Starting phenix.real_space_refine on Thu Mar 14 20:24:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a09_11602/03_2024/7a09_11602_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a09_11602/03_2024/7a09_11602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a09_11602/03_2024/7a09_11602.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a09_11602/03_2024/7a09_11602.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a09_11602/03_2024/7a09_11602_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a09_11602/03_2024/7a09_11602_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 8 7.16 5 Zn 4 6.06 5 P 1793 5.49 5 Mg 3 5.21 5 S 413 5.16 5 C 69976 2.51 5 N 22210 2.21 5 O 27761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a GLU 208": "OE1" <-> "OE2" Residue "a GLU 209": "OE1" <-> "OE2" Residue "p GLU 122": "OE1" <-> "OE2" Residue "d ARG 68": "NH1" <-> "NH2" Residue "d GLU 79": "OE1" <-> "OE2" Residue "d GLU 80": "OE1" <-> "OE2" Residue "d PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 258": "OE1" <-> "OE2" Residue "d GLU 268": "OE1" <-> "OE2" Residue "Q GLU 46": "OE1" <-> "OE2" Residue "q GLU 60": "OE1" <-> "OE2" Residue "q GLU 97": "OE1" <-> "OE2" Residue "q PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 198": "NH1" <-> "NH2" Residue "q ARG 200": "NH1" <-> "NH2" Residue "q PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 252": "NH1" <-> "NH2" Residue "W ARG 2": "NH1" <-> "NH2" Residue "W ARG 23": "NH1" <-> "NH2" Residue "r GLU 35": "OE1" <-> "OE2" Residue "r GLU 91": "OE1" <-> "OE2" Residue "r GLU 165": "OE1" <-> "OE2" Residue "r ARG 170": "NH1" <-> "NH2" Residue "r GLU 208": "OE1" <-> "OE2" Residue "s GLU 42": "OE1" <-> "OE2" Residue "s GLU 50": "OE1" <-> "OE2" Residue "s GLU 52": "OE1" <-> "OE2" Residue "s GLU 131": "OE1" <-> "OE2" Residue "s GLU 167": "OE1" <-> "OE2" Residue "s GLU 188": "OE1" <-> "OE2" Residue "t GLU 132": "OE1" <-> "OE2" Residue "t GLU 151": "OE1" <-> "OE2" Residue "t GLU 191": "OE1" <-> "OE2" Residue "t GLU 194": "OE1" <-> "OE2" Residue "c GLU 21": "OE1" <-> "OE2" Residue "c GLU 34": "OE1" <-> "OE2" Residue "c ARG 162": "NH1" <-> "NH2" Residue "n GLU 7": "OE1" <-> "OE2" Residue "n TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 49": "OE1" <-> "OE2" Residue "n GLU 52": "OE1" <-> "OE2" Residue "n GLU 103": "OE1" <-> "OE2" Residue "n GLU 130": "OE1" <-> "OE2" Residue "m TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 103": "OE1" <-> "OE2" Residue "m GLU 119": "OE1" <-> "OE2" Residue "m GLU 142": "OE1" <-> "OE2" Residue "y GLU 7": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 16": "NH1" <-> "NH2" Residue "z PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 80": "NH1" <-> "NH2" Residue "T GLU 23": "OE1" <-> "OE2" Residue "w GLU 37": "OE1" <-> "OE2" Residue "b ARG 54": "NH1" <-> "NH2" Residue "b GLU 61": "OE1" <-> "OE2" Residue "b ARG 178": "NH1" <-> "NH2" Residue "e ARG 55": "NH1" <-> "NH2" Residue "e GLU 106": "OE1" <-> "OE2" Residue "e GLU 160": "OE1" <-> "OE2" Residue "e GLU 176": "OE1" <-> "OE2" Residue "e GLU 195": "OE1" <-> "OE2" Residue "e GLU 197": "OE1" <-> "OE2" Residue "v ARG 36": "NH1" <-> "NH2" Residue "v GLU 87": "OE1" <-> "OE2" Residue "v GLU 117": "OE1" <-> "OE2" Residue "v GLU 125": "OE1" <-> "OE2" Residue "g GLU 53": "OE1" <-> "OE2" Residue "g ARG 71": "NH1" <-> "NH2" Residue "g ARG 125": "NH1" <-> "NH2" Residue "k ARG 14": "NH1" <-> "NH2" Residue "x PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 44": "OE1" <-> "OE2" Residue "x TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 19": "NH1" <-> "NH2" Residue "h GLU 111": "OE1" <-> "OE2" Residue "h GLU 113": "OE1" <-> "OE2" Residue "P GLU 90": "OE1" <-> "OE2" Residue "S GLU 52": "OE1" <-> "OE2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "S ARG 66": "NH1" <-> "NH2" Residue "S ARG 67": "NH1" <-> "NH2" Residue "l ARG 12": "NH1" <-> "NH2" Residue "l PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 116": "NH1" <-> "NH2" Residue "V ARG 88": "NH1" <-> "NH2" Residue "V ARG 100": "NH1" <-> "NH2" Residue "V GLU 223": "OE1" <-> "OE2" Residue "V GLU 269": "OE1" <-> "OE2" Residue "V GLU 282": "OE1" <-> "OE2" Residue "i ARG 104": "NH1" <-> "NH2" Residue "i ARG 121": "NH1" <-> "NH2" Residue "i ARG 146": "NH1" <-> "NH2" Residue "i ARG 150": "NH1" <-> "NH2" Residue "j ARG 11": "NH1" <-> "NH2" Residue "j GLU 53": "OE1" <-> "OE2" Residue "j GLU 95": "OE1" <-> "OE2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ARG 66": "NH1" <-> "NH2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 501": "NH1" <-> "NH2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B ARG 505": "NH1" <-> "NH2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "B GLU 551": "OE1" <-> "OE2" Residue "B GLU 560": "OE1" <-> "OE2" Residue "A ARG 7": "NH1" <-> "NH2" Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 298": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A ARG 353": "NH1" <-> "NH2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ARG 406": "NH1" <-> "NH2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A ARG 489": "NH1" <-> "NH2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A GLU 548": "OE1" <-> "OE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 571": "NH1" <-> "NH2" Residue "A ARG 572": "NH1" <-> "NH2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A GLU 595": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C ARG 450": "NH1" <-> "NH2" Residue "C GLU 454": "OE1" <-> "OE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C GLU 492": "OE1" <-> "OE2" Residue "C GLU 498": "OE1" <-> "OE2" Residue "C ARG 563": "NH1" <-> "NH2" Residue "C GLU 666": "OE1" <-> "OE2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C ARG 719": "NH1" <-> "NH2" Residue "C GLU 722": "OE1" <-> "OE2" Residue "C GLU 735": "OE1" <-> "OE2" Residue "C GLU 812": "OE1" <-> "OE2" Residue "C GLU 830": "OE1" <-> "OE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "E GLU 314": "OE1" <-> "OE2" Residue "E PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 369": "NH1" <-> "NH2" Residue "F GLU 145": "OE1" <-> "OE2" Residue "F GLU 181": "OE1" <-> "OE2" Residue "F GLU 193": "OE1" <-> "OE2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "F GLU 291": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H GLU 217": "OE1" <-> "OE2" Residue "H GLU 229": "OE1" <-> "OE2" Residue "H ARG 249": "NH1" <-> "NH2" Residue "H GLU 252": "OE1" <-> "OE2" Residue "K GLU 39": "OE1" <-> "OE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "L GLU 211": "OE1" <-> "OE2" Residue "L GLU 245": "OE1" <-> "OE2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L GLU 298": "OE1" <-> "OE2" Residue "L GLU 365": "OE1" <-> "OE2" Residue "M GLU 84": "OE1" <-> "OE2" Residue "M GLU 88": "OE1" <-> "OE2" Residue "M GLU 143": "OE1" <-> "OE2" Residue "M ARG 166": "NH1" <-> "NH2" Residue "M ARG 206": "NH1" <-> "NH2" Residue "M GLU 235": "OE1" <-> "OE2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M GLU 309": "OE1" <-> "OE2" Residue "M ARG 330": "NH1" <-> "NH2" Residue "M ARG 340": "NH1" <-> "NH2" Residue "J ARG 22": "NH1" <-> "NH2" Residue "J ARG 33": "NH1" <-> "NH2" Residue "J GLU 40": "OE1" <-> "OE2" Residue "J GLU 52": "OE1" <-> "OE2" Residue "J GLU 82": "OE1" <-> "OE2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 190": "NH1" <-> "NH2" Residue "J GLU 193": "OE1" <-> "OE2" Residue "J GLU 211": "OE1" <-> "OE2" Residue "J GLU 242": "OE1" <-> "OE2" Residue "J GLU 273": "OE1" <-> "OE2" Residue "J ARG 306": "NH1" <-> "NH2" Residue "J ARG 323": "NH1" <-> "NH2" Residue "J ARG 390": "NH1" <-> "NH2" Residue "J ARG 395": "NH1" <-> "NH2" Residue "J GLU 400": "OE1" <-> "OE2" Residue "J GLU 466": "OE1" <-> "OE2" Residue "J GLU 495": "OE1" <-> "OE2" Residue "J GLU 519": "OE1" <-> "OE2" Residue "J ARG 567": "NH1" <-> "NH2" Residue "J ARG 568": "NH1" <-> "NH2" Residue "N ARG 26": "NH1" <-> "NH2" Residue "N GLU 75": "OE1" <-> "OE2" Residue "N GLU 169": "OE1" <-> "OE2" Residue "N ARG 183": "NH1" <-> "NH2" Residue "N GLU 194": "OE1" <-> "OE2" Residue "N ARG 218": "NH1" <-> "NH2" Residue "N ARG 271": "NH1" <-> "NH2" Residue "N ARG 329": "NH1" <-> "NH2" Residue "N GLU 333": "OE1" <-> "OE2" Residue "N GLU 352": "OE1" <-> "OE2" Residue "N ARG 362": "NH1" <-> "NH2" Residue "N ARG 402": "NH1" <-> "NH2" Residue "N ARG 434": "NH1" <-> "NH2" Residue "N ARG 462": "NH1" <-> "NH2" Residue "N GLU 475": "OE1" <-> "OE2" Residue "N GLU 503": "OE1" <-> "OE2" Residue "4 ARG 200": "NH1" <-> "NH2" Residue "4 ARG 211": "NH1" <-> "NH2" Residue "4 ARG 261": "NH1" <-> "NH2" Residue "4 ARG 285": "NH1" <-> "NH2" Residue "4 ARG 308": "NH1" <-> "NH2" Residue "O GLU 16": "OE1" <-> "OE2" Residue "O GLU 28": "OE1" <-> "OE2" Residue "O ARG 56": "NH1" <-> "NH2" Residue "O ARG 74": "NH1" <-> "NH2" Residue "O ARG 112": "NH1" <-> "NH2" Residue "O GLU 171": "OE1" <-> "OE2" Residue "O ARG 172": "NH1" <-> "NH2" Residue "O GLU 202": "OE1" <-> "OE2" Residue "Y GLU 74": "OE1" <-> "OE2" Residue "Y PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 34": "NH1" <-> "NH2" Residue "Z GLU 75": "OE1" <-> "OE2" Residue "Z PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 122168 Number of models: 1 Model: "" Number of chains: 61 Chain: "a" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1705 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "p" 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: "d" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1674 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "Q" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "q" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2031 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 14, 'TRANS': 240} Chain: "W" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 230 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "r" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1794 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "s" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1399 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain breaks: 3 Chain: "t" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1638 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain breaks: 1 Chain: "c" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1499 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "n" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1119 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain breaks: 1 Chain: "m" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "y" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "z" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 999 Classifications: {'peptide': 122} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 116} Chain: "R" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "T" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 354 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain breaks: 1 Chain: "2" Number of atoms: 36717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1721, 36717 Inner-chain residues flagged as termini: ['pdbres=" U 2 140 "', 'pdbres=" U 2 287 "', 'pdbres=" G 2 330 "', 'pdbres=" C 2 746 "', 'pdbres=" C 2 791 "', 'pdbres=" G 2 841 "', 'pdbres=" G 21424 "', 'pdbres=" A 21438 "', 'pdbres=" G 21771 "'] Classifications: {'RNA': 1721} Modifications used: {'5*END': 10, 'rna2p_pur': 142, 'rna2p_pyr': 121, 'rna3p_pur': 769, 'rna3p_pyr': 689} Link IDs: {'rna2p': 262, 'rna3p': 1458} Chain breaks: 3 Chain: "w" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1011 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "b" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1745 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain: "e" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1495 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "u" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 799 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain: "v" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 861 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 1 Chain: "o" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 980 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "g" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1100 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "k" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1162 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "x" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1094 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain: "h" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 780 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 557 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "S" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 479 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "l" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 450 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "U" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 465 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain breaks: 1 Chain: "V" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2314 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 10, 'TRANS': 285} Chain breaks: 2 Chain: "i" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 939 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "j" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1080 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain: "G" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 712 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "I" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 1497 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 261} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 965 Unresolved non-hydrogen angles: 1241 Unresolved non-hydrogen dihedrals: 823 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 21, 'TYR:plan': 10, 'ASN:plan1': 16, 'TRP:plan': 5, 'HIS:plan': 11, 'PHE:plan': 18, 'GLU:plan': 18, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 570 Chain: "B" Number of atoms: 2966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 2966 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 388} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 509} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1526 Unresolved non-hydrogen angles: 1965 Unresolved non-hydrogen dihedrals: 1337 Unresolved non-hydrogen chiralities: 109 Planarities with less than four sites: {'GLN:plan1': 22, 'ASP:plan': 30, 'TYR:plan': 14, 'ASN:plan1': 16, 'TRP:plan': 16, 'HIS:plan': 13, 'PHE:plan': 26, 'GLU:plan': 23, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 886 Chain: "A" Number of atoms: 5385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5385 Classifications: {'peptide': 692} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 25, 'TRANS': 666} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 444 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 206 Chain: "C" Number of atoms: 5113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5113 Classifications: {'peptide': 633} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 17, 'TRANS': 615} Chain breaks: 5 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3437 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 404} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2090 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 10, 'TRANS': 258} Chain: "H" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2413 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 10, 'TRANS': 284} Chain breaks: 2 Chain: "K" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1750 Classifications: {'peptide': 217} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 3, 'TRANS': 210} Chain: "L" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3111 Classifications: {'peptide': 372} Link IDs: {'CIS': 5, 'PTRANS': 11, 'TRANS': 355} Chain: "M" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2718 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "J" Number of atoms: 4541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4541 Classifications: {'peptide': 576} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 30, 'TRANS': 543} Chain breaks: 1 Chain: "N" Number of atoms: 3617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3617 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 19, 'TRANS': 427} Chain breaks: 2 Chain: "X" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 390 Classifications: {'peptide': 78} Link IDs: {'TRANS': 77} Chain: "f" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1603 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 2, 'rna3p_pur': 31, 'rna3p_pyr': 31} Link IDs: {'rna2p': 12, 'rna3p': 62} Chain: "4" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1080 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 57 Chain: "O" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2138 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 9, 'TRANS': 286} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 138 Chain: "Y" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 2156 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 315} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain breaks: 2 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1043 Unresolved non-hydrogen angles: 1328 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 133 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 15, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 1, 'HIS:plan': 8, 'PHE:plan': 8, 'GLU:plan': 23, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 444 Chain: "Z" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 106} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 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: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 76 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'SF4': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "f" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5272 SG CYS Q 23 91.210 170.184 115.994 1.00 17.89 S ATOM 5293 SG CYS Q 26 91.177 169.287 112.436 1.00 19.75 S ATOM 5676 SG CYS Q 74 93.171 167.056 114.908 1.00 19.65 S ATOM 5695 SG CYS Q 77 94.388 170.269 113.560 1.00 26.43 S ATOM 69955 SG CYS U 121 200.385 155.674 52.446 1.00 86.67 S ATOM 69991 SG CYS U 126 200.013 153.994 55.958 1.00 94.06 S ATOM 70128 SG CYS U 144 198.991 156.499 53.548 1.00 89.35 S ATOM A04JX SG CYS J 29 95.184 110.083 66.030 1.00 27.13 S ATOM A04PH SG CYS J 55 95.687 103.722 64.776 1.00 26.34 S ATOM A04QH SG CYS J 61 91.446 104.997 68.352 1.00 19.51 S ATOM A04PZ SG CYS J 58 96.541 106.515 70.276 1.00 23.48 S ATOM A04H0 SG CYS J 16 82.250 105.268 63.676 1.00 42.35 S ATOM A04I4 SG CYS J 21 80.206 109.952 66.352 1.00 50.53 S ATOM A04J3 SG CYS J 25 86.636 109.189 65.658 1.00 36.46 S ATOM A04RD SG CYS J 65 83.369 105.863 69.078 1.00 31.45 S ATOM A0CXG SG CYS 4 302 102.189 166.843 37.823 1.00 72.10 S Time building chain proxies: 45.32, per 1000 atoms: 0.37 Number of scatterers: 122168 At special positions: 0 Unit cell: (231.921, 264.75, 314.523, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 Fe 8 26.01 S 413 16.00 P 1793 15.00 Mg 3 11.99 O 27761 8.00 N 22210 7.00 C 69976 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: 39.70 Conformation dependent library (CDL) restraints added in 11.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 J 601 " pdb="FE4 SF4 J 601 " - pdb=" SG CYS J 58 " pdb="FE2 SF4 J 601 " - pdb=" SG CYS J 55 " pdb="FE3 SF4 J 601 " - pdb=" SG CYS J 61 " pdb="FE1 SF4 J 601 " - pdb=" SG CYS J 29 " pdb="FE2 SF4 J 601 " - pdb=" SG CYS J 38 " pdb=" SF4 J 602 " pdb="FE2 SF4 J 602 " - pdb=" SG CYS J 21 " pdb="FE4 SF4 J 602 " - pdb=" SG CYS J 65 " pdb="FE1 SF4 J 602 " - pdb=" SG CYS J 16 " pdb="FE3 SF4 J 602 " - pdb=" SG CYS J 25 " Number of angles added : 27 Zn2+ tetrahedral coordination pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 302 " pdb=" ZN Q 201 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 74 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 26 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 77 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 23 " pdb=" ZN U 500 " pdb="ZN ZN U 500 " - pdb=" SG CYS U 144 " pdb="ZN ZN U 500 " - pdb=" SG CYS U 121 " pdb="ZN ZN U 500 " - pdb=" SG CYS U 126 " Number of angles added : 6 21522 Ramachandran restraints generated. 