448 Ramachandran restraints generated. 9724 Oldfield, 0 Emsley, 9724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19448 Ramachandran restraints generated. 9724 Oldfield, 0 Emsley, 9724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1379 residues out of total 8689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1367 time to evaluate : 6.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 revert: symmetry clash 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: 12 outliers final: 6 residues processed: 1373 average time/residue: 0.9434 time to fit residues: 2268.0794 Evaluate side-chains 948 residues out of total 8689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 942 time to evaluate : 6.922 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.8109 time to fit residues: 17.9194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1147 random chunks: chunk 1030 optimal weight: 20.0000 chunk 784 optimal weight: 20.0000 chunk 541 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 497 optimal weight: 7.9990 chunk 700 optimal weight: 10.0000 chunk 1047 optimal weight: 7.9990 chunk 1108 optimal weight: 10.0000 chunk 547 optimal weight: 8.9990 chunk 992 optimal weight: 40.0000 chunk 298 optimal weight: 10.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 553 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN B 106 HIS B 112 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 HIS E 61 GLN ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN G 25 GLN H 49 HIS H 65 GLN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 ASN K 2 GLN K 33 GLN L 113 GLN L 272 HIS R 9 HIS S 70 HIS S 187 HIS S 225 GLN V 79 HIS V 95 HIS V 118 ASN V 149 GLN Y 11 GLN Y 24 HIS Y 86 GLN a 61 GLN ** b 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 45 ASN f 72 GLN ** h 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 36 GLN ** p 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 107 GLN r 41 ASN ** r 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 269 ASN ** u 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 312 GLN u 372 ASN u 432 GLN u 442 GLN v 272 GLN ** v 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 325 GLN ** x 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 465 HIS ** y 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 623 GLN y 858 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 115427 Z= 0.393 Angle : 0.873 18.558 164969 Z= 0.454 Chirality : 0.046 0.340 20337 Planarity : 0.007 0.128 14592 Dihedral : 21.692 178.051 37300 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 27.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.10 % Favored : 93.85 % Rotamer: Outliers : 0.17 % Allowed : 5.59 % Favored : 94.24 % 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: -1.53 (0.08), residues: 9724 helix: -0.10 (0.08), residues: 3884 sheet: -1.03 (0.14), residues: 1270 loop : -1.81 (0.09), residues: 4570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP a 64 HIS 0.019 0.002 HIS V 79 PHE 0.038 0.003 PHE y 714 TYR 0.035 0.003 TYR c 302 ARG 0.015 0.001 ARG M 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19448 Ramachandran restraints generated. 9724 Oldfield, 0 Emsley, 9724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19448 Ramachandran restraints generated. 9724 Oldfield, 0 Emsley, 9724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1157 residues out of total 8689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1146 time to evaluate : 7.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 outliers start: 11 outliers final: 6 residues processed: 1150 average time/residue: 0.9325 time to fit residues: 1880.7450 Evaluate side-chains 822 residues out of total 8689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 816 time to evaluate : 6.965 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.8975 time to fit residues: 18.3052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1147 random chunks: chunk 923 optimal weight: 8.9990 chunk 629 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 825 optimal weight: 20.0000 chunk 457 optimal weight: 20.0000 chunk 946 optimal weight: 6.9990 chunk 766 optimal weight: 10.0000 chunk 1 optimal weight: 50.0000 chunk 566 optimal weight: 5.9990 chunk 995 optimal weight: 40.0000 chunk 279 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 HIS F 89 GLN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 GLN K 35 ASN ** M 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 155 GLN T 63 HIS V 118 ASN V 149 GLN Y 11 GLN ** Y 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 86 GLN ** b 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 107 GLN s 263 GLN s 264 GLN ** u 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 236 GLN u 316 GLN ** x 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 334 ASN ** y 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 115427 Z= 0.272 Angle : 0.731 18.150 164969 Z= 0.385 Chirality : 0.042 0.349 20337 Planarity : 0.006 0.124 14592 Dihedral : 21.670 178.977 37300 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.58 % Favored : 94.37 % Rotamer: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % 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: -1.28 (0.08), residues: 9724 helix: 0.17 (0.08), residues: 3875 sheet: -1.00 (0.14), residues: 1266 loop : -1.68 (0.09), residues: 4583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP S 45 HIS 0.014 0.002 HIS b 79 PHE 0.070 0.002 PHE s 219 TYR 0.035 0.002 TYR Y 96 ARG 0.013 0.001 ARG G 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19448 Ramachandran restraints generated. 9724 Oldfield, 0 Emsley, 9724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19448 Ramachandran restraints generated. 9724 Oldfield, 0 Emsley, 9724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 8689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1150 time to evaluate : 7.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 outliers start: 2 outliers final: 1 residues processed: 1151 average time/residue: 0.9419 time to fit residues: 1901.4596 Evaluate side-chains 840 residues out of total 8689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 839 time to evaluate : 6.995 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.8665 time to fit residues: 10.2751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1147 random chunks: chunk 373 optimal weight: 6.9990 chunk 998 optimal weight: 50.0000 chunk 219 optimal weight: 20.0000 chunk 650 optimal weight: 9.9990 chunk 273 optimal weight: 10.0000 chunk 1109 optimal weight: 30.0000 chunk 921 optimal weight: 0.0270 chunk 513 optimal weight: 9.9990 chunk 92 optimal weight: 40.0000 chunk 367 optimal weight: 6.9990 chunk 582 optimal weight: 3.9990 overall best weight: 5.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN C 8 HIS ** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 HIS E 92 ASN F 89 GLN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN I 123 HIS K 21 ASN M 31 ASN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 ASN V 118 ASN V 149 GLN Y 11 GLN ** Y 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 142 GLN ** b 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 HIS o 288 HIS p 36 GLN ** p 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 107 GLN r 11 HIS s 266 GLN ** u 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 236 GLN v 216 HIS ** x 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 296 ASN ** x 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 338 GLN y 509 HIS ** y 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 115427 Z= 0.267 Angle : 0.722 18.081 164969 Z= 0.380 Chirality : 0.041 0.324 20337 Planarity : 0.005 0.124 14592 Dihedral : 21.618 179.525 37300 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.15 % Favored : 93.81 % Rotamer: Outliers : 0.08 % Allowed : 2.42 % Favored : 97.50 % 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: -1.16 (0.08), residues: 9724 helix: 0.37 (0.08), residues: 3858 sheet: -1.06 (0.14), residues: 1241 loop : -1.67 (0.09), residues: 4625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP L 60 HIS 0.010 0.002 HIS o 288 PHE 0.033 0.002 PHE q 28 TYR 0.032 0.002 TYR c 246 ARG 0.019 0.001 ARG y 781 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19448 Ramachandran restraints generated. 9724 Oldfield, 0 Emsley, 9724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19448 Ramachandran restraints generated. 9724 Oldfield, 0 Emsley, 9724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1105 residues out of total 8689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1100 time to evaluate : 7.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 outliers start: 5 outliers final: 2 residues processed: 1104 average time/residue: 0.9612 time to fit residues: 1872.9615 Evaluate side-chains 816 residues out of total 8689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 814 time to evaluate : 7.205 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.8389 time to fit residues: 12.3412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1147 random chunks: chunk 1069 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 632 optimal weight: 0.9990 chunk 810 optimal weight: 20.0000 chunk 627 optimal weight: 1.9990 chunk 934 optimal weight: 7.9990 chunk 619 optimal weight: 8.9990 chunk 1105 optimal weight: 8.9990 chunk 691 optimal weight: 10.0000 chunk 673 optimal weight: 2.9990 chunk 510 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 HIS F 89 GLN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 GLN I 58 HIS J 82 GLN L 136 HIS N 193 HIS ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 113 GLN ** Q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 ASN V 149 GLN Y 11 GLN ** Y 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 80 GLN ** b 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 288 HIS ** p 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 107 GLN u 44 GLN ** u 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 68 GLN x 296 ASN ** y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 415 ASN ** y 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 115427 Z= 0.191 Angle : 0.673 17.661 164969 Z= 0.355 Chirality : 0.039 0.333 20337 Planarity : 0.005 0.121 14592 Dihedral : 21.506 179.413 37300 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.49 % Favored : 94.47 % Rotamer: Outliers : 0.09 % Allowed : 1.62 % Favored : 98.28 % 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: -0.97 (0.08), residues: 9724 helix: 0.58 (0.08), residues: 3885 sheet: -1.02 (0.14), residues: 1276 loop : -1.61 (0.09), residues: 4563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP u 43 HIS 0.011 0.001 HIS G 91 PHE 0.029 0.002 PHE N 108 TYR 0.027 0.002 TYR c 246 ARG 0.011 0.001 ARG y 781 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19448 Ramachandran restraints generated. 