10761 Oldfield, 0 Emsley, 10761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 20646 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: 363 helices and 111 sheets defined 46.5% alpha, 15.0% beta 411 base pairs and 907 stacking pairs defined. Time for finding SS restraints: 66.92 Creating SS restraints... Processing helix chain 'a' and resid 11 through 22 Processing helix chain 'a' and resid 31 through 39 removed outlier: 5.382A pdb=" N GLN a 36 " --> pdb=" O PHE a 32 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TYR a 37 " --> pdb=" O GLN a 33 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE a 38 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N TYR a 39 " --> pdb=" O GLU a 35 " (cutoff:3.500A) Processing helix chain 'a' and resid 50 through 68 removed outlier: 3.550A pdb=" N ALA a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE a 68 " --> pdb=" O ALA a 64 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 95 removed outlier: 4.003A pdb=" N GLN a 84 " --> pdb=" O ARG a 80 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ARG a 85 " --> pdb=" O ASN a 81 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA a 86 " --> pdb=" O THR a 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 126 through 131 removed outlier: 4.064A pdb=" N HIS a 131 " --> pdb=" O PRO a 127 " (cutoff:3.500A) Processing helix chain 'a' and resid 132 through 141 removed outlier: 4.759A pdb=" N SER a 138 " --> pdb=" O LEU a 134 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR a 139 " --> pdb=" O THR a 135 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL a 140 " --> pdb=" O GLU a 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 167 through 187 Processing helix chain 'a' and resid 198 through 204 removed outlier: 4.601A pdb=" N TYR a 202 " --> pdb=" O MET a 198 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE a 203 " --> pdb=" O PRO a 199 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TYR a 204 " --> pdb=" O ASP a 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 198 through 204' Processing helix chain 'a' and resid 206 through 216 removed outlier: 4.825A pdb=" N ALA a 216 " --> pdb=" O LYS a 212 " (cutoff:3.500A) Processing helix chain 'p' and resid 23 through 29 removed outlier: 5.501A pdb=" N LYS p 27 " --> pdb=" O ASP p 23 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS p 28 " --> pdb=" O PRO p 24 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASP p 29 " --> pdb=" O PHE p 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 23 through 29' Processing helix chain 'p' and resid 57 through 63 removed outlier: 3.555A pdb=" N GLY p 61 " --> pdb=" O ILE p 57 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU p 62 " --> pdb=" O ALA p 58 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS p 63 " --> pdb=" O SER p 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 57 through 63' Processing helix chain 'p' and resid 70 through 76 removed outlier: 3.723A pdb=" N GLN p 75 " --> pdb=" O LEU p 71 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASN p 76 " --> pdb=" O ALA p 72 " (cutoff:3.500A) Processing helix chain 'p' and resid 106 through 115 removed outlier: 3.588A pdb=" N MET p 113 " --> pdb=" O LYS p 109 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL p 114 " --> pdb=" O MET p 110 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LYS p 115 " --> pdb=" O CYS p 111 " (cutoff:3.500A) Processing helix chain 'p' and resid 157 through 179 removed outlier: 4.012A pdb=" N VAL p 176 " --> pdb=" O MET p 172 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR p 178 " --> pdb=" O ARG p 174 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ASN p 179 " --> pdb=" O GLU p 175 " (cutoff:3.500A) Processing helix chain 'p' and resid 180 through 191 removed outlier: 3.556A pdb=" N ILE p 189 " --> pdb=" O VAL p 185 " (cutoff:3.500A) Proline residue: p 190 - end of helix Processing helix chain 'p' and resid 192 through 203 removed outlier: 3.836A pdb=" N GLN p 202 " --> pdb=" O GLU p 198 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER p 203 " --> pdb=" O LYS p 199 " (cutoff:3.500A) Processing helix chain 'p' and resid 224 through 233 removed outlier: 3.707A pdb=" N LEU p 228 " --> pdb=" O GLU p 224 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 73 removed outlier: 4.457A pdb=" N ASP d 72 " --> pdb=" O ARG d 68 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N MET d 73 " --> pdb=" O LEU d 69 " (cutoff:3.500A) Processing helix chain 'd' and resid 77 through 85 removed outlier: 4.189A pdb=" N ILE d 81 " --> pdb=" O SER d 77 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE d 84 " --> pdb=" O GLU d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 91 through 98 removed outlier: 3.737A pdb=" N ASP d 95 " --> pdb=" O SER d 91 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 162 removed outlier: 3.681A pdb=" N ILE d 162 " --> pdb=" O ALA d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 207 through 218 removed outlier: 3.875A pdb=" N LEU d 213 " --> pdb=" O VAL d 209 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY d 218 " --> pdb=" O LEU d 214 " (cutoff:3.500A) Processing helix chain 'd' and resid 232 through 250 removed outlier: 3.801A pdb=" N LYS d 246 " --> pdb=" O ASP d 242 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR d 247 " --> pdb=" O ALA d 243 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TYR d 248 " --> pdb=" O ILE d 244 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N SER d 249 " --> pdb=" O SER d 245 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR d 250 " --> pdb=" O LYS d 246 " (cutoff:3.500A) Processing helix chain 'd' and resid 264 through 270 removed outlier: 4.117A pdb=" N THR d 270 " --> pdb=" O TYR d 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 57 removed outlier: 4.604A pdb=" N ARG Q 51 " --> pdb=" O ALA Q 47 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASP Q 52 " --> pdb=" O ALA Q 48 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 82 removed outlier: 3.553A pdb=" N ILE Q 79 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) Processing helix chain 'Q' and resid 88 through 95 removed outlier: 4.845A pdb=" N LYS Q 93 " --> pdb=" O ARG Q 89 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASP Q 94 " --> pdb=" O GLU Q 90 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARG Q 95 " --> pdb=" O ALA Q 91 " (cutoff:3.500A) Processing helix chain 'q' and resid 43 through 49 Processing helix chain 'q' and resid 57 through 68 removed outlier: 3.711A pdb=" N VAL q 61 " --> pdb=" O THR q 57 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS q 62 " --> pdb=" O GLY q 58 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLN q 67 " --> pdb=" O LYS q 63 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG q 68 " --> pdb=" O ILE q 64 " (cutoff:3.500A) Processing helix chain 'q' and resid 115 through 120 removed outlier: 4.030A pdb=" N LYS q 120 " --> pdb=" O PRO q 116 " (cutoff:3.500A) Processing helix chain 'q' and resid 247 through 256 removed outlier: 3.696A pdb=" N LEU q 256 " --> pdb=" O ARG q 252 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 24 removed outlier: 4.579A pdb=" N SER W 24 " --> pdb=" O MET W 20 " (cutoff:3.500A) Processing helix chain 'r' and resid 20 through 29 removed outlier: 5.021A pdb=" N LEU r 24 " --> pdb=" O ASP r 20 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N THR r 26 " --> pdb=" O ARG r 22 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N PHE r 27 " --> pdb=" O LYS r 23 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU r 29 " --> pdb=" O ARG r 25 " (cutoff:3.500A) Processing helix chain 'r' and resid 38 through 43 removed outlier: 5.406A pdb=" N GLY r 42 " --> pdb=" O ALA r 38 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLU r 43 " --> pdb=" O ASP r 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 38 through 43' Processing helix chain 'r' and resid 137 through 146 removed outlier: 3.885A pdb=" N ILE r 141 " --> pdb=" O ARG r 137 " (cutoff:3.500A) Processing helix chain 'r' and resid 152 through 157 removed outlier: 4.818A pdb=" N TYR r 156 " --> pdb=" O ASP r 152 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL r 157 " --> pdb=" O VAL r 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 152 through 157' Processing helix chain 'r' and resid 181 through 221 removed outlier: 3.697A pdb=" N LEU r 185 " --> pdb=" O THR r 181 " (cutoff:3.500A) Processing helix chain 's' and resid 18 through 31 removed outlier: 4.024A pdb=" N GLU s 31 " --> pdb=" O LEU s 27 " (cutoff:3.500A) Processing helix chain 's' and resid 65 through 77 removed outlier: 4.385A pdb=" N LYS s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ILE s 75 " --> pdb=" O SER s 71 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL s 77 " --> pdb=" O GLN s 73 " (cutoff:3.500A) Processing helix chain 's' and resid 78 through 88 removed outlier: 4.896A pdb=" N SER s 88 " --> pdb=" O GLU s 84 " (cutoff:3.500A) Processing helix chain 's' and resid 117 through 122 removed outlier: 3.925A pdb=" N THR s 121 " --> pdb=" O PRO s 117 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU s 122 " --> pdb=" O ARG s 118 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 117 through 122' Processing helix chain 's' and resid 123 through 135 removed outlier: 4.279A pdb=" N VAL s 134 " --> pdb=" O LEU s 130 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N PHE s 135 " --> pdb=" O GLU s 131 " (cutoff:3.500A) Processing helix chain 's' and resid 159 through 164 removed outlier: 4.574A pdb=" N GLN s 163 " --> pdb=" O ASP s 159 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASN s 164 " --> pdb=" O LYS s 160 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 159 through 164' Processing helix chain 's' and resid 169 through 181 Processing helix chain 't' and resid 87 through 94 removed outlier: 4.485A pdb=" N VAL t 91 " --> pdb=" O ASN t 87 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR t 93 " --> pdb=" O GLU t 89 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS t 94 " --> pdb=" O LEU t 90 " (cutoff:3.500A) Processing helix chain 't' and resid 106 through 117 removed outlier: 3.897A pdb=" N ARG t 110 " --> pdb=" O SER t 106 " (cutoff:3.500A) Processing helix chain 't' and resid 130 through 138 removed outlier: 4.314A pdb=" N GLU t 135 " --> pdb=" O PRO t 131 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE t 136 " --> pdb=" O GLU t 132 " (cutoff:3.500A) Processing helix chain 't' and resid 143 through 156 removed outlier: 3.895A pdb=" N LYS t 147 " --> pdb=" O LYS t 143 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS t 148 " --> pdb=" O LYS t 144 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASN t 155 " --> pdb=" O GLU t 151 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA t 156 " --> pdb=" O ARG t 152 " (cutoff:3.500A) Processing helix chain 't' and resid 159 through 169 removed outlier: 4.230A pdb=" N GLN t 167 " --> pdb=" O GLU t 163 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN t 168 " --> pdb=" O GLU t 164 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY t 169 " --> pdb=" O GLN t 165 " (cutoff:3.500A) Processing helix chain 't' and resid 192 through 206 removed outlier: 3.918A pdb=" N LYS t 206 " --> pdb=" O ILE t 202 " (cutoff:3.500A) Processing helix chain 'c' and resid 21 through 36 Processing helix chain 'c' and resid 39 through 63 removed outlier: 4.223A pdb=" N VAL c 43 " --> pdb=" O ASN c 39 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL c 46 " --> pdb=" O GLU c 42 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR c 62 " --> pdb=" O ARG c 58 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU c 63 " --> pdb=" O GLU c 59 " (cutoff:3.500A) Processing helix chain 'c' and resid 67 through 85 removed outlier: 4.393A pdb=" N ASN c 75 " --> pdb=" O LEU c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 93 through 100 removed outlier: 3.859A pdb=" N ILE c 97 " --> pdb=" O LYS c 93 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU c 98 " --> pdb=" O LEU c 94 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLY c 99 " --> pdb=" O ASP c 95 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU c 100 " --> pdb=" O TYR c 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 93 through 100' Processing helix chain 'c' and resid 101 through 109 removed outlier: 3.788A pdb=" N PHE c 105 " --> pdb=" O LYS c 101 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU c 107 " --> pdb=" O GLU c 103 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG c 108 " --> pdb=" O ASP c 104 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG c 109 " --> pdb=" O PHE c 105 " (cutoff:3.500A) Processing helix chain 'c' and resid 110 through 118 removed outlier: 3.711A pdb=" N LEU c 117 " --> pdb=" O GLN c 113 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY c 118 " --> pdb=" O VAL c 114 " (cutoff:3.500A) Processing helix chain 'c' and resid 122 through 133 removed outlier: 3.721A pdb=" N ARG c 133 " --> pdb=" O LEU c 129 " (cutoff:3.500A) Processing helix chain 'c' and resid 150 through 155 removed outlier: 4.372A pdb=" N LYS c 155 " --> pdb=" O LEU c 151 " (cutoff:3.500A) Processing helix chain 'c' and resid 171 through 180 removed outlier: 3.912A pdb=" N LYS c 179 " --> pdb=" O ARG c 175 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LYS c 180 " --> pdb=" O LYS c 176 " (cutoff:3.500A) Processing helix chain 'n' and resid 47 through 53 removed outlier: 3.614A pdb=" N ILE n 51 " --> pdb=" O PRO n 47 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY n 53 " --> pdb=" O GLU n 49 " (cutoff:3.500A) Processing helix chain 'm' and resid 29 through 44 removed outlier: 3.814A pdb=" N VAL m 33 " --> pdb=" O THR m 29 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS m 43 " --> pdb=" O LYS m 39 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLY m 44 " --> pdb=" O LEU m 40 " (cutoff:3.500A) Processing helix chain 'm' and resid 46 through 57 Processing helix chain 'm' and resid 62 through 67 removed outlier: 3.562A pdb=" N VAL m 66 " --> pdb=" O GLN m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 70 through 79 removed outlier: 3.998A pdb=" N LYS m 78 " --> pdb=" O ILE m 74 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 106 removed outlier: 3.748A pdb=" N ARG m 104 " --> pdb=" O LYS m 100 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG m 106 " --> pdb=" O LEU m 102 " (cutoff:3.500A) Processing helix chain 'm' and resid 108 through 133 removed outlier: 3.512A pdb=" N LYS m 112 " --> pdb=" O ASP m 108 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR m 131 " --> pdb=" O ARG m 127 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS m 132 " --> pdb=" O TYR m 128 " (cutoff:3.500A) Processing helix chain 'm' and resid 145 through 150 removed outlier: 4.447A pdb=" N LEU m 149 " --> pdb=" O THR m 145 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL m 150 " --> pdb=" O ALA m 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 145 through 150' Processing helix chain 'y' and resid 56 through 63 removed outlier: 3.759A pdb=" N ARG y 60 " --> pdb=" O CYS y 56 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET y 62 " --> pdb=" O ALA y 58 " (cutoff:3.500A) Processing helix chain 'y' and resid 64 through 77 removed outlier: 3.517A pdb=" N SER y 68 " --> pdb=" O GLU y 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 21 removed outlier: 3.588A pdb=" N ASP D 9 " --> pdb=" O ASN D 5 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 45 removed outlier: 3.777A pdb=" N HIS D 44 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY D 45 " --> pdb=" O MET D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 removed outlier: 4.854A pdb=" N GLU D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYS D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP D 89 " --> pdb=" O ASP D 85 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU D 94 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 120 Processing helix chain 'z' and resid 36 through 49 Processing helix chain 'z' and resid 51 through 56 removed outlier: 4.628A pdb=" N ILE z 55 " --> pdb=" O THR z 51 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE z 56 " --> pdb=" O PRO z 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 51 through 56' Processing helix chain 'z' and resid 78 through 86 Processing helix chain 'z' and resid 87 through 95 removed outlier: 3.812A pdb=" N HIS z 94 " --> pdb=" O ARG z 90 " (cutoff:3.500A) Processing helix chain 'z' and resid 103 through 118 removed outlier: 5.380A pdb=" N ARG z 107 " --> pdb=" O SER z 103 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS z 116 " --> pdb=" O ASN z 112 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL z 117 " --> pdb=" O ARG z 113 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ARG z 118 " --> pdb=" O MET z 114 " (cutoff:3.500A) Processing helix chain 'z' and resid 119 through 126 removed outlier: 4.677A pdb=" N ALA z 123 " --> pdb=" O GLY z 119 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN z 124 " --> pdb=" O THR z 120 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL z 125 " --> pdb=" O ALA z 121 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLY z 126 " --> pdb=" O LYS z 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 119 through 126' Processing helix chain 'R' and resid 11 through 18 removed outlier: 4.667A pdb=" N LYS R 18 " --> pdb=" O GLU R 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 16 removed outlier: 4.821A pdb=" N GLY T 14 " --> pdb=" O GLY T 10 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 42 removed outlier: 3.563A pdb=" N ARG T 34 " --> pdb=" O GLY T 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 6 through 20 removed outlier: 3.672A pdb=" N LYS w 10 " --> pdb=" O THR w 6 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA w 13 " --> pdb=" O VAL w 9 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG w 14 " --> pdb=" O LYS w 10 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS w 19 " --> pdb=" O VAL w 15 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TYR w 20 " --> pdb=" O ILE w 16 " (cutoff:3.500A) Processing helix chain 'w' and resid 27 through 39 removed outlier: 3.633A pdb=" N ASN w 31 " --> pdb=" O ASP w 27 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG w 33 " --> pdb=" O HIS w 29 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU w 36 " --> pdb=" O LYS w 32 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU w 37 " --> pdb=" O ARG w 33 " (cutoff:3.500A) Processing helix chain 'w' and resid 43 through 64 removed outlier: 3.686A pdb=" N ARG w 47 " --> pdb=" O SER w 43 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN w 62 " --> pdb=" O MET w 58 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG w 63 " --> pdb=" O LYS w 59 " (cutoff:3.500A) Processing helix chain 'w' and resid 71 through 81 removed outlier: 4.292A pdb=" N GLU w 75 " --> pdb=" O ILE w 71 " (cutoff:3.500A) Processing helix chain 'w' and resid 99 through 110 Processing helix chain 'b' and resid 6 through 30 removed outlier: 4.081A pdb=" N ALA b 30 " --> pdb=" O THR b 26 " (cutoff:3.500A) Processing helix chain 'b' and resid 54 through 60 removed outlier: 4.400A pdb=" N VAL b 58 " --> pdb=" O ARG b 54 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY b 60 " --> pdb=" O GLN b 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 63 through 77 removed outlier: 3.660A pdb=" N ARG b 67 " --> pdb=" O GLY b 63 " (cutoff:3.500A) Processing helix chain 'b' and resid 93 through 98 removed outlier: 5.637A pdb=" N ALA b 98 " --> pdb=" O ARG b 94 " (cutoff:3.500A) Processing helix chain 'b' and resid 99 through 112 removed outlier: 3.516A pdb=" N GLY b 111 " --> pdb=" O TYR b 107 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY b 112 " --> pdb=" O LYS b 108 " (cutoff:3.500A) Processing helix chain 'b' and resid 114 through 130 Processing helix chain 'b' and resid 161 through 167 removed outlier: 4.712A pdb=" N ASN b 165 " --> pdb=" O GLY b 161 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR b 166 " --> pdb=" O ASP b 162 " (cutoff:3.500A) Processing helix chain 'e' and resid 35 through 40 removed outlier: 4.394A pdb=" N ALA e 40 " --> pdb=" O GLN e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 61 through 66 removed outlier: 4.480A pdb=" N GLN e 65 " --> pdb=" O PHE e 61 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N CYS e 66 " --> pdb=" O ARG e 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 61 through 66' Processing helix chain 'e' and resid 67 through 78 removed outlier: 3.708A pdb=" N MET e 77 " --> pdb=" O THR e 73 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N MET e 78 " --> pdb=" O ASN e 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 105 removed outlier: 3.842A pdb=" N THR e 89 " --> pdb=" O LYS e 85 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 120 removed outlier: 3.801A pdb=" N GLY e 120 " --> pdb=" O ILE e 116 " (cutoff:3.500A) Processing helix chain 'e' and resid 142 through 163 removed outlier: 4.867A pdb=" N GLY e 157 " --> pdb=" O LEU e 153 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLU e 160 " --> pdb=" O THR e 156 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA e 162 " --> pdb=" O ALA e 158 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE e 163 " --> pdb=" O ARG e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 168 through 183 removed outlier: 4.550A pdb=" N GLY e 183 " --> pdb=" O ASN e 179 " (cutoff:3.500A) Processing helix chain 'e' and resid 187 through 204 removed outlier: 4.211A pdb=" N ALA e 200 " --> pdb=" O LEU e 196 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG e 204 " --> pdb=" O ALA e 200 " (cutoff:3.500A) Processing helix chain 'u' and resid 4 through 19 Processing helix chain 'u' and resid 41 through 56 removed outlier: 3.533A pdb=" N VAL u 45 " --> pdb=" O PRO u 41 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG u 55 " --> pdb=" O SER u 51 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY u 56 " --> pdb=" O LEU u 52 " (cutoff:3.500A) Processing helix chain 'u' and resid 72 through 84 removed outlier: 3.675A pdb=" N LEU u 83 " --> pdb=" O LEU u 79 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N HIS u 84 " --> pdb=" O ARG u 80 " (cutoff:3.500A) Processing helix chain 'v' and resid 14 through 29 removed outlier: 4.806A pdb=" N LEU v 18 " --> pdb=" O VAL v 14 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU v 20 " --> pdb=" O THR v 16 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL v 21 " --> pdb=" O ALA v 17 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU v 22 " --> pdb=" O LEU v 18 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR v 24 " --> pdb=" O GLU v 20 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE v 27 " --> pdb=" O LYS v 23 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP v 29 " --> pdb=" O ALA v 25 " (cutoff:3.500A) Processing helix chain 'v' and resid 34 through 45 removed outlier: 3.939A pdb=" N ALA v 39 " --> pdb=" O ILE v 35 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS v 44 " --> pdb=" O LYS v 40 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARG v 45 " --> pdb=" O ALA v 41 " (cutoff:3.500A) Processing helix chain 'v' and resid 63 through 73 removed outlier: 4.021A pdb=" N CYS v 69 " --> pdb=" O VAL v 65 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ALA v 70 " --> pdb=" O GLU v 66 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLU v 71 " --> pdb=" O ALA v 67 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N HIS v 72 " --> pdb=" O LEU v 68 " (cutoff:3.500A) Processing helix chain 'v' and resid 81 through 90 removed outlier: 3.795A pdb=" N LEU v 85 " --> pdb=" O ASP v 81 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLY v 90 " --> pdb=" O GLY v 86 " (cutoff:3.500A) Processing helix chain 'v' and resid 118 through 127 removed outlier: 5.323A pdb=" N ASP v 122 " --> pdb=" O SER v 118 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL v 123 " --> pdb=" O GLN v 119 " (cutoff:3.500A) Processing helix chain 'o' and resid 21 through 29 removed outlier: 5.907A pdb=" N ASP o 27 " --> pdb=" O ASP o 23 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N MET o 28 " --> pdb=" O GLN o 24 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N SER o 29 " --> pdb=" O LEU o 25 " (cutoff:3.500A) Processing helix chain 'o' and resid 30 through 38 removed outlier: 5.200A pdb=" N GLN o 35 " --> pdb=" O GLU o 31 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU o 36 " --> pdb=" O GLN o 32 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER o 38 " --> pdb=" O MET o 34 " (cutoff:3.500A) Processing helix chain 'o' and resid 39 through 48 Processing helix chain 'o' and resid 50 through 67 removed outlier: 4.488A pdb=" N ALA o 67 " --> pdb=" O ALA o 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 58 removed outlier: 4.196A pdb=" N GLN g 48 " --> pdb=" O PRO g 44 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N TYR g 49 " --> pdb=" O ARG g 45 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LYS g 50 " --> pdb=" O THR g 46 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU g 51 " --> pdb=" O LEU g 47 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU g 52 " --> pdb=" O GLN g 48 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU g 53 " --> pdb=" O TYR g 49 " (cutoff:3.500A) Proline residue: g 54 - end of helix Processing helix chain 'g' and resid 59 through 67 removed outlier: 4.400A pdb=" N PHE g 63 " --> pdb=" O GLY g 59 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASP g 67 " --> pdb=" O PHE g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 77 through 99 removed outlier: 3.612A pdb=" N ILE g 81 " --> pdb=" O HIS g 77 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN g 86 " --> pdb=" O TYR g 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 101 through 116 removed outlier: 3.718A pdb=" N LYS g 105 " --> pdb=" O ASP g 101 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN g 114 " --> pdb=" O ASP g 110 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR g 115 " --> pdb=" O ILE g 111 " (cutoff:3.500A) Processing helix chain 'k' and resid 25 through 32 removed outlier: 4.047A pdb=" N THR k 31 " --> pdb=" O ALA k 27 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ALA k 32 " --> pdb=" O PHE k 28 " (cutoff:3.500A) Processing helix chain 'k' and resid 37 through 49 removed outlier: 3.891A pdb=" N VAL k 43 " --> pdb=" O ARG k 39 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASP k 49 " --> pdb=" O LEU k 45 " (cutoff:3.500A) Processing helix chain 'k' and resid 60 through 74 Proline residue: k 74 - end of helix Processing helix chain 'k' and resid 100 through 118 removed outlier: 3.868A pdb=" N ASP k 104 " --> pdb=" O ALA k 100 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN k 105 " --> pdb=" O ASN k 101 " (cutoff:3.500A) Processing helix chain 'k' and resid 119 through 128 Processing helix chain 'x' and resid 5 through 10 removed outlier: 3.904A pdb=" N VAL x 9 " --> pdb=" O THR x 5 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ASN x 10 " --> pdb=" O VAL x 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 5 through 10' Processing helix chain 'x' and resid 11 through 26 removed outlier: 3.694A pdb=" N VAL x 15 " --> pdb=" O GLN x 11 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG x 16 " --> pdb=" O GLN x 12 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA x 20 " --> pdb=" O ARG x 16 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER x 25 " --> pdb=" O PHE x 21 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY x 26 " --> pdb=" O LEU x 22 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 67 removed outlier: 4.044A pdb=" N THR x 55 " --> pdb=" O ASN x 51 " (cutoff:3.500A) Processing helix chain 'x' and resid 71 through 80 removed outlier: 4.328A pdb=" N LYS x 77 " --> pdb=" O GLY x 73 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR x 79 " --> pdb=" O MET x 75 " (cutoff:3.500A) Processing helix chain 'x' and resid 96 through 111 removed outlier: 3.991A pdb=" N ALA x 100 " --> pdb=" O SER x 96 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS x 111 " --> pdb=" O LEU x 107 " (cutoff:3.500A) Processing helix chain 'x' and resid 124 through 142 removed outlier: 3.883A pdb=" N LEU x 131 " --> pdb=" O GLY x 127 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE x 134 " --> pdb=" O ASP x 130 " (cutoff:3.500A) Processing helix chain 'x' and resid 31 through 36 removed outlier: 3.705A pdb=" N VAL x 34 " --> pdb=" O PRO x 31 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASP x 35 " --> pdb=" O GLU x 32 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR x 36 " --> pdb=" O TRP x 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 31 through 36' Processing helix chain 'h' and resid 28 through 47 removed outlier: 4.412A pdb=" N LEU h 32 " --> pdb=" O ASN h 28 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU h 45 " --> pdb=" O ARG h 41 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS h 46 " --> pdb=" O GLY h 42 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN h 47 " --> pdb=" O ALA h 43 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 103 removed outlier: 4.038A pdb=" N VAL h 98 " --> pdb=" O PRO h 94 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR h 102 " --> pdb=" O VAL h 98 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N SER h 103 " --> pdb=" O LYS h 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 66 removed outlier: 3.754A pdb=" N TYR P 55 " --> pdb=" O ASP P 51 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP P 56 " --> pdb=" O LYS P 52 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LYS P 57 " --> pdb=" O ALA P 53 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL P 62 " --> pdb=" O LEU P 58 " (cutoff:3.500A) Proline residue: P 63 - end of helix removed outlier: 6.020A pdb=" N LYS P 66 " --> pdb=" O VAL P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 78 removed outlier: 3.995A pdb=" N GLU P 75 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG P 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS P 78 " --> pdb=" O SER P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 95 removed outlier: 3.675A pdb=" N LEU P 92 " --> pdb=" O LEU P 88 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER P 93 " --> pdb=" O GLN P 89 " (cutoff:3.500A) Processing helix chain 'l' and resid 15 through 20 removed outlier: 4.336A pdb=" N ARG l 19 " --> pdb=" O GLY l 15 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N SER l 20 " --> pdb=" O GLN l 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 15 through 20' Processing helix chain 'l' and resid 39 through 47 Processing helix chain 'U' and resid 100 through 106 removed outlier: 4.479A pdb=" N LYS U 104 " --> pdb=" O LEU U 100 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TYR U 105 " --> pdb=" O ALA U 101 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TYR U 106 " --> pdb=" O VAL U 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 100 through 106' Processing helix chain 'i' and resid 57 through 63 removed outlier: 4.744A pdb=" N LYS i 61 " --> pdb=" O THR i 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL i 62 " --> pdb=" O GLY i 58 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N LYS i 63 " --> pdb=" O GLY i 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 57 through 63' Processing helix chain 'i' and resid 64 through 69 removed outlier: 3.817A pdb=" N GLU i 68 " --> pdb=" O ALA i 64 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER i 69 " --> pdb=" O ASP i 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 64 through 69' Processing helix chain 'i' and resid 70 through 89 removed outlier: 4.152A pdb=" N GLU i 87 " --> pdb=" O GLN i 83 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU i 88 " --> pdb=" O ARG i 84 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY i 89 " --> pdb=" O CYS i 85 " (cutoff:3.500A) Processing helix chain 'i' and resid 111 through 123 removed outlier: 3.543A pdb=" N ALA i 120 " --> pdb=" O LEU i 116 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY i 123 " --> pdb=" O LEU i 119 " (cutoff:3.500A) Processing helix chain 'j' and resid 9 through 24 removed outlier: 3.657A pdb=" N ASP j 19 " --> pdb=" O SER j 15 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TRP j 22 " --> pdb=" O ARG j 18 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N HIS j 23 " --> pdb=" O ASP j 19 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP j 24 " --> pdb=" O GLN j 20 " (cutoff:3.500A) Processing helix chain 'j' and resid 25 through 32 removed outlier: 3.576A pdb=" N LYS j 29 " --> pdb=" O LYS j 25 " (cutoff:3.500A) Processing helix chain 'j' and resid 33 through 39 removed outlier: 3.868A pdb=" N LYS j 37 " --> pdb=" O GLY j 33 " (cutoff:3.500A) Processing helix chain 'j' and resid 89 through 95 removed outlier: 4.681A pdb=" N PHE j 93 " --> pdb=" O GLY j 89 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE j 94 " --> pdb=" O CYS j 90 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLU j 95 " --> pdb=" O LEU j 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 89 through 95' Processing helix chain 'j' and resid 129 through 136 Processing helix chain 'G' and resid 96 through 107 removed outlier: 4.048A pdb=" N ALA G 105 " --> pdb=" O ARG G 101 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR G 106 " --> pdb=" O SER G 102 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY G 107 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 213 removed outlier: 4.426A pdb=" N GLU B 201 " --> pdb=" O PRO B 197 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LYS B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LYS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 251 removed outlier: 3.660A pdb=" N ALA B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 4.021A pdb=" N LEU B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR B 295 " --> pdb=" O GLY B 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 289 through 295' Processing helix chain 'B' and resid 459 through 464 removed outlier: 5.009A pdb=" N ILE B 464 " --> pdb=" O LYS B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 722 removed outlier: 3.814A pdb=" N ILE B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B 722 " --> pdb=" O LYS B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 744 removed outlier: 5.235A pdb=" N ARG B 736 " --> pdb=" O GLU B 732 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU B 737 " --> pdb=" O GLN B 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 22 removed outlier: 4.151A pdb=" N ALA A 11 " --> pdb=" O ARG A 7 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 12 " --> pdb=" O PRO A 8 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 37 removed outlier: 3.719A pdb=" N ALA A 27 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 62 removed outlier: 3.543A pdb=" N ILE A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.535A pdb=" N ALA A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 116 removed outlier: 4.026A pdb=" N GLU A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 removed outlier: 5.566A pdb=" N LEU A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 removed outlier: 3.709A pdb=" N ARG A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 165 removed outlier: 4.193A pdb=" N ARG A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 189 removed outlier: 3.612A pdb=" N TYR A 174 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 212 removed outlier: 3.819A pdb=" N PHE A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N HIS A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 244 Processing helix chain 'A' and resid 245 through 264 removed outlier: 3.717A pdb=" N SER A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LYS A 264 " --> pdb=" O PHE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 287 removed outlier: 4.009A pdb=" N THR A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 308 removed outlier: 5.111A pdb=" N GLU A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ARG A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 329 removed outlier: 4.513A pdb=" N MET A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 343 removed outlier: 4.249A pdb=" N ALA A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 removed outlier: 3.907A pdb=" N LYS A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ARG A 353 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 355 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 378 removed outlier: 3.624A pdb=" N LEU A 370 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N MET A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A 375 " --> pdb=" O ILE A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 395 removed outlier: 4.223A pdb=" N ASP A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LEU A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 418 removed outlier: 4.151A pdb=" N GLN A 417 " --> pdb=" O TRP A 413 " (cutoff:3.500A) Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 427 through 447 removed outlier: 3.615A pdb=" N ILE A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 Proline residue: A 460 - end of helix Processing helix chain 'A' and resid 463 through 477 Processing helix chain 'A' and resid 514 through 522 removed outlier: 4.557A pdb=" N ASN A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN A 522 " --> pdb=" O GLN A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 538 removed outlier: 4.158A pdb=" N LYS A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 567 removed outlier: 6.980A pdb=" N ARG A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LYS A 563 " --> pdb=" O LYS A 559 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N HIS A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN A 566 " --> pdb=" O ARG A 562 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARG A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 601 removed outlier: 3.873A pdb=" N LEU A 601 " --> pdb=" O ARG A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 640 Processing helix chain 'A' and resid 642 through 685 Proline residue: A 666 - end of helix Processing helix chain 'A' and resid 707 through 725 Processing helix chain 'C' and resid 51 through 74 removed outlier: 4.331A pdb=" N LEU C 60 " --> pdb=" O ARG C 56 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 94 removed outlier: 4.231A pdb=" N ALA C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS C 94 " --> pdb=" O TYR C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 124 removed outlier: 4.632A pdb=" N ILE C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE C 109 " --> pdb=" O PHE C 105 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU C 122 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ASP C 123 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LYS C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 149 removed outlier: 7.288A pdb=" N ALA C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS C 136 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU C 138 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 340 removed outlier: 4.207A pdb=" N VAL C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE C 330 " --> pdb=" O HIS C 326 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLN C 338 " --> pdb=" O ASN C 334 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA C 339 " --> pdb=" O GLU C 335 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 362 removed outlier: 3.635A pdb=" N GLU C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU C 354 " --> pdb=" O GLN C 350 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA C 362 " --> pdb=" O VAL C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 386 removed outlier: 4.216A pdb=" N LYS C 375 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASN C 386 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 416 removed outlier: 5.484A pdb=" N ALA C 414 " --> pdb=" O ASP C 410 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASN C 415 " --> pdb=" O ILE C 411 " (cutoff:3.500A) Proline residue: C 416 - end of helix Processing helix chain 'C' and resid 443 through 463 removed outlier: 4.923A pdb=" N LEU C 447 " --> pdb=" O CYS C 443 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 462 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASP C 463 " --> pdb=" O MET C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 493 removed outlier: 4.026A pdb=" N VAL C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS C 474 " --> pdb=" O VAL C 470 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ASP C 475 " --> pdb=" O GLU C 471 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU C 476 " --> pdb=" O HIS C 472 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA C 477 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLN C 478 " --> pdb=" O LYS C 474 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU C 490 " --> pdb=" O VAL C 486 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU C 491 " --> pdb=" O GLN C 487 