9724 Oldfield, 0 Emsley, 9724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19448 Ramachandran restraints generated. 9724 Oldfield, 0 Emsley, 9724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 8689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1102 time to evaluate : 7.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 6 outliers final: 2 residues processed: 1106 average time/residue: 0.9316 time to fit residues: 1821.6473 Evaluate side-chains 814 residues out of total 8689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 812 time to evaluate : 7.026 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.8072 time to fit residues: 11.8177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1147 random chunks: chunk 683 optimal weight: 8.9990 chunk 441 optimal weight: 6.9990 chunk 660 optimal weight: 2.9990 chunk 333 optimal weight: 20.0000 chunk 217 optimal weight: 10.0000 chunk 214 optimal weight: 30.0000 chunk 702 optimal weight: 10.0000 chunk 753 optimal weight: 0.6980 chunk 546 optimal weight: 5.9990 chunk 103 optimal weight: 40.0000 chunk 868 optimal weight: 7.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 HIS F 89 GLN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 ASN K 33 GLN N 193 HIS ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 ASN V 149 GLN Y 11 GLN ** a 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 36 GLN ** p 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.6205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 115427 Z= 0.241 Angle : 0.701 17.732 164969 Z= 0.368 Chirality : 0.040 0.355 20337 Planarity : 0.005 0.123 14592 Dihedral : 21.509 179.261 37300 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.37 % Favored : 93.58 % Rotamer: Outliers : 0.03 % Allowed : 1.40 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.94 (0.08), residues: 9724 helix: 0.61 (0.08), residues: 3893 sheet: -1.01 (0.14), residues: 1273 loop : -1.60 (0.09), residues: 4558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP 6 347 HIS 0.008 0.001 HIS O 101 PHE 0.033 0.002 PHE q 28 TYR 0.040 0.002 TYR H 31 ARG 0.009 0.001 ARG T 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19448 Ramachandran restraints generated. 9724 Oldfield, 0 Emsley, 9724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19448 Ramachandran restraints generated. 9724 Oldfield, 0 Emsley, 9724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 8689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1043 time to evaluate : 6.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 2 outliers final: 1 residues processed: 1044 average time/residue: 0.9444 time to fit residues: 1744.6041 Evaluate side-chains 785 residues out of total 8689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 784 time to evaluate : 6.964 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.7639 time to fit residues: 10.3286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1147 random chunks: chunk 1005 optimal weight: 50.0000 chunk 1059 optimal weight: 40.0000 chunk 966 optimal weight: 3.9990 chunk 1030 optimal weight: 20.0000 chunk 1058 optimal weight: 0.9980 chunk 620 optimal weight: 8.9990 chunk 448 optimal weight: 8.9990 chunk 808 optimal weight: 30.0000 chunk 316 optimal weight: 20.0000 chunk 930 optimal weight: 10.0000 chunk 974 optimal weight: 2.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 HIS ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 193 HIS ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 ASN ** V 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 11 GLN ** b 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 296 GLN ** c 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 10 ASN ** d 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 107 GLN q 72 ASN ** r 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 512 GLN ** v 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.6480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 115427 Z= 0.239 Angle : 0.699 17.554 164969 Z= 0.368 Chirality : 0.040 0.358 20337 Planarity : 0.005 0.123 14592 Dihedral : 21.543 179.355 37300 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.21 % Favored : 93.75 % Rotamer: Outliers : 0.03 % Allowed : 0.63 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.91 (0.08), residues: 9724 helix: 0.65 (0.08), residues: 3887 sheet: -0.97 (0.14), residues: 1259 loop : -1.62 (0.09), residues: 4578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP 1 482 HIS 0.008 0.001 HIS a 44 PHE 0.029 0.002 PHE O 25 TYR 0.028 0.002 TYR v 242 ARG 0.026 0.001 ARG y 781 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19448 Ramachandran restraints generated. 9724 Oldfield, 0 Emsley, 9724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19448 Ramachandran restraints generated. 