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLU C 492 " --> pdb=" O ARG C 488 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS C 493 " --> pdb=" O TYR C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 511 removed outlier: 3.625A pdb=" N ARG C 501 " --> pdb=" O GLU C 497 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ILE C 502 " --> pdb=" O GLU C 498 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 505 " --> pdb=" O ARG C 501 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N HIS C 509 " --> pdb=" O LEU C 505 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR C 510 " --> pdb=" O ARG C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 558 Processing helix chain 'C' and resid 561 through 580 removed outlier: 3.958A pdb=" N ARG C 565 " --> pdb=" O THR C 561 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS C 579 " --> pdb=" O HIS C 575 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N SER C 580 " --> pdb=" O HIS C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 593 removed outlier: 3.974A pdb=" N ALA C 585 " --> pdb=" O ARG C 581 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS C 593 " --> pdb=" O MET C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 602 removed outlier: 4.742A pdb=" N GLN C 599 " --> pdb=" O GLN C 595 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N HIS C 600 " --> pdb=" O ASP C 596 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA C 601 " --> pdb=" O ASN C 597 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP C 602 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 624 removed outlier: 4.315A pdb=" N LEU C 608 " --> pdb=" O PRO C 604 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN C 623 " --> pdb=" O CYS C 619 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY C 624 " --> pdb=" O ALA C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 639 removed outlier: 4.662A pdb=" N ASP C 635 " --> pdb=" O ASN C 631 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE C 636 " --> pdb=" O ALA C 632 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN C 637 " --> pdb=" O LEU C 633 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER C 639 " --> pdb=" O ASP C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 647 removed outlier: 4.449A pdb=" N LEU C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY C 647 " --> pdb=" O LYS C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 670 removed outlier: 5.390A pdb=" N GLU C 663 " --> pdb=" O ASN C 659 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LYS C 664 " --> pdb=" O GLN C 660 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL C 665 " --> pdb=" O GLU C 661 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU C 666 " --> pdb=" O GLN C 662 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG C 668 " --> pdb=" O LYS C 664 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN C 670 " --> pdb=" O GLU C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 698 removed outlier: 3.866A pdb=" N HIS C 676 " --> pdb=" O PRO C 672 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE C 677 " --> pdb=" O PHE C 673 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N ASN C 678 " --> pdb=" O HIS C 674 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N LEU C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N GLU C 680 " --> pdb=" O HIS C 676 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU C 681 " --> pdb=" O ILE C 677 " (cutoff:3.500A) Proline residue: C 696 - end of helix Processing helix chain 'C' and resid 711 through 724 removed outlier: 4.029A pdb=" N ARG C 723 " --> pdb=" O ARG C 719 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN C 724 " --> pdb=" O VAL C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 747 removed outlier: 3.788A pdb=" N ALA C 743 " --> pdb=" O ALA C 739 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET C 746 " --> pdb=" O LYS C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 758 removed outlier: 4.353A pdb=" N ASN C 758 " --> pdb=" O SER C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 765 removed outlier: 4.017A pdb=" N GLY C 763 " --> pdb=" O GLU C 759 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS C 764 " --> pdb=" O LYS C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 800 removed outlier: 4.104A pdb=" N VAL C 775 " --> pdb=" O GLU C 771 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER C 796 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER C 797 " --> pdb=" O PHE C 793 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL C 798 " --> pdb=" O THR C 794 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TYR C 799 " --> pdb=" O TYR C 795 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASP C 800 " --> pdb=" O SER C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 812 Processing helix chain 'C' and resid 814 through 829 removed outlier: 3.543A pdb=" N ILE C 827 " --> pdb=" O SER C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 878 removed outlier: 3.569A pdb=" N GLU C 861 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL C 873 " --> pdb=" O ASN C 869 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN C 878 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 102 removed outlier: 4.878A pdb=" N VAL C 102 " --> pdb=" O VAL C 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 102' Processing helix chain 'E' and resid 6 through 15 removed outlier: 3.855A pdb=" N HIS E 12 " --> pdb=" O THR E 8 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N PHE E 13 " --> pdb=" O ARG E 9 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LEU E 14 " --> pdb=" O ILE E 10 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ASP E 15 " --> pdb=" O ALA E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 30 removed outlier: 4.287A pdb=" N PHE E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Proline residue: E 21 - end of helix Processing helix chain 'E' and resid 33 through 49 removed outlier: 4.143A pdb=" N LEU E 37 " --> pdb=" O ASN E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 62 Processing helix chain 'E' and resid 67 through 95 removed outlier: 4.081A pdb=" N ARG E 71 " --> pdb=" O PRO E 67 " (cutoff:3.500A) Proline residue: E 90 - end of helix Processing helix chain 'E' and resid 99 through 104 removed outlier: 5.138A pdb=" N GLN E 103 " --> pdb=" O GLU E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 121 removed outlier: 3.794A pdb=" N PHE E 114 " --> pdb=" O GLY E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 142 removed outlier: 5.468A pdb=" N LEU E 128 " --> pdb=" O ARG E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 158 Processing helix chain 'E' and resid 160 through 180 removed outlier: 4.436A pdb=" N ASN E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA E 165 " --> pdb=" O THR E 161 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N LEU E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N SER E 167 " --> pdb=" O ARG E 163 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN E 180 " --> pdb=" O GLU E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 199 Processing helix chain 'E' and resid 203 through 226 removed outlier: 3.652A pdb=" N SER E 207 " --> pdb=" O SER E 203 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASN E 224 " --> pdb=" O PHE E 220 " (cutoff:3.500A) Proline residue: E 226 - end of helix Processing helix chain 'E' and resid 228 through 236 Processing helix chain 'E' and resid 239 through 249 removed outlier: 4.377A pdb=" N ALA E 245 " --> pdb=" O GLN E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 263 removed outlier: 4.575A pdb=" N TYR E 256 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR E 259 " --> pdb=" O ARG E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 285 removed outlier: 5.586A pdb=" N LYS E 275 " --> pdb=" O ARG E 271 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP E 276 " --> pdb=" O GLN E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 301 Processing helix chain 'E' and resid 305 through 322 removed outlier: 4.537A pdb=" N ASN E 321 " --> pdb=" O SER E 317 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP E 322 " --> pdb=" O VAL E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 348 removed outlier: 3.621A pdb=" N LEU E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU E 330 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASP E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE E 332 " --> pdb=" O CYS E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 361 removed outlier: 4.244A pdb=" N LEU E 356 " --> pdb=" O SER E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 379 removed outlier: 4.318A pdb=" N ASN E 377 " --> pdb=" O ASN E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 430 removed outlier: 4.614A pdb=" N SER E 410 " --> pdb=" O GLU E 406 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU E 411 " --> pdb=" O LYS E 407 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE E 422 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASN E 427 " --> pdb=" O GLU E 423 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER E 430 " --> pdb=" O LEU E 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 109 removed outlier: 4.690A pdb=" N ARG F 108 " --> pdb=" O ASP F 104 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 164 removed outlier: 3.567A pdb=" N SER F 164 " --> pdb=" O HIS F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 194 removed outlier: 4.788A pdb=" N VAL F 184 " --> pdb=" O THR F 180 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE F 186 " --> pdb=" O HIS F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 254 Processing helix chain 'F' and resid 267 through 294 Processing helix chain 'F' and resid 302 through 314 removed outlier: 4.333A pdb=" N GLN F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 357 removed outlier: 4.118A pdb=" N PHE F 323 " --> pdb=" O VAL F 319 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU F 357 " --> pdb=" O LYS F 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 56 removed outlier: 3.819A pdb=" N VAL H 46 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLU H 56 " --> pdb=" O HIS H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 111 removed outlier: 4.073A pdb=" N VAL H 110 " --> pdb=" O SER H 106 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN H 111 " --> pdb=" O LEU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 144 removed outlier: 3.711A pdb=" N LEU H 134 " --> pdb=" O THR H 130 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE H 144 " --> pdb=" O TYR H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 160 removed outlier: 3.630A pdb=" N THR H 157 " --> pdb=" O ASP H 153 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN H 159 " --> pdb=" O ILE H 155 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY H 160 " --> pdb=" O LYS H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 180 Processing helix chain 'H' and resid 183 through 191 removed outlier: 4.020A pdb=" N ASN H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 199 removed outlier: 4.308A pdb=" N PHE H 198 " --> pdb=" O PHE H 194 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N GLU H 199 " --> pdb=" O GLU H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 222 removed outlier: 3.974A pdb=" N ASN H 212 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 289 removed outlier: 5.615A pdb=" N LEU H 239 " --> pdb=" O SER H 235 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLN H 289 " --> pdb=" O ASN H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 349 removed outlier: 5.078A pdb=" N LEU H 317 " --> pdb=" O ARG H 313 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU H 347 " --> pdb=" O MET H 343 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU H 349 " --> pdb=" O GLN H 345 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 16 removed outlier: 4.582A pdb=" N GLN K 6 " --> pdb=" O ALA K 2 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS K 13 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LYS K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 23 removed outlier: 4.214A pdb=" N ASN K 22 " --> pdb=" O ILE K 18 " (cutoff:3.500A) Proline residue: K 23 - end of helix No H-bonds generated for 'chain 'K' and resid 18 through 23' Processing helix chain 'K' and resid 24 through 39 removed outlier: 5.040A pdb=" N THR K 28 " --> pdb=" O GLU K 24 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 58 removed outlier: 4.069A pdb=" N ASN K 47 " --> pdb=" O ASP K 43 " (cutoff:3.500A) Proline residue: K 58 - end of helix Processing helix chain 'K' and resid 62 through 77 removed outlier: 3.908A pdb=" N THR K 66 " --> pdb=" O GLN K 62 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 89 removed outlier: 4.140A pdb=" N LEU K 84 " --> pdb=" O THR K 80 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE K 89 " --> pdb=" O CYS K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 96 removed outlier: 5.612A pdb=" N GLU K 96 " --> pdb=" O ALA K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 112 removed outlier: 6.786A pdb=" N GLN K 101 " --> pdb=" O ARG K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 119 Processing helix chain 'K' and resid 125 through 132 removed outlier: 4.812A pdb=" N GLU K 129 " --> pdb=" O MET K 125 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N THR K 132 " --> pdb=" O LEU K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 150 Processing helix chain 'K' and resid 154 through 163 Processing helix chain 'K' and resid 166 through 178 removed outlier: 3.573A pdb=" N VAL K 172 " --> pdb=" O SER K 168 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TYR K 177 " --> pdb=" O TRP K 173 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY K 178 " --> pdb=" O MET K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 218 removed outlier: 4.161A pdb=" N VAL K 210 " --> pdb=" O ASP K 206 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER K 212 " --> pdb=" O ASP K 208 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE K 213 " --> pdb=" O SER K 209 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER K 216 " --> pdb=" O SER K 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 197 removed outlier: 4.064A pdb=" N GLU K 194 " --> pdb=" O SER K 191 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER K 195 " --> pdb=" O GLN K 192 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE K 196 " --> pdb=" O GLU K 193 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS K 197 " --> pdb=" O GLU K 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 191 through 197' Processing helix chain 'L' and resid 183 through 203 removed outlier: 4.562A pdb=" N ILE L 187 " --> pdb=" O LEU L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 208 through 218 removed outlier: 4.782A pdb=" N ILE L 212 " --> pdb=" O SER L 208 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 247 removed outlier: 3.515A pdb=" N ASN L 229 " --> pdb=" O HIS L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 258 Processing helix chain 'L' and resid 259 through 265 removed outlier: 5.637A pdb=" N HIS L 263 " --> pdb=" O GLU L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 274 through 291 removed outlier: 4.208A pdb=" N LEU L 278 " --> pdb=" O LEU L 274 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA L 290 " --> pdb=" O ASP L 286 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE L 291 " --> pdb=" O TYR L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 303 removed outlier: 5.628A pdb=" N SER L 303 " --> pdb=" O LEU L 299 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 327 Processing helix chain 'L' and resid 328 through 341 removed outlier: 5.223A pdb=" N ARG L 334 " --> pdb=" O GLN L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 376 removed outlier: 4.344A pdb=" N ILE L 360 " --> pdb=" O LYS L 356 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR L 376 " --> pdb=" O ALA L 372 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 384 removed outlier: 6.386A pdb=" N ASP L 383 " --> pdb=" O PRO L 379 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLU L 384 " --> pdb=" O MET L 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 379 through 384' Processing helix chain 'L' and resid 388 through 400 removed outlier: 4.758A pdb=" N LYS L 397 " --> pdb=" O LYS L 393 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG L 400 " --> pdb=" O ASP L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 422 removed outlier: 4.584A pdb=" N TYR L 409 " --> pdb=" O ASP L 405 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU L 410 " --> pdb=" O PRO L 406 " (cutoff:3.500A) Proline residue: L 418 - end of helix removed outlier: 4.736A pdb=" N LEU L 421 " --> pdb=" O CYS L 417 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER L 422 " --> pdb=" O PRO L 418 " (cutoff:3.500A) Processing helix chain 'L' and resid 435 through 462 Proline residue: L 439 - end of helix removed outlier: 3.961A pdb=" N GLN L 442 " --> pdb=" O GLU L 438 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS L 445 " --> pdb=" O LEU L 441 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL L 446 " --> pdb=" O GLN L 442 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP L 449 " --> pdb=" O LYS L 445 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLU L 450 " --> pdb=" O VAL L 446 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL L 451 " --> pdb=" O PHE L 447 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN L 452 " --> pdb=" O SER L 448 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLN L 453 " --> pdb=" O ASP L 449 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER L 458 " --> pdb=" O GLN L 454 " (cutoff:3.500A) Processing helix chain 'L' and resid 471 through 483 Processing helix chain 'L' and resid 489 through 498 removed outlier: 4.581A pdb=" N HIS L 495 " --> pdb=" O LEU L 491 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS L 496 " --> pdb=" O VAL L 492 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET L 497 " --> pdb=" O PHE L 493 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS L 498 " --> pdb=" O LYS L 494 " (cutoff:3.500A) Processing helix chain 'L' and resid 524 through 551 removed outlier: 4.427A pdb=" N ILE L 528 " --> pdb=" O ASP L 524 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS L 549 " --> pdb=" O ARG L 545 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 26 removed outlier: 4.670A pdb=" N ALA M 15 " --> pdb=" O GLU M 11 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER M 24 " --> pdb=" O ALA M 20 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS M 25 " --> pdb=" O TYR M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 52 removed outlier: 5.342A pdb=" N VAL M 51 " --> pdb=" O GLU M 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 74 removed outlier: 5.630A pdb=" N MET M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE M 73 " --> pdb=" O SER M 69 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU M 74 " --> pdb=" O LEU M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 96 removed outlier: 4.734A pdb=" N GLU M 95 " --> pdb=" O VAL M 91 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLY M 96 " --> pdb=" O LYS M 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 114 removed outlier: 3.554A pdb=" N ASP M 114 " --> pdb=" O PHE M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 134 removed outlier: 5.188A pdb=" N TYR M 121 " --> pdb=" O THR M 117 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N THR M 122 " --> pdb=" O PRO M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 154 removed outlier: 4.102A pdb=" N VAL M 147 " --> pdb=" O GLU M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 176 removed outlier: 4.424A pdb=" N LYS M 161 " --> pdb=" O THR M 157 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS M 176 " --> pdb=" O LEU M 172 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 192 removed outlier: 4.302A pdb=" N LYS M 183 " --> pdb=" O ASP M 179 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR M 192 " --> pdb=" O LEU M 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 215 removed outlier: 4.920A pdb=" N ALA M 200 " --> pdb=" O ASN M 196 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG M 201 " --> pdb=" O ALA M 197 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL M 202 " --> pdb=" O SER M 198 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASP M 203 " --> pdb=" O GLN M 199 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ALA M 204 " --> pdb=" O ALA M 200 " (cutoff:3.500A) Proline residue: M 215 - end of helix Processing helix chain 'M' and resid 226 through 233 removed outlier: 4.990A pdb=" N GLU M 233 " --> pdb=" O VAL M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 236 through 246 removed outlier: 4.518A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER M 246 " --> pdb=" O THR M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 259 removed outlier: 3.593A pdb=" N TYR M 252 " --> pdb=" O LYS M 248 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE M 255 " --> pdb=" O SER M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 260 through 266 removed outlier: 4.856A pdb=" N LEU M 266 " --> pdb=" O PHE M 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 269 through 289 removed outlier: 4.219A pdb=" N ASN M 273 " --> pdb=" O LEU M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 302 removed outlier: 3.836A pdb=" N MET M 297 " --> pdb=" O SER M 293 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU M 301 " --> pdb=" O MET M 297 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 319 removed outlier: 4.151A pdb=" N ALA M 310 " --> pdb=" O ASP M 306 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS M 319 " --> pdb=" O ALA M 315 " (cutoff:3.500A) Processing helix chain 'M' and resid 343 through 372 removed outlier: 3.854A pdb=" N TRP M 347 " --> pdb=" O GLY M 343 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER M 372 " --> pdb=" O LEU M 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 22 removed outlier: 3.977A pdb=" N CYS J 21 " --> pdb=" O LYS J 17 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG J 22 " --> pdb=" O PRO J 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 17 through 22' Processing helix chain 'J' and resid 23 through 29 removed outlier: 3.907A pdb=" N LYS J 27 " --> pdb=" O GLN J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 35 removed outlier: 4.169A pdb=" N GLY J 35 " --> pdb=" O VAL J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 65 removed outlier: 4.250A pdb=" N LYS J 63 " --> pdb=" O GLY J 59 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS J 64 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N CYS J 65 " --> pdb=" O CYS J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 59 through 65' Processing helix chain 'J' and resid 115 through 125 removed outlier: 3.618A pdb=" N LEU J 120 " --> pdb=" O LYS J 116 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY J 125 " --> pdb=" O LYS J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 148 removed outlier: 3.598A pdb=" N TYR J 146 " --> pdb=" O GLU J 142 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG J 148 " --> pdb=" O LEU J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 162 removed outlier: 4.224A pdb=" N ASN J 154 " --> pdb=" O SER J 150 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP J 162 " --> pdb=" O LYS J 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 181 removed outlier: 5.617A pdb=" N ILE J 176 " --> pdb=" O TYR J 172 " (cutoff:3.500A) Proline residue: J 177 - end of helix removed outlier: 5.424A pdb=" N LYS J 181 " --> pdb=" O PRO J 177 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 192 removed outlier: 4.649A pdb=" N ARG J 190 " --> pdb=" O SER J 186 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS J 191 " --> pdb=" O ILE J 187 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ASP J 192 " --> pdb=" O LEU J 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 205 removed outlier: 5.865A pdb=" N VAL J 200 " --> pdb=" O THR J 196 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS J 201 " --> pdb=" O GLN J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 211 removed outlier: 6.863A pdb=" N LYS J 210 " --> pdb=" O LEU J 206 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLU J 211 " --> pdb=" O THR J 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 206 through 211' Processing helix chain 'J' and resid 218 through 234 removed outlier: 6.324A pdb=" N LYS J 234 " --> pdb=" O VAL J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 248 through 263 removed outlier: 3.703A pdb=" N LEU J 262 " --> pdb=" O THR J 258 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE J 263 " --> pdb=" O ILE J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 275 through 283 removed outlier: 6.213A pdb=" N LEU J 279 " --> pdb=" O ASP J 275 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP J 280 " --> pdb=" O LEU J 276 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR J 281 " --> pdb=" O SER J 277 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER J 283 " --> pdb=" O LEU J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 304 through 315 Processing helix chain 'J' and resid 384 through 394 removed outlier: 3.732A pdb=" N ARG J 390 " --> pdb=" O THR J 386 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET J 391 " --> pdb=" O THR J 387 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU J 392 " --> pdb=" O PHE J 388 " (cutoff:3.500A) Processing helix chain 'J' and resid 423 through 428 Processing helix chain 'J' and resid 444 through 449 Proline residue: J 448 - end of helix No H-bonds generated for 'chain 'J' and resid 444 through 449' Processing helix chain 'J' and resid 450 through 456 removed outlier: 4.920A pdb=" N ILE J 454 " --> pdb=" O GLN J 450 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASP J 456 " --> pdb=" O GLU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 463 through 478 removed outlier: 4.226A pdb=" N LYS J 478 " --> pdb=" O LEU J 474 " (cutoff:3.500A) Processing helix chain 'J' and resid 493 through 512 removed outlier: 3.591A pdb=" N LEU J 498 " --> pdb=" O SER J 494 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET J 499 " --> pdb=" O GLU J 495 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA J 500 " --> pdb=" O GLN J 496 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA J 501 " --> pdb=" O ARG J 497 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N HIS J 510 " --> pdb=" O ARG J 506 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS J 512 " --> pdb=" O ILE J 508 " (cutoff:3.500A) Processing helix chain 'J' and resid 521 through 529 removed outlier: 4.147A pdb=" N ALA J 529 " --> pdb=" O ALA J 525 " (cutoff:3.500A) Processing helix chain 'J' and resid 551 through 563 removed outlier: 3.758A pdb=" N SER J 560 " --> pdb=" O ASN J 556 " (cutoff:3.500A) Processing helix chain 'J' and resid 582 through 592 removed outlier: 3.956A pdb=" N VAL J 586 " --> pdb=" O SER J 582 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN J 588 " --> pdb=" O LYS J 584 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER J 591 " --> pdb=" O GLU J 587 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 60 removed outlier: 3.757A pdb=" N ASN N 57 " --> pdb=" O LYS N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 182 removed outlier: 4.540A pdb=" N LEU N 179 " --> pdb=" O ASP N 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 204 through 209 removed outlier: 4.530A pdb=" N ARG N 208 " --> pdb=" O LYS N 204 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE N 209 " --> pdb=" O ALA N 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 204 through 209' Processing helix chain 'N' and resid 232 through 240 removed outlier: 4.234A pdb=" N LYS N 240 " --> pdb=" O ARG N 236 " (cutoff:3.500A) Processing helix chain 'N' and resid 248 through 258 removed outlier: 3.800A pdb=" N SER N 257 " --> pdb=" O ALA N 253 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N CYS N 258 " --> pdb=" O THR N 254 " (cutoff:3.500A) Processing helix chain 'N' and resid 308 through 327 removed outlier: 4.806A pdb=" N GLN N 325 " --> pdb=" O HIS N 321 " (cutoff:3.500A) Processing helix chain 'N' and resid 400 through 405 removed outlier: 5.099A pdb=" N CYS N 404 " --> pdb=" O ASP N 400 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN N 405 " --> pdb=" O SER N 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 400 through 405' Processing helix chain 'N' and resid 408 through 413 Processing helix chain 'N' and resid 416 through 428 removed outlier: 3.633A pdb=" N VAL N 420 " --> pdb=" O GLN N 416 " (cutoff:3.500A) Processing helix chain 'N' and resid 429 through 443 removed outlier: 4.144A pdb=" N GLY N 443 " --> pdb=" O ALA N 439 " (cutoff:3.500A) Processing helix chain 'N' and resid 472 through 481 removed outlier: 4.501A pdb=" N ILE N 480 " --> pdb=" O PHE N 476 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN N 481 " --> pdb=" O ALA N 477 " (cutoff:3.500A) Processing helix chain 'N' and resid 483 through 499 removed outlier: 4.126A pdb=" N LEU N 491 " --> pdb=" O ALA N 487 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 24 removed outlier: 4.240A pdb=" N ALA X 24 " --> pdb=" O ALA X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 64 removed outlier: 3.680A pdb=" N ALA X 64 " --> pdb=" O ALA X 60 " (cutoff:3.500A) Processing helix chain '4' and resid 177 through 185 removed outlier: 3.788A pdb=" N PHE 4 184 " --> pdb=" O LEU 4 180 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ASN 4 185 " --> pdb=" O ASN 4 181 " (cutoff:3.500A) Processing helix chain '4' and resid 221 through 230 removed outlier: 4.269A pdb=" N ILE 4 225 " --> pdb=" O ASN 4 221 " (cutoff:3.500A) Processing helix chain '4' and resid 232 through 245 removed outlier: 5.147A pdb=" N GLY 4 245 " --> pdb=" O LEU 4 241 " (cutoff:3.500A) Processing helix chain '4' and resid 263 through 278 removed outlier: 4.737A pdb=" N ASN 4 269 " --> pdb=" O LYS 4 265 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL 4 270 " --> pdb=" O GLN 4 266 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 63 removed outlier: 4.161A pdb=" N ARG O 63 " --> pdb=" O ASN O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 117 Processing helix chain 'O' and resid 122 through 142 removed outlier: 4.625A pdb=" N TRP O 135 " --> pdb=" O GLN O 131 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL O 136 " --> pdb=" O ARG O 132 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N PHE O 137 " --> pdb=" O THR O 133 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASP O 138 " --> pdb=" O ALA O 134 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASP O 139 " --> pdb=" O TRP O 135 " (cutoff:3.500A) Processing helix chain 'O' and resid 144 through 158 removed outlier: 6.663A pdb=" N ALA O 148 " --> pdb=" O PRO O 144 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR O 149 " --> pdb=" O GLY O 145 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA O 151 " --> pdb=" O GLY O 147 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N VAL O 156 " --> pdb=" O PHE O 152 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER O 157 " --> pdb=" O LYS O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 159 through 164 Processing helix chain 'O' and resid 169 through 183 removed outlier: 3.535A pdb=" N ILE O 176 " --> pdb=" O ARG O 172 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ASN O 177 " --> pdb=" O GLU O 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 205 through 218 removed outlier: 4.718A pdb=" N SER O 218 " --> pdb=" O GLY O 214 " (cutoff:3.500A) Processing helix chain 'O' and resid 242 through 263 removed outlier: 4.448A pdb=" N SER O 248 " --> pdb=" O THR O 244 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL O 249 " --> pdb=" O GLU O 245 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU O 263 " --> pdb=" O GLU O 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 281 through 297 Processing helix chain 'Y' and resid 55 through 63 removed outlier: 4.300A pdb=" N LYS Y 59 " --> pdb=" O SER Y 55 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY Y 63 " --> pdb=" O LYS Y 59 " (cutoff:3.500A) Processing helix chain 'Y' and resid 139 through 146 removed outlier: 4.579A pdb=" N ALA Y 143 " --> pdb=" O ASP Y 139 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET Y 145 " --> pdb=" O LEU Y 141 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU Y 146 " --> pdb=" O MET Y 142 " (cutoff:3.500A) Processing helix chain 'Y' and resid 165 through 179 removed outlier: 4.550A pdb=" N GLU Y 172 " --> pdb=" O PRO Y 168 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N HIS Y 173 " --> pdb=" O GLN Y 169 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU Y 178 " --> pdb=" O LEU Y 174 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE Y 179 " --> pdb=" O ALA Y 175 " (cutoff:3.500A) Processing helix chain 'Y' and resid 195 through 214 removed outlier: 4.022A pdb=" N GLN Y 199 " --> pdb=" O VAL Y 195 " (cutoff:3.500A) Processing helix chain 'Y' and resid 230 through 239 removed outlier: 3.510A pdb=" N VAL Y 234 " --> pdb=" O TYR Y 230 " (cutoff:3.500A) Processing helix chain 'Y' and resid 64 through 69 removed outlier: 4.279A pdb=" N ARG Y 68 " --> pdb=" O HIS Y 65 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE Y 69 " --> pdb=" O THR Y 66 " (cutoff:3.500A) Processing helix chain 'Z' and resid 11 through 20 removed outlier: 4.222A pdb=" N ASP Z 15 " --> pdb=" O ASP Z 11 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA Z 16 " --> pdb=" O PRO Z 12 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 68 removed outlier: 5.068A pdb=" N ALA Z 62 " --> pdb=" O LYS Z 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 89 through 101 removed outlier: 4.591A pdb=" N ILE Z 93 " --> pdb=" O GLN Z 89 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLY Z 101 " --> pdb=" O LEU Z 97 " (cutoff:3.500A) Processing helix chain 'Z' and resid 104 through 109 removed outlier: 4.513A pdb=" N GLN Z 107 " --> pdb=" O LYS Z 104 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU Z 108 " --> pdb=" O ASP Z 105 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LYS Z 109 " --> pdb=" O ASP Z 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 104 through 109' Processing sheet with id= 1, first strand: chain 'a' and resid 96 through 99 Processing sheet with id= 2, first strand: chain 'p' and resid 45 through 48 removed outlier: 4.128A pdb=" N GLY p 45 " --> pdb=" O VAL p 33 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'p' and resid 65 through 69 removed outlier: 5.029A pdb=" N ARG p 65 " --> pdb=" O THR p 88 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N HIS p 101 " --> pdb=" O MET p 217 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET p 217 " --> pdb=" O HIS p 101 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N ARG p 213 " --> pdb=" O LEU p 105 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS p 214 " --> pdb=" O PHE p 138 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU p 134 " --> pdb=" O LEU p 218 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N THR p 119 " --> pdb=" O THR p 143 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'd' and resid 103 through 107 removed outlier: 6.809A pdb=" N PHE d 127 " --> pdb=" O LEU d 107 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'd' and resid 183 through 187 removed outlier: 4.489A pdb=" N ALA d 198 " --> pdb=" O ASP d 221 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ASP d 221 " --> pdb=" O ALA d 198 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'd' and resid 124 through 131 Processing sheet with id= 7, first strand: chain 'Q' and resid 20 through 24 removed outlier: 4.293A pdb=" N ARG Q 28 " --> pdb=" O CYS Q 23 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'Q' and resid 36 through 43 Processing sheet with id= 9, first strand: chain 'q' and resid 89 through 93 Processing sheet with id= 10, first strand: chain 'q' and resid 121 through 126 removed outlier: 4.577A pdb=" N ASP q 158 " --> pdb=" O VAL q 126 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP q 171 " --> pdb=" O GLN q 161 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'q' and resid 128 through 131 Processing sheet with id= 12, first strand: chain 'q' and resid 180 through 184 removed outlier: 6.922A pdb=" N LEU q 180 " --> pdb=" O ILE q 228 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASN q 224 " --> pdb=" O THR q 184 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'q' and resid 197 through 200 removed outlier: 3.551A pdb=" N PHE q 218 " --> pdb=" O VAL q 210 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASN q 216 " --> pdb=" O ASP q 212 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'r' and resid 11 through 17 removed outlier: 3.837A pdb=" N LEU r 109 " --> pdb=" O LYS r 2 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL r 49 " --> pdb=" O VAL r 114 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'r' and resid 72 through 76 Processing sheet with id= 16, first strand: chain 'r' and resid 159 through 163 Processing sheet with id= 17, first strand: chain 'r' and resid 53 through 56 No H-bonds generated for sheet with id= 17 Processing sheet with id= 18, first strand: chain 's' and resid 47 through 53 removed outlier: 3.671A pdb=" N ALA s 47 " --> pdb=" O PHE s 63 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N HIS s 91 " --> pdb=" O LYS s 58 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 's' and resid 141 through 146 removed outlier: 3.540A pdb=" N GLY s 141 " --> pdb=" O HIS s 157 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ASP s 184 " --> pdb=" O ARG s 152 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 't' and resid 42 through 48 removed outlier: 6.321A pdb=" N ARG t 42 " --> pdb=" O LEU t 58 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN t 52 " --> pdb=" O VAL t 48 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 't' and resid 72 through 76 removed outlier: 3.660A pdb=" N CYS t 72 " --> pdb=" O TRP t 67 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN t 64 " --> pdb=" O ALA t 185 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 't' and resid 79 through 82 removed outlier: 3.853A pdb=" N ASP t 80 " --> pdb=" O LEU t 103 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE t 101 " --> pdb=" O VAL t 82 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N CYS t 100 " --> pdb=" O ILE t 175 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'n' and resid 71 through 76 removed outlier: 5.665A pdb=" N ARG n 71 " --> pdb=" O GLU n 130 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR n 127 " --> pdb=" O LEU n 143 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'n' and resid 84 through 97 No H-bonds generated for sheet with id= 24 Processing sheet with id= 25, first strand: chain 'n' and resid 124 through 127 removed outlier: 3.705A pdb=" N LYS n 144 " --> pdb=" O THR n 127 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'y' and resid 15 through 18 removed outlier: 4.440A pdb=" N ARG y 15 " --> pdb=" O ILE y 24 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ARG y 22 " --> pdb=" O CYS y 17 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'y' and resid 32 through 38 removed outlier: 5.161A pdb=" N GLN y 49 " --> pdb=" O GLU y 38 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'D' and resid 23 through 28 removed outlier: 5.932A pdb=" N ARG D 23 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLU D 49 " --> pdb=" O ASN D 64 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'z' and resid 5 through 10 removed outlier: 4.380A pdb=" N VAL z 24 " --> pdb=" O ARG z 10 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'z' and resid 59 through 62 removed outlier: 5.374A pdb=" N GLY z 59 " --> pdb=" O PHE z 72 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE z 72 " --> pdb=" O GLY z 59 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'z' and resid 20 through 28 removed outlier: 3.787A pdb=" N GLY z 73 " --> pdb=" O MET z 23 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'R' and resid 43 through 48 removed outlier: 7.060A pdb=" N TYR R 31 " --> pdb=" O SER R 48 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N PHE R 32 " --> pdb=" O LYS R 82 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG R 80 " --> pdb=" O ASP R 34 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'R' and resid 63 through 66 removed outlier: 7.027A pdb=" N LEU R 63 " --> pdb=" O THR R 74 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'b' and resid 46 through 52 removed outlier: 3.882A pdb=" N GLU b 85 " --> pdb=" O THR b 46 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE b 48 " --> pdb=" O GLU b 85 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'b' and resid 148 