9724 Oldfield, 0 Emsley, 9724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 8689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1027 time to evaluate : 7.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 outliers start: 2 outliers final: 1 residues processed: 1028 average time/residue: 0.9812 time to fit residues: 1789.3459 Evaluate side-chains 779 residues out of total 8689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 778 time to evaluate : 6.985 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.7635 time to fit residues: 10.0616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1147 random chunks: chunk 1026 optimal weight: 0.7980 chunk 676 optimal weight: 9.9990 chunk 1089 optimal weight: 6.9990 chunk 664 optimal weight: 5.9990 chunk 516 optimal weight: 9.9990 chunk 757 optimal weight: 30.0000 chunk 1142 optimal weight: 8.9990 chunk 1051 optimal weight: 30.0000 chunk 909 optimal weight: 20.0000 chunk 94 optimal weight: 0.0470 chunk 702 optimal weight: 5.9990 overall best weight: 3.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 127 ASN N 193 HIS ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 ASN ** V 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 11 GLN Y 86 GLN ** b 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 278 GLN ** p 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 390 HIS ** x 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 660 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.6630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 115427 Z= 0.207 Angle : 0.684 17.539 164969 Z= 0.359 Chirality : 0.039 0.352 20337 Planarity : 0.005 0.122 14592 Dihedral : 21.511 179.446 37300 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.33 % Favored : 93.63 % Rotamer: Outliers : 0.03 % Allowed : 0.38 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 9724 helix: 0.73 (0.09), residues: 3883 sheet: -0.95 (0.14), residues: 1244 loop : -1.58 (0.09), residues: 4597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP y 766 HIS 0.007 0.001 HIS H 19 PHE 0.049 0.002 PHE n 34 TYR 0.026 0.002 TYR i 46 ARG 0.012 0.001 ARG y 781 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19448 Ramachandran restraints generated. 9724 Oldfield, 0 Emsley, 9724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19448 Ramachandran restraints generated. 9724 Oldfield, 0 Emsley, 9724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1027 residues out of total 8689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1025 time to evaluate : 9.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 2 outliers final: 1 residues processed: 1025 average time/residue: 0.9489 time to fit residues: 1724.5315 Evaluate side-chains 784 residues out of total 8689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 783 time to evaluate : 6.979 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASN P 26 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.7660 time to fit residues: 10.2220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1147 random chunks: chunk 557 optimal weight: 6.9990 chunk 722 optimal weight: 4.9990 chunk 969 optimal weight: 4.9990 chunk 278 optimal weight: 9.9990 chunk 839 optimal weight: 30.0000 chunk 134 optimal weight: 50.0000 chunk 252 optimal weight: 30.0000 chunk 911 optimal weight: 6.9990 chunk 381 optimal weight: 0.0470 chunk 935 optimal weight: 10.0000 chunk 115 optimal weight: 0.2980 overall best weight: 3.4684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 HIS ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 127 ASN N 193 HIS ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 ASN ** V 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 11 GLN ** b 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 36 GLN ** p 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 390 HIS ** x 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 615 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.067466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.051311 restraints weight = 771444.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.051192 restraints weight = 456245.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.051480 restraints weight = 300916.373| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 216 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 216 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.6783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 115427 Z= 0.192 Angle : 0.669 17.387 164969 Z= 0.351 Chirality : 0.039 0.351 20337 Planarity : 0.005 0.122 14592 Dihedral : 21.467 179.541 37300 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.05 % Favored : 93.91 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.76 (0.09), residues: 9724 helix: 0.81 (0.09), residues: 3895 sheet: -0.94 (0.14), residues: 1275 loop : -1.56 (0.09), residues: 4554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP y 766 HIS 0.007 0.001 HIS O 101 PHE 0.039 0.002 PHE n 34 TYR 0.026 0.002 TYR i 46 ARG 0.011 0.001 ARG y 781 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29777.64 seconds wall clock time: 519 minutes 17.60 seconds (31157.60 seconds total)