through 153 removed outlier: 3.775A pdb=" N GLY b 140 " --> pdb=" O LYS b 148 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL b 138 " --> pdb=" O MET b 150 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE b 152 " --> pdb=" O VAL b 136 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY b 133 " --> pdb=" O MET b 189 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY b 180 " --> pdb=" O LEU b 177 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL b 186 " --> pdb=" O ALA b 171 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'e' and resid 123 through 129 Processing sheet with id= 37, first strand: chain 'u' and resid 20 through 24 Processing sheet with id= 38, first strand: chain 'v' and resid 30 through 33 removed outlier: 7.987A pdb=" N GLY v 30 " --> pdb=" O LYS v 112 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL v 110 " --> pdb=" O ALA v 32 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER v 54 " --> pdb=" O VAL v 79 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'o' and resid 75 through 79 removed outlier: 4.542A pdb=" N SER o 92 " --> pdb=" O ILE o 107 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'g' and resid 9 through 15 Processing sheet with id= 41, first strand: chain 'x' and resid 81 through 84 Processing sheet with id= 42, first strand: chain 'x' and resid 113 through 116 removed outlier: 5.100A pdb=" N GLY x 120 " --> pdb=" O ASP x 116 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'h' and resid 58 through 67 removed outlier: 3.597A pdb=" N ILE h 63 " --> pdb=" O PHE h 80 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N THR h 76 " --> pdb=" O LYS h 67 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE h 89 " --> pdb=" O ILE h 22 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'P' and resid 97 through 100 removed outlier: 6.720A pdb=" N ILE P 108 " --> pdb=" O VAL P 100 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'S' and resid 9 through 14 removed outlier: 4.358A pdb=" N ASP S 54 " --> pdb=" O VAL S 14 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'S' and resid 18 through 22 removed outlier: 3.830A pdb=" N GLY S 19 " --> pdb=" O GLN S 29 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'U' and resid 138 through 141 removed outlier: 4.207A pdb=" N LEU U 146 " --> pdb=" O CYS U 141 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'V' and resid 19 through 23 removed outlier: 4.177A pdb=" N GLN V 20 " --> pdb=" O ALA V 34 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA V 34 " --> pdb=" O GLN V 20 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE V 31 " --> pdb=" O TRP V 43 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP V 43 " --> pdb=" O ILE V 31 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER V 33 " --> pdb=" O ILE V 41 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR V 39 " --> pdb=" O SER V 35 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'V' and resid 67 through 72 removed outlier: 6.317A pdb=" N PHE V 77 " --> pdb=" O SER V 72 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLN V 76 " --> pdb=" O LEU V 92 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA V 78 " --> pdb=" O TRP V 90 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU V 89 " --> pdb=" O THR V 98 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR V 96 " --> pdb=" O ASP V 91 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'V' and resid 110 through 114 removed outlier: 3.738A pdb=" N SER V 110 " --> pdb=" O GLY V 123 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N GLN V 119 " --> pdb=" O SER V 114 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR V 128 " --> pdb=" O SER V 124 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'V' and resid 153 through 156 removed outlier: 5.290A pdb=" N CYS V 153 " --> pdb=" O CYS V 168 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N HIS V 188 " --> pdb=" O VAL V 174 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'V' and resid 197 through 201 removed outlier: 3.829A pdb=" N ALA V 208 " --> pdb=" O THR V 199 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU V 206 " --> pdb=" O SER V 201 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER V 209 " --> pdb=" O MET V 217 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLY V 214 " --> pdb=" O GLY V 232 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU V 218 " --> pdb=" O TYR V 228 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'V' and resid 247 through 251 removed outlier: 4.272A pdb=" N LEU V 248 " --> pdb=" O TRP V 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TRP V 259 " --> pdb=" O LEU V 248 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP V 268 " --> pdb=" O ILE V 258 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'V' and resid 288 through 292 removed outlier: 6.283A pdb=" N THR V 297 " --> pdb=" O SER V 292 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLN V 296 " --> pdb=" O VAL V 312 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU V 306 " --> pdb=" O TYR V 302 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'V' and resid 86 through 89 No H-bonds generated for sheet with id= 55 Processing sheet with id= 56, first strand: chain 'i' and resid 40 through 46 removed outlier: 5.823A pdb=" N ILE i 95 " --> pdb=" O GLY i 127 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'i' and resid 94 through 99 removed outlier: 5.812A pdb=" N ALA i 99 " --> pdb=" O VAL i 132 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'j' and resid 46 through 50 removed outlier: 6.597A pdb=" N LEU j 101 " --> pdb=" O VAL j 123 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'j' and resid 52 through 59 removed outlier: 3.791A pdb=" N GLU j 53 " --> pdb=" O ARG j 71 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ALA j 65 " --> pdb=" O ALA j 59 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS j 79 " --> pdb=" O LEU j 74 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'G' and resid 33 through 36 removed outlier: 6.660A pdb=" N LEU G 78 " --> pdb=" O ILE G 92 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'G' and resid 46 through 51 removed outlier: 4.655A pdb=" N VAL G 55 " --> pdb=" O CYS G 51 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'I' and resid 1 through 6 removed outlier: 3.786A pdb=" N VAL I 309 " --> pdb=" O LEU I 6 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LYS I 298 " --> pdb=" O PHE I 314 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N SER I 299 " --> pdb=" O HIS I 294 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER I 290 " --> pdb=" O GLY I 303 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'I' and resid 15 through 19 removed outlier: 5.896A pdb=" N LEU I 24 " --> pdb=" O ASN I 19 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASP I 23 " --> pdb=" O SER I 39 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL I 36 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU I 43 " --> pdb=" O TYR I 38 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'I' and resid 56 through 60 removed outlier: 7.714A pdb=" N LYS I 65 " --> pdb=" O CYS I 81 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER I 71 " --> pdb=" O SER I 75 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N SER I 75 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'I' and resid 98 through 102 removed outlier: 4.361A pdb=" N THR I 98 " --> pdb=" O SER I 111 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE I 107 " --> pdb=" O ASP I 102 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASN I 106 " --> pdb=" O LEU I 127 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE I 121 " --> pdb=" O THR I 112 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'I' and resid 151 through 155 removed outlier: 5.917A pdb=" N CYS I 160 " --> pdb=" O GLY I 155 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN I 171 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS I 165 " --> pdb=" O GLU I 169 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU I 169 " --> pdb=" O HIS I 165 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL I 182 " --> pdb=" O GLN I 172 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'I' and resid 193 through 197 removed outlier: 3.545A pdb=" N ASP I 193 " --> pdb=" O ALA I 206 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N MET I 202 " --> pdb=" O SER I 197 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N THR I 201 " --> pdb=" O SER I 217 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU I 214 " --> pdb=" O GLN I 223 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU I 221 " --> pdb=" O ASP I 216 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'I' and resid 234 through 238 removed outlier: 4.544A pdb=" N HIS I 243 " --> pdb=" O SER I 238 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ASP I 242 " --> pdb=" O LEU I 272 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE I 269 " --> pdb=" O PHE I 278 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU I 276 " --> pdb=" O HIS I 271 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'I' and resid 33 through 36 Processing sheet with id= 70, first strand: chain 'I' and resid 210 through 214 removed outlier: 5.565A pdb=" N ASN I 210 " --> pdb=" O THR I 228 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'I' and resid 266 through 269 removed outlier: 3.584A pdb=" N GLY I 279 " --> pdb=" O PHE I 269 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'B' and resid 219 through 222 removed outlier: 3.892A pdb=" N ASN B 219 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE B 233 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU B 235 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE B 187 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG B 262 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'B' and resid 305 through 310 No H-bonds generated for sheet with id= 73 Processing sheet with id= 74, first strand: chain 'B' and resid 314 through 317 No H-bonds generated for sheet with id= 74 Processing sheet with id= 75, first strand: chain 'B' and resid 357 through 362 removed outlier: 4.048A pdb=" N ILE B 357 " --> pdb=" O PHE B 371 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN B 369 " --> pdb=" O LEU B 359 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLY B 361 " --> pdb=" O GLN B 367 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN B 367 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'B' and resid 377 through 382 removed outlier: 4.097A pdb=" N SER B 382 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TYR B 387 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG B 386 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE B 409 " --> pdb=" O ARG B 386 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TRP B 407 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'B' and resid 470 through 473 removed outlier: 4.461A pdb=" N ILE B 478 " --> pdb=" O SER B 473 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ASN B 477 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE B 481 " --> pdb=" O THR B 494 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B 494 " --> pdb=" O PHE B 481 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 509 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL B 493 " --> pdb=" O ARG B 507 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'B' and resid 515 through 520 removed outlier: 4.142A pdb=" N LYS B 516 " --> pdb=" O LYS B 529 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS B 529 " --> pdb=" O LYS B 516 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N HIS B 518 " --> pdb=" O CYS B 527 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N CYS B 527 " --> pdb=" O HIS B 518 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TYR B 525 " --> pdb=" O GLN B 520 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASN B 543 " --> pdb=" O VAL B 530 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'B' and resid 567 through 571 removed outlier: 3.751A pdb=" N ALA B 569 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LYS B 576 " --> pdb=" O GLU B 571 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N SER B 575 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL B 579 " --> pdb=" O SER B 590 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N SER B 590 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE B 591 " --> pdb=" O ILE B 603 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'B' and resid 621 through 628 removed outlier: 6.049A pdb=" N GLN B 621 " --> pdb=" O THR B 640 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR B 640 " --> pdb=" O GLN B 621 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ALA B 634 " --> pdb=" O GLY B 627 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU B 635 " --> pdb=" O ILE B 648 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE B 648 " --> pdb=" O LEU B 635 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE B 637 " --> pdb=" O MET B 646 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET B 646 " --> pdb=" O PHE B 637 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR B 644 " --> pdb=" O ASP B 639 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'B' and resid 655 through 660 removed outlier: 3.534A pdb=" N GLU B 658 " --> pdb=" O VAL B 667 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TYR B 665 " --> pdb=" O ASP B 660 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ALA B 680 " --> pdb=" O VAL B 670 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'A' and resid 482 through 486 Processing sheet with id= 83, first strand: chain 'C' and resid 418 through 421 Processing sheet with id= 84, first strand: chain 'C' and resid 833 through 837 removed outlier: 4.068A pdb=" N THR C 841 " --> pdb=" O ASP C 836 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'F' and resid 128 through 131 removed outlier: 3.669A pdb=" N VAL F 131 " --> pdb=" O ARG F 93 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR F 236 " --> pdb=" O ARG F 90 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'F' and resid 133 through 137 removed outlier: 3.753A pdb=" N ILE F 117 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP F 172 " --> pdb=" O ILE F 198 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'H' and resid 164 through 168 removed outlier: 4.136A pdb=" N THR H 123 " --> pdb=" O TYR H 152 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLY H 118 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY H 65 " --> pdb=" O TYR H 120 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER H 122 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL H 63 " --> pdb=" O SER H 122 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL H 66 " --> pdb=" O CYS H 81 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N CYS H 81 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU H 68 " --> pdb=" O THR H 79 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN H 38 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'K' and resid 179 through 182 removed outlier: 3.596A pdb=" N SER K 180 " --> pdb=" O PHE K 188 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN K 186 " --> pdb=" O ASP K 182 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'M' and resid 322 through 326 removed outlier: 7.008A pdb=" N TYR M 322 " --> pdb=" O SER M 335 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'J' and resid 6 through 12 removed outlier: 4.171A pdb=" N THR J 6 " --> pdb=" O LEU J 75 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA J 69 " --> pdb=" O ASN J 12 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN J 321 " --> pdb=" O ILE J 72 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'J' and resid 38 through 41 removed outlier: 8.189A pdb=" N CYS J 38 " --> pdb=" O SER J 51 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TRP J 49 " --> pdb=" O GLU J 40 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'J' and resid 84 through 87 removed outlier: 6.759A pdb=" N PHE J 92 " --> pdb=" O TYR J 87 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'J' and resid 166 through 170 removed outlier: 3.530A pdb=" N MET J 239 " --> pdb=" O ILE J 167 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL J 109 " --> pdb=" O CYS J 287 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'J' and resid 360 through 365 removed outlier: 3.567A pdb=" N GLU J 361 " --> pdb=" O LYS J 541 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL J 544 " --> pdb=" O ASP J 536 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL J 534 " --> pdb=" O ASN J 546 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG J 531 " --> pdb=" O ILE J 374 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU J 373 " --> pdb=" O LYS J 513 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA J 515 " --> pdb=" O GLU J 373 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET J 375 " --> pdb=" O ALA J 515 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL J 518 " --> pdb=" O ILE J 485 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP J 486 " --> pdb=" O LYS J 412 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'J' and resid 566 through 569 removed outlier: 4.069A pdb=" N ARG J 574 " --> pdb=" O ASP J 569 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'N' and resid 214 through 217 removed outlier: 5.667A pdb=" N HIS N 463 " --> pdb=" O LEU N 217 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'N' and resid 334 through 337 removed outlier: 5.863A pdb=" N GLY N 197 " --> pdb=" O PHE N 337 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU N 194 " --> pdb=" O TYR N 360 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG N 359 " --> pdb=" O CYS N 375 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL N 373 " --> pdb=" O ARG N 361 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE N 369 " --> pdb=" O LEU N 365 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG N 374 " --> pdb=" O ALA N 247 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE N 278 " --> pdb=" O PHE N 246 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE N 277 " --> pdb=" O GLN N 270 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TRP N 265 " --> pdb=" O LYS N 510 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LYS N 505 " --> pdb=" O LEU N 522 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'N' and resid 379 through 383 removed outlier: 4.893A pdb=" N GLU N 387 " --> pdb=" O GLY N 383 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU N 398 " --> pdb=" O VAL N 452 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY N 467 " --> pdb=" O TYR N 451 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'X' and resid 30 through 34 removed outlier: 3.919A pdb=" N ALA X 30 " --> pdb=" O ALA X 49 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA X 45 " --> pdb=" O ALA X 34 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA X 2 " --> pdb=" O ALA X 50 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA X 3 " --> pdb=" O ALA X 78 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA X 74 " --> pdb=" O ALA X 7 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain '4' and resid 208 through 212 removed outlier: 3.841A pdb=" N GLN 4 208 " --> pdb=" O VAL 4 220 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL 4 212 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS 4 216 " --> pdb=" O VAL 4 212 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain '4' and resid 288 through 293 removed outlier: 8.523A pdb=" N ASP 4 288 " --> pdb=" O GLU 4 303 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N GLU 4 303 " --> pdb=" O ASP 4 288 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER 4 307 " --> pdb=" O CYS 4 302 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'O' and resid 30 through 36 removed outlier: 3.743A pdb=" N ILE O 41 " --> pdb=" O LEU O 35 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'O' and resid 73 through 77 removed outlier: 3.649A pdb=" N ARG O 74 " --> pdb=" O ASP O 83 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP O 76 " --> pdb=" O TYR O 81 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR O 81 " --> pdb=" O ASP O 76 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'O' and resid 189 through 195 removed outlier: 6.363A pdb=" N ARG O 233 " --> pdb=" O ILE O 229 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR O 237 " --> pdb=" O LYS O 225 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N THR O 239 " --> pdb=" O PRO O 223 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'Y' and resid 81 through 90 removed outlier: 5.703A pdb=" N GLY Y 82 " --> pdb=" O SER Y 131 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N SER Y 131 " --> pdb=" O GLY Y 82 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA Y 84 " --> pdb=" O HIS Y 129 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N HIS Y 129 " --> pdb=" O ALA Y 84 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA Y 86 " --> pdb=" O VAL Y 127 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL Y 127 " --> pdb=" O ALA Y 86 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ILE Y 88 " --> pdb=" O LYS Y 125 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASN Y 123 " --> pdb=" O LYS Y 90 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE Y 42 " --> pdb=" O VAL Y 127 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N SER Y 131 " --> pdb=" O ILE Y 44 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR Y 46 " --> pdb=" O SER Y 131 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA Y 154 " --> pdb=" O ASN Y 43 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY Y 45 " --> pdb=" O ALA Y 154 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU Y 158 " --> pdb=" O ILE Y 47 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU Y 186 " --> pdb=" O ALA Y 155 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU Y 157 " --> pdb=" O LEU Y 186 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN Y 190 " --> pdb=" O ILE Y 159 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'Y' and resid 254 through 258 removed outlier: 3.703A pdb=" N ALA Y 360 " --> pdb=" O PRO Y 254 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU Y 256 " --> pdb=" O LEU Y 358 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU Y 358 " --> pdb=" O LEU Y 256 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN Y 356 " --> pdb=" O VAL Y 258 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'Y' and resid 260 through 263 removed outlier: 3.967A pdb=" N ARG Y 260 " --> pdb=" O GLY Y 280 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'Y' and resid 293 through 296 removed outlier: 4.108A pdb=" N VAL Y 296 " --> pdb=" O ILE Y 314 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE Y 318 " --> pdb=" O LYS Y 342 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LYS Y 342 " --> pdb=" O ILE Y 318 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'Y' and resid 370 through 373 Processing sheet with id=110, first strand: chain 'Y' and resid 411 through 415 removed outlier: 5.087A pdb=" N ALA Y 442 " --> pdb=" O ASN Y 407 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain 'Z' and resid 32 through 38 removed outlier: 4.623A pdb=" N LYS Z 42 " --> pdb=" O ARG Z 38 " (cutoff:3.500A) 3735 hydrogen bonds defined for protein. 11109 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1044 hydrogen bonds 1706 hydrogen bond angles 0 basepair planarities 411 basepair parallelities 907 stacking parallelities Total time for adding SS restraints: 82.97 Time building geometry restraints manager: 43.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.34: 34706 1.34 - 1.57: 89139 1.57 - 1.81: 4142 1.81 - 2.04: 47 2.04 - 2.28: 24 Bond restraints: 128058 Sorted by residual: bond pdb=" C3' ATP J 605 " pdb=" C4' ATP J 605 " ideal model delta sigma weight residual 1.526 1.275 0.251 1.10e-02 8.26e+03 5.21e+02 bond pdb=" C1' ATP J 605 " pdb=" C2' ATP J 605 " ideal model delta sigma weight residual 1.531 1.265 0.266 1.20e-02 6.94e+03 4.90e+02 bond pdb=" C2' ADP J 603 " pdb=" C3' ADP J 603 " ideal model delta sigma weight residual 1.524 1.240 0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" CG PRO N 512 " pdb=" CD PRO N 512 " ideal model delta sigma weight residual 1.503 1.103 0.400 3.40e-02 8.65e+02 1.38e+02 bond pdb=" C1' ATP J 605 " pdb=" O4' ATP J 605 " ideal model delta sigma weight residual 1.416 1.564 -0.148 1.30e-02 5.92e+03 1.29e+02 ... (remaining 128053 not shown) Histogram of bond angle deviations from ideal: 73.61 - 88.89: 26 88.89 - 104.16: 7835 104.16 - 119.43: 113099 119.43 - 134.70: 60796 134.70 - 149.97: 13 Bond angle restraints: 181769 Sorted by residual: angle pdb=" PA ATP J 605 " pdb=" O3A ATP J 605 " pdb=" PB ATP J 605 " ideal model delta sigma weight residual 136.83 117.21 19.62 1.00e+00 1.00e+00 3.85e+02 angle pdb=" N PRO N 512 " pdb=" CD PRO N 512 " pdb=" CG PRO N 512 " ideal model delta sigma weight residual 103.20 76.69 26.51 1.50e+00 4.44e-01 3.12e+02 angle pdb=" PB ATP J 605 " pdb=" O3B ATP J 605 " pdb=" PG ATP J 605 " ideal model delta sigma weight residual 139.87 122.82 17.05 1.00e+00 1.00e+00 2.91e+02 angle pdb=" CB PRO N 512 " pdb=" CG PRO N 512 " pdb=" CD PRO N 512 " ideal model delta sigma weight residual 106.10 148.11 -42.01 3.20e+00 9.77e-02 1.72e+02 angle pdb=" CA PRO N 512 " pdb=" CB PRO N 512 " pdb=" CG PRO N 512 " ideal model delta sigma weight residual 104.50 80.10 24.40 1.90e+00 2.77e-01 1.65e+02 ... (remaining 181764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 74499 35.78 - 71.56: 5050 71.56 - 107.34: 616 107.34 - 143.12: 11 143.12 - 178.90: 30 Dihedral angle restraints: 80206 sinusoidal: 48377 harmonic: 31829 Sorted by residual: dihedral pdb=" CA ALA Y 51 " pdb=" C ALA Y 51 " pdb=" N HIS Y 52 " pdb=" CA HIS Y 52 " ideal model delta harmonic sigma weight residual 180.00 -124.09 -55.91 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA THR O 184 " pdb=" C THR O 184 " pdb=" N PRO O 185 " pdb=" CA PRO O 185 " ideal model delta harmonic sigma weight residual -180.00 -126.80 -53.20 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CA HIS L 432 " pdb=" C HIS L 432 " pdb=" N PRO L 433 " pdb=" CA PRO L 433 " ideal model delta harmonic sigma weight residual 180.00 133.34 46.66 0 5.00e+00 4.00e-02 8.71e+01 ... (remaining 80203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 21699 0.165 - 0.330: 311 0.330 - 0.495: 12 0.495 - 0.659: 0 0.659 - 0.824: 1 Chirality restraints: 22023 Sorted by residual: chirality pdb=" CB ILE L 333 " pdb=" CA ILE L 333 " pdb=" CG1 ILE L 333 " pdb=" CG2 ILE L 333 " both_signs ideal model delta sigma weight residual False 2.64 1.82 0.82 2.00e-01 2.50e+01 1.70e+01 chirality pdb=" CB VAL M 186 " pdb=" CA VAL M 186 " pdb=" CG1 VAL M 186 " pdb=" CG2 VAL M 186 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" C1' G 2 470 " pdb=" O4' G 2 470 " pdb=" C2' G 2 470 " pdb=" N9 G 2 470 " both_signs ideal model delta sigma weight residual False 2.46 2.03 0.43 2.00e-01 2.50e+01 4.57e+00 ... (remaining 22020 not shown) Planarity restraints: 16598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS L 432 " -0.079 5.00e-02 4.00e+02 1.20e-01 2.31e+01 pdb=" N PRO L 433 " 0.208 5.00e-02 4.00e+02 pdb=" CA PRO L 433 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO L 433 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE d 236 " -0.034 2.00e-02 2.50e+03 3.50e-02 2.15e+01 pdb=" CG PHE d 236 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE d 236 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE d 236 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE d 236 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE d 236 " -0.019 2.00e-02 2.50e+03 pdb=" CZ PHE d 236 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP N 168 " 0.037 2.00e-02 2.50e+03 2.90e-02 2.11e+01 pdb=" CG TRP N 168 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP N 168 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP N 168 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP N 168 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP N 168 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP N 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP N 168 " 0.015 2.00e-02 2.50e+03 pdb=" CZ3 TRP N 168 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP N 168 " 0.002 2.00e-02 2.50e+03 ... (remaining 16595 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 926 2.52 - 3.12: 84523 3.12 - 3.71: 202754 3.71 - 4.31: 282026 4.31 - 4.90: 435524 Nonbonded interactions: 1005753 Sorted by model distance: nonbonded pdb=" CE2 TYR E 132 " pdb=" ND2 ASN E 164 " model vdw 1.928 3.420 nonbonded pdb=" OE1 GLN J 414 " pdb="MG MG J 606 " model vdw 1.988 2.170 nonbonded pdb=" CD2 TYR E 132 " pdb=" ND2 ASN E 164 " model vdw 2.011 3.420 nonbonded pdb=" OG1 THR Y 78 " pdb="MG MG Y 502 " model vdw 2.026 2.170 nonbonded pdb=" OG1 THR J 386 " pdb="MG MG J 606 " model vdw 2.062 2.170 ... (remaining 1005748 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 17.180 Check model and map are aligned: 1.260 Set scattering table: 0.800 Process input model: 354.430 Find NCS groups from input model: 3.100 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 382.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 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 : 0.010 0.400 128058 Z= 0.635 Angle : 1.214 42.006 181769 Z= 0.639 Chirality : 0.062 0.824 22023 Planarity : 0.007 0.120 16598 Dihedral : 21.000 178.902 59560 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.98 % Favored : 90.97 % Rotamer: Outliers : 0.02 % Allowed : 0.73 % Favored : 99.25 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.11 % Twisted Proline : 1.50 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.07), residues: 10761 helix: -1.50 (0.07), residues: 4164 sheet: -1.65 (0.13), residues: 1489 loop : -2.56 (0.08), residues: 5108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.004 TRP N 168 HIS 0.018 0.003 HIS H 209 PHE 0.080 0.004 PHE d 236 TYR 0.050 0.004 TYR E 116 ARG 0.027 0.001 ARG i 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21522 Ramachandran restraints generated. 10761 Oldfield, 0 Emsley, 10761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21522 Ramachandran restraints generated. 10761 Oldfield, 0 Emsley, 10761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1451 residues out of total 9568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1449 time to evaluate : 8.026 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: y 50 PHE cc_start: 0.7119 (m-80) cc_final: 0.6689 (m-80) REVERT: o 62 LYS cc_start: 0.7605 (tttt) cc_final: 0.7277 (mmmt) REVERT: k 79 ILE cc_start: 0.7584 (mt) cc_final: 0.7116 (mt) REVERT: j 88 ASP cc_start: 0.7709 (t0) cc_final: 0.7399 (t0) REVERT: G 81 LEU cc_start: 0.7759 (mt) cc_final: 0.6652 (mt) REVERT: B 486 ASP cc_start: 0.7456 (m-30) cc_final: 0.6976 (m-30) REVERT: B 492 ARG cc_start: 0.7088 (mmt90) cc_final: 0.6709 (tpp80) REVERT: B 550 ARG cc_start: 0.7106 (mmm-85) cc_final: 0.6903 (mmt-90) REVERT: B 561 MET cc_start: 0.3191 (mmt) cc_final: 0.1408 (ttp) REVERT: C 691 MET cc_start: 0.6293 (tmm) cc_final: 0.6051 (tmm) REVERT: C 744 MET cc_start: 0.6953 (tmm) cc_final: 0.6724 (tmm) REVERT: C 832 MET cc_start: 0.4563 (mmp) cc_final: 0.4325 (mmt) REVERT: E 150 TYR cc_start: 0.4352 (m-10) cc_final: 0.3901 (m-80) REVERT: F 221 MET cc_start: 0.5128 (mmm) cc_final: 0.4584 (mtm) REVERT: F 231 MET cc_start: 0.3790 (mmt) cc_final: 0.3301 (mtt) REVERT: H 103 MET cc_start: -0.2726 (mmt) cc_final: -0.3047 (tpt) REVERT: H 215 MET cc_start: 0.3666 (ppp) cc_final: 0.3305 (ppp) REVERT: K 48 LEU cc_start: 0.4253 (tp) cc_final: 0.3857 (mt) REVERT: K 88 MET cc_start: -0.3247 (ttt) cc_final: -0.3961 (mtt) REVERT: K 125 MET cc_start: -0.1898 (tpt) cc_final: -0.2180 (mtt) REVERT: L 272 PHE cc_start: 0.2493 (p90) cc_final: 0.2238 (m-80) REVERT: L 497 MET cc_start: 0.3868 (ptm) cc_final: 0.3595 (ptt) REVERT: M 285 MET cc_start: 0.4675 (mtt) cc_final: 0.3887 (mtt) REVERT: N 28 MET cc_start: 0.6310 (tmm) cc_final: 0.5905 (tmm) REVERT: 4 200 ARG cc_start: 0.6638 (mmm160) cc_final: 0.4843 (ttp80) REVERT: O 20 MET cc_start: 0.6611 (mmm) cc_final: 0.6358 (tpp) REVERT: O 236 MET cc_start: 0.3819 (mtt) cc_final: 0.3436 (mmt) REVERT: Z 72 THR cc_start: 0.7832 (p) cc_final: 0.7601 (p) outliers start: 2 outliers final: 0 residues processed: 1451 average time/residue: 1.0570 time to fit residues: 2596.6825 Evaluate side-chains 967 residues out of total 9568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 967 time to evaluate : 7.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1250 random chunks: chunk 1055 optimal weight: 0.9990 chunk 947 optimal weight: 10.0000 chunk 525 optimal weight: 5.9990 chunk 323 optimal weight: 40.0000 chunk 639 optimal weight: 8.9990 chunk 506 optimal weight: 7.9990 chunk 979 optimal weight: 20.0000 chunk 379 optimal weight: 10.0000 chunk 595 optimal weight: 8.9990 chunk 729 optimal weight: 4.9990 chunk 1135 optimal weight: 0.3980 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 36 GLN Q 72 HIS ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 110 ASN ** s 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 44 ASN s 68 GLN ** s 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 99 ASN t 111 GLN t 165 GLN ** n 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 106 GLN T 15 GLN w 74 GLN ** b 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 74 ASN ** k 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 101 ASN k 105 ASN ** x 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 117 ASN j 77 ASN G 37 GLN ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 ASN B 538 GLN A 25 GLN A 44 GLN A 73 GLN A 270 GLN A 274 ASN ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 610 ASN ** C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN E 390 HIS ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 HIS H 114 HIS ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 261 ASN ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 GLN L 223 ASN ** L 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 452 GLN ** M 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 233 GLN ** N 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 221 ASN ** O 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 154 HIS ** Z 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 128058 Z= 0.235 Angle : 0.691 14.785 181769 Z= 0.357 Chirality : 0.042 0.334 22023 Planarity : 0.005 0.105 16598 Dihedral : 21.791 179.583 39964 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.47 % Favored : 93.50 % Rotamer: Outliers : 1.48 % Allowed : 10.07 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.11 % Twisted Proline : 0.75 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.08), residues: 10761 helix: -0.58 (0.08), residues: 4202 sheet: -1.38 (0.13), residues: 1532 loop : -2.32 (0.08), residues: 5027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP N 409 HIS 0.011 0.001 HIS L 432 PHE 0.032 0.002 PHE u 16 TYR 0.023 0.002 TYR o 37 ARG 0.009 0.001 ARG t 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21522 Ramachandran restraints generated. 10761 Oldfield, 0 Emsley, 10761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21522 Ramachandran restraints generated. 10761 Oldfield, 0 Emsley, 10761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 9568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1097 time to evaluate : 9.352 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: p 78 GLU cc_start: 0.7526 (pm20) cc_final: 0.6649 (pm20) REVERT: d 221 ASP cc_start: 0.6950 (p0) cc_final: 0.6600 (p0) REVERT: y 1 MET cc_start: 0.6704 (tpp) cc_final: 0.4967 (tpp) REVERT: e 78 MET cc_start: 0.5812 (OUTLIER) cc_final: 0.5094 (tmm) REVERT: u 64 TRP cc_start: 0.5708 (m-10) cc_final: 0.5500 (m-10) REVERT: v 36 ARG cc_start: 0.5595 (tpt90) cc_final: 0.4963 (ttt180) REVERT: o 37 TYR cc_start: 0.6642 (m-80) cc_final: 0.6363 (m-80) REVERT: o 62 LYS cc_start: 0.7530 (tttt) cc_final: 0.7245 (mmmt) REVERT: k 105 ASN cc_start: 0.6569 (OUTLIER) cc_final: 0.6046 (t0) REVERT: h 33 GLU cc_start: 0.5803 (mt-10) cc_final: 0.5163 (mt-10) REVERT: i 106 LYS cc_start: 0.8000 (mttm) cc_final: 0.7779 (mttp) REVERT: G 81 LEU cc_start: 0.7279 (mt) cc_final: 0.6942 (mt) REVERT: B 481 PHE cc_start: 0.5329 (p90) cc_final: 0.4924 (p90) REVERT: B 492 ARG cc_start: 0.6959 (mmt90) cc_final: 0.6610 (tpp80) REVERT: B 561 MET cc_start: 0.2530 (mmt) cc_final: 0.1204 (ttp) REVERT: A 32 TYR cc_start: 0.7370 (t80) cc_final: 0.7035 (t80) REVERT: A 318 MET cc_start: 0.4920 (tmm) cc_final: 0.4383 (tmm) REVERT: A 567 ARG cc_start: 0.5041 (ptt90) cc_final: 0.4614 (ptt180) REVERT: C 744 MET cc_start: 0.6855 (tmm) cc_final: 0.6445 (tmm) REVERT: F 221 MET cc_start: 0.5104 (mmm) cc_final: 0.4450 (mtm) REVERT: K 48 LEU cc_start: 0.4657 (tp) cc_final: 0.4250 (mt) REVERT: K 88 MET cc_start: -0.3226 (ttt) cc_final: -0.4077 (mtt) REVERT: K 174 MET cc_start: 0.3264 (mtt) cc_final: 0.3061 (mtt) REVERT: L 200 TYR cc_start: 0.1313 (OUTLIER) cc_final: 0.0981 (t80) REVERT: L 497 MET cc_start: 0.3185 (ptm) cc_final: 0.2912 (ptt) REVERT: N 73 HIS cc_start: 0.7032 (t70) cc_final: 0.6273 (t70) REVERT: N 180 MET cc_start: 0.6291 (mpp) cc_final: 0.6053 (mpp) REVERT: N 387 GLU cc_start: 0.4792 (pp20) cc_final: 0.4543 (pp20) REVERT: 4 200 ARG cc_start: 0.6544 (mmm160) cc_final: 0.4920 (ttp80) REVERT: Y 324 GLU cc_start: 0.3257 (tm-30) cc_final: 0.2639 (mp0) REVERT: Z 72 THR cc_start: 0.7964 (p) cc_final: 0.7671 (p) outliers start: 124 outliers final: 80 residues processed: 1154 average time/residue: 1.0322 time to fit residues: 2071.0612 Evaluate side-chains 1022 residues out of total 9568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 939 time to evaluate : 7.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain p residue 62 LEU Chi-restraints excluded: chain p residue 108 ASP Chi-restraints excluded: chain d residue 104 ASP Chi-restraints excluded: chain d residue 206 SER Chi-restraints excluded: chain d residue 271 ASP Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain r residue 19 ASP Chi-restraints excluded: chain r residue 82 SER Chi-restraints excluded: chain s residue 88 SER Chi-restraints excluded: chain t residue 186 ASP Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 71 LEU Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain m residue 83 ASP Chi-restraints excluded: chain y residue 39 VAL Chi-restraints excluded: chain y residue 66 ASP Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain z residue 98 GLU Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 78 MET Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 140 ASP Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain u residue 77 GLN Chi-restraints excluded: chain u residue 93 THR Chi-restraints excluded: chain v residue 75 ASN Chi-restraints excluded: chain v residue 82 ASN Chi-restraints excluded: chain o residue 34 MET Chi-restraints excluded: chain g residue 20 THR Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 19 ASN Chi-restraints excluded: chain k residue 105 ASN Chi-restraints excluded: chain x residue 49 ASP Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain S residue 32 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain l residue 53 ILE Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain V residue 5 MET Chi-restraints excluded: chain V residue 89 LEU Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 65 ASP Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain i residue 107 THR Chi-restraints excluded: chain i residue 131 ASP Chi-restraints excluded: chain j residue 115 ILE Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 825 MET Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain E residue 390 HIS Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 261 ASN Chi-restraints excluded: chain H residue 352 ASN Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain L residue 200 TYR Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 229 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 163 ASP Chi-restraints excluded: chain J residue 273 GLU Chi-restraints excluded: chain J residue 288 CYS Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain 4 residue 201 LYS Chi-restraints excluded: chain 4 residue 225 ILE Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain Z residue 53 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1250 random chunks: chunk 630 optimal weight: 8.9990 chunk 352 optimal weight: 10.0000 chunk 944 optimal weight: 8.9990 chunk 772 optimal weight: 9.9990 chunk 313 optimal weight: 30.0000 chunk 1137 optimal weight: 5.9990 chunk 1228 optimal weight: 0.0980 chunk 1012 optimal weight: 20.0000 chunk 1127 optimal weight: 0.8980 chunk 387 optimal weight: 30.0000 chunk 912 optimal weight: 20.0000 overall best weight: 4.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 17 HIS ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 68 GLN ** s 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 165 ASN ** v 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 GLN k 135 HIS ** x 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 77 ASN B 497 GLN ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 610 ASN ** C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN F 302 ASN F 345 GLN ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 255 GLN H 324 ASN H 328 GLN ** H 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 238 HIS 4 235 HIS O 67 ASN ** Z 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 128058 Z= 0.264 Angle : 0.661 13.960 181769 Z= 0.341 Chirality : 0.042 0.324 22023 Planarity : 0.005 0.090 16598 Dihedral : 21.601 179.844 39964 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.19 % Favored : 92.78 % Rotamer: Outliers : 2.29 % Allowed : 13.68 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.11 % Twisted Proline : 0.75 % Twisted General : 0.05 % 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: -1.86 (0.08), residues: 10761 helix: -0.16 (0.08), residues: 4235 sheet: -1.28 (0.13), residues: 1505 loop : -2.17 (0.08), residues: 5021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 179 HIS 0.025 0.001 HIS E 390 PHE 0.031 0.002 PHE s 72 TYR 0.027 0.002 TYR A 391 ARG 0.008 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21522 Ramachandran restraints generated. 10761 Oldfield, 0 Emsley, 10761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21522 Ramachandran restraints generated. 10761 Oldfield, 0 Emsley, 10761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1181 residues out of total 9568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 989 time to evaluate : 7.896 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: p 79 VAL cc_start: 0.9324 (OUTLIER) cc_final: 0.9118 (p) REVERT: d 221 ASP cc_start: 0.7147 (p0) cc_final: 0.6741 (p0) REVERT: s 73 GLN cc_start: 0.6428 (mt0) cc_final: 0.6196 (mt0) REVERT: b 198 ILE cc_start: 0.7064 (pt) cc_final: 0.6828 (pt) REVERT: u 24 LYS cc_start: 0.6786 (mmtm) cc_final: 0.6540 (tppt) REVERT: u 64 TRP cc_start: 0.5704 (m-10) cc_final: 0.5499 (m-10) REVERT: o 51 ARG cc_start: 0.6736 (mmm-85) cc_final: 0.5880 (tpt170) REVERT: k 83 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.7058 (m-80) REVERT: h 28 ASN cc_start: 0.5836 (OUTLIER) cc_final: 0.5468 (p0) REVERT: V 138 CYS cc_start: 0.3983 (t) cc_final: 0.3631 (t) REVERT: V 156 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.7372 (m-10) REVERT: B 481 PHE cc_start: 0.5641 (p90) cc_final: 0.5287 (p90) REVERT: B 509 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.6052 (mt) REVERT: B 550 ARG cc_start: 0.6883 (mtp85) cc_final: 0.6535 (mmt-90) REVERT: B 561 MET cc_start: 0.2637 (mmt) cc_final: 0.1400 (ttp) REVERT: A 318 MET cc_start: 0.5236 (tmm) cc_final: 0.4631 (tmm) REVERT: C 744 MET cc_start: 0.6949 (tmm) cc_final: 0.6692 (tmm) REVERT: E 256 TYR cc_start: 0.6464 (OUTLIER) cc_final: 0.6240 (m-80) REVERT: F 221 MET cc_start: 0.5095 (mmm) cc_final: 0.4394 (mtm) REVERT: L 200 TYR cc_start: 0.1534 (OUTLIER) cc_final: 0.1224 (t80) REVERT: J 189 ASP cc_start: 0.6946 (p0) cc_final: 0.6688 (p0) REVERT: J 307 GLU cc_start: 0.5685 (pt0) cc_final: 0.5356 (pt0) REVERT: N 28 MET cc_start: 0.6002 (tmm) cc_final: 0.5614 (tmm) REVERT: N 387 GLU cc_start: 0.4992 (pp20) cc_final: 0.4461 (pt0) REVERT: 4 200 ARG cc_start: 0.6462 (mmm160) cc_final: 0.4899 (ttp80) REVERT: 4 261 ARG cc_start: 0.4573 (mtt-85) cc_final: 0.4347 (ttm-80) REVERT: Z 72 THR cc_start: 0.8150 (p) cc_final: 0.7875 (p) outliers start: 192 outliers final: 114 residues processed: 1105 average time/residue: 1.0455 time to fit residues: 2020.2578 Evaluate side-chains 1030 residues out of total 9568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 909 time to evaluate : 7.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 87 VAL Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain p residue 62 LEU Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 108 ASP Chi-restraints excluded: chain d residue 104 ASP Chi-restraints excluded: chain d residue 206 SER Chi-restraints excluded: chain d residue 257 LYS Chi-restraints excluded: chain d residue 271 ASP Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain r residue 19 ASP Chi-restraints excluded: chain r residue 82 SER Chi-restraints excluded: chain r residue 126 ASP Chi-restraints excluded: chain s residue 88 SER Chi-restraints excluded: chain t residue 150 ASP Chi-restraints excluded: chain t residue 186 ASP Chi-restraints excluded: chain c residue 62 THR Chi-restraints excluded: chain c residue 71 LEU Chi-restraints excluded: chain m residue 83 ASP Chi-restraints excluded: chain m residue 125 LEU Chi-restraints excluded: chain y residue 39 VAL Chi-restraints excluded: chain y residue 42 VAL Chi-restraints excluded: chain y residue 66 ASP Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain z residue 98 GLU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain w residue 96 ILE Chi-restraints excluded: chain w residue 117 LEU Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 97 PHE Chi-restraints excluded: chain e residue 140 ASP Chi-restraints excluded: chain e residue 203 ASN Chi-restraints excluded: chain v residue 82 ASN Chi-restraints excluded: chain o residue 34 MET Chi-restraints excluded: chain o residue 126 VAL Chi-restraints excluded: chain g residue 20 THR Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 77 TYR Chi-restraints excluded: chain k residue 83 PHE Chi-restraints excluded: chain k residue 105 ASN Chi-restraints excluded: chain x residue 49 ASP Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain h residue 28 ASN Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain P residue 101 SER Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain S residue 32 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain l residue 53 ILE Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain V residue 5 MET Chi-restraints excluded: chain V residue 153 CYS Chi-restraints excluded: chain V residue 156 PHE Chi-restraints excluded: chain i residue 45 THR Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 67 ASP Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain i residue 107 THR Chi-restraints excluded: chain i residue 131 ASP Chi-restraints excluded: chain j residue 115 ILE Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 514 ASP Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 627 LYS Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 256 TYR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 142 HIS Chi-restraints excluded: chain H residue 352 ASN Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain L residue 200 TYR Chi-restraints excluded: chain L residue 288 TYR Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 229 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 163 ASP Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 270 ILE Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 273 GLU Chi-restraints excluded: chain J residue 288 CYS Chi-restraints excluded: chain J residue 421 THR Chi-restraints excluded: chain J residue 445 VAL Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 182 MET Chi-restraints excluded: chain 4 residue 225 ILE Chi-restraints excluded: chain O residue 10 HIS Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 69 CYS Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain Z residue 46 THR Chi-restraints excluded: chain Z residue 73 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1250 random chunks: chunk 1123 optimal weight: 20.0000 chunk 854 optimal weight: 6.9990 chunk 590 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 542 optimal weight: 30.0000 chunk 763 optimal weight: 30.0000 chunk 1141 optimal weight: 40.0000 chunk 1208 optimal weight: 8.9990 chunk 596 optimal weight: 4.9990 chunk 1081 optimal weight: 6.9990 chunk 325 optimal weight: 20.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 68 GLN ** s 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 165 ASN ** u 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 92 HIS ** h 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 15 ASN j 77 ASN ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 HIS ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 ASN ** C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 432 HIS ** J 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 73 HIS ** Z 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 128058 Z= 0.267 Angle : 0.645 15.348 181769 Z= 0.331 Chirality : 0.041 0.298 22023 Planarity : 0.005 0.108 16598 Dihedral : 21.508 179.062 39964 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.03 % Favored : 92.95 % Rotamer: Outliers : 2.86 % Allowed : 16.29 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.11 % Twisted Proline : 0.75 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.08), residues: 10761 helix: 0.06 (0.08), residues: 4261 sheet: -1.27 (0.13), residues: 1538 loop : -2.06 (0.08), residues: 4962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 179 HIS 0.013 0.001 HIS N 73 PHE 0.029 0.002 PHE s 72 TYR 0.025 0.002 TYR C 106 ARG 0.008 0.000 ARG W 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21522 Ramachandran restraints generated. 10761 Oldfield, 0 Emsley, 10761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21522 Ramachandran restraints generated. 10761 Oldfield, 0 Emsley, 10761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 9568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 946 time to evaluate : 8.037 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: p 78 GLU cc_start: 0.7540 (pm20) cc_final: 0.7247 (pm20) REVERT: d 221 ASP cc_start: 0.7188 (p0) cc_final: 0.6751 (p0) REVERT: m 103 GLU cc_start: 0.6958 (pp20) cc_final: 0.6705 (pp20) REVERT: T 36 MET cc_start: 0.7111 (ttp) cc_final: 0.6871 (ttp) REVERT: e 79 HIS cc_start: 0.5783 (OUTLIER) cc_final: 0.5356 (t-90) REVERT: o 51 ARG cc_start: 0.6992 (mmm-85) cc_final: 0.6132 (tpt170) REVERT: k 15 VAL cc_start: 0.7528 (m) cc_final: 0.7249 (p) REVERT: k 83 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.6990 (m-80) REVERT: k 105 ASN cc_start: 0.6500 (OUTLIER) cc_final: 0.6237 (t0) REVERT: x 88 MET cc_start: 0.7855 (mmt) cc_final: 0.6928 (mmt) REVERT: h 28 ASN cc_start: 0.5767 (OUTLIER) cc_final: 0.5430 (p0) REVERT: h 100 GLN cc_start: 0.7339 (mp-120) cc_final: 0.6962 (mp10) REVERT: P 55 TYR cc_start: 0.3661 (OUTLIER) cc_final: 0.3069 (m-80) REVERT: V 156 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.7329 (m-10) REVERT: B 481 PHE cc_start: 0.5565 (p90) cc_final: 0.4909 (p90) REVERT: B 550 ARG cc_start: 0.6982 (mtp85) cc_final: 0.6407 (mmt-90) REVERT: B 561 MET cc_start: 0.2810 (mmt) cc_final: 0.1450 (ttp) REVERT: A 318 MET cc_start: 0.5382 (tmm) cc_final: 0.4719 (tmm) REVERT: E 417 MET cc_start: 0.4669 (mmm) cc_final: 0.4438 (mmt) REVERT: F 221 MET cc_start: 0.5066 (mmm) cc_final: 0.4290 (mtm) REVERT: L 200 TYR cc_start: 0.1717 (OUTLIER) cc_final: 0.1445 (t80) REVERT: J 307 GLU cc_start: 0.5808 (pt0) cc_final: 0.5515 (pt0) REVERT: N 314 MET cc_start: 0.7315 (mmm) cc_final: 0.6911 (tmm) REVERT: N 387 GLU cc_start: 0.5232 (pp20) cc_final: 0.4798 (pt0) REVERT: 4 200 ARG cc_start: 0.6484 (mmm160) cc_final: 0.4897 (ttp80) REVERT: 4 261 ARG cc_start: 0.4608 (mtt-85) cc_final: 0.4227 (ttm110) REVERT: 4 273 ARG cc_start: 0.8026 (ttm170) cc_final: 0.7818 (ttm110) REVERT: O 152 PHE cc_start: 0.6821 (OUTLIER) cc_final: 0.5964 (t80) REVERT: Z 72 THR cc_start: 0.8208 (p) cc_final: 0.7960 (p) outliers start: 240 outliers final: 152 residues processed: 1099 average time/residue: 0.9992 time to fit residues: 1925.2842 Evaluate side-chains 1036 residues out of total 9568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 876 time to evaluate : 8.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 87 VAL Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain p residue 62 LEU Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 108 ASP Chi-restraints excluded: chain p residue 143 THR Chi-restraints excluded: chain d residue 170 TRP Chi-restraints excluded: chain d residue 206 SER Chi-restraints excluded: chain d residue 257 LYS Chi-restraints excluded: chain d residue 268 GLU Chi-restraints excluded: chain d residue 271 ASP Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 247 THR Chi-restraints excluded: chain r residue 19 ASP Chi-restraints excluded: chain r residue 41 LEU Chi-restraints excluded: chain r residue 82 SER Chi-restraints excluded: chain r residue 126 ASP Chi-restraints excluded: chain s residue 88 SER Chi-restraints excluded: chain t residue 150 ASP Chi-restraints excluded: chain t residue 186 ASP Chi-restraints excluded: chain c residue 95 ASP Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 80 MET Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 83 ASP Chi-restraints excluded: chain m residue 125 LEU Chi-restraints excluded: chain y residue 39 VAL Chi-restraints excluded: chain y residue 42 VAL Chi-restraints excluded: chain y residue 50 PHE Chi-restraints excluded: chain y residue 66 ASP Chi-restraints excluded: chain D residue 30 CYS Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain z residue 70 THR Chi-restraints excluded: chain z residue 74 MET Chi-restraints excluded: chain z residue 98 GLU Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain w residue 9 VAL Chi-restraints excluded: chain w residue 71 ILE Chi-restraints excluded: chain w residue 96 ILE Chi-restraints excluded: chain w residue 98 VAL Chi-restraints excluded: chain w residue 117 LEU Chi-restraints excluded: chain b residue 175 VAL Chi-restraints excluded: chain e residue 25 THR Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 79 HIS Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 97 PHE Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain e residue 140 ASP Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 203 ASN Chi-restraints excluded: chain v residue 82 ASN Chi-restraints excluded: chain o residue 34 MET Chi-restraints excluded: chain o residue 96 VAL Chi-restraints excluded: chain o residue 126 VAL Chi-restraints excluded: chain g residue 20 THR Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 50 ILE Chi-restraints excluded: chain k residue 69 THR Chi-restraints excluded: chain k residue 77 TYR Chi-restraints excluded: chain k residue 83 PHE Chi-restraints excluded: chain k residue 105 ASN Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain x residue 49 ASP Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain h residue 28 ASN Chi-restraints excluded: chain h residue 35 VAL Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 92 HIS Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain S residue 32 VAL Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain l residue 53 ILE Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain V residue 5 MET Chi-restraints excluded: chain V residue 156 PHE Chi-restraints excluded: chain V residue 194 TYR Chi-restraints excluded: chain i residue 45 THR Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 67 ASP Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain i residue 107 THR Chi-restraints excluded: chain j residue 115 ILE Chi-restraints excluded: chain j residue 125 VAL Chi-restraints excluded: chain G residue 59 CYS Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 142 HIS Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 216 TRP Chi-restraints excluded: chain H residue 319 ILE Chi-restraints excluded: chain H residue 352 ASN Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain L residue 200 TYR Chi-restraints excluded: chain L residue 288 TYR Chi-restraints excluded: chain L residue 321 PHE Chi-restraints excluded: chain L residue 371 LEU Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 229 VAL Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 163 ASP Chi-restraints excluded: chain J residue 196 THR Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 273 GLU Chi-restraints excluded: chain J residue 288 CYS Chi-restraints excluded: chain J residue 392 LEU Chi-restraints excluded: chain J residue 421 THR Chi-restraints excluded: chain J residue 445 VAL Chi-restraints excluded: chain J residue 572 ASN Chi-restraints excluded: chain N residue 170 VAL Chi-restraints excluded: chain N residue 182 MET Chi-restraints excluded: chain N residue 186 GLU Chi-restraints excluded: chain N residue 234 VAL Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 225 ILE Chi-restraints excluded: chain O residue 20 MET Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 83 ASP Chi-restraints excluded: chain O residue 152 PHE Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain O residue 229 ILE Chi-restraints excluded: chain Z residue 46 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1250 random chunks: chunk 1006 optimal weight: 20.0000 chunk 685 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 899 optimal weight: 8.9990 chunk 498 optimal weight: 0.9980 chunk 1031 optimal weight: 5.9990 chunk 835 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 616 optimal weight: 4.9990 chunk 1084 optimal weight: 20.0000 chunk 304 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 25 GLN ** s 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 165 ASN b 179 GLN ** u 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 105 ASN ** x 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 196 ASN j 77 ASN ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 ASN ** C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 ASN ** E 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 HIS ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 273 GLN H 337 ASN ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 578 ASN ** Z 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 128058 Z= 0.245 Angle : 0.627 15.857 181769 Z= 0.321 Chirality : 0.040 0.282 22023 Planarity : 0.004 0.090 16598 Dihedral : 21.447 179.023 39964 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.09 % Favored : 92.88 % Rotamer: Outliers : 3.14 % Allowed : 17.67 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.11 % Twisted Proline : 0.75 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.08), residues: 10761 helix: 0.25 (0.08), residues: 4259 sheet: -1.19 (0.13), residues: 1568 loop : -1.99 (0.08), residues: 4934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 179 HIS 0.036 0.001 HIS h 92 PHE 0.029 0.002 PHE K 4 TYR 0.025 0.002 TYR L 318 ARG 0.016 0.000 ARG F 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21522 Ramachandran restraints generated. 10761 Oldfield, 0 Emsley, 10761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21522 Ramachandran restraints generated. 10761 Oldfield, 0 Emsley, 10761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 9568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 932 time to evaluate : 7.264 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: p 78 GLU cc_start: 0.7547 (pm20) cc_final: 0.7258 (pm20) REVERT: d 221 ASP cc_start: 0.7135 (p0) cc_final: 0.6752 (p0) REVERT: s 73 GLN cc_start: 0.6385 (OUTLIER) cc_final: 0.5898 (mt0) REVERT: T 36 MET cc_start: 0.7080 (ttp) cc_final: 0.6861 (ttp) REVERT: e 79 HIS cc_start: 0.5721 (OUTLIER) cc_final: 0.5282 (t-90) REVERT: o 51 ARG cc_start: 0.7183 (mmm-85) cc_final: 0.6254 (tpt-90) REVERT: k 15 VAL cc_start: 0.7526 (m) cc_final: 0.7235 (p) REVERT: k 83 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.6995 (m-80) REVERT: x 88 MET cc_start: 0.7851 (mmt) cc_final: 0.6928 (mmt) REVERT: h 28 ASN cc_start: 0.5864 (OUTLIER) cc_final: 0.5519 (p0) REVERT: h 100 GLN cc_start: 0.7356 (mp-120) cc_final: 0.7008 (mp10) REVERT: B 497 GLN cc_start: 0.5218 (OUTLIER) cc_final: 0.4981 (mt0) REVERT: B 509 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5855 (mt) REVERT: B 550 ARG cc_start: 0.6923 (mtp85) cc_final: 0.6370 (mmt-90) REVERT: B 561 MET cc_start: 0.3095 (mmt) cc_final: 0.1740 (ttp) REVERT: A 318 MET cc_start: 0.5408 (tmm) cc_final: 0.4782 (tmm) REVERT: C 744 MET cc_start: 0.7016 (tmm) cc_final: 0.6742 (tmm) REVERT: E 417 MET cc_start: 0.4901 (mmm) cc_final: 0.4641 (mmt) REVERT: F 196 ASN cc_start: 0.3884 (OUTLIER) cc_final: 0.3531 (p0) REVERT: F 221 MET cc_start: 0.4877 (mmm) cc_final: 0.4244 (mtm) REVERT: L 200 TYR cc_start: 0.1719 (OUTLIER) cc_final: 0.1471 (t80) REVERT: L 288 TYR cc_start: 0.2066 (OUTLIER) cc_final: 0.1420 (t80) REVERT: L 318 TYR cc_start: 0.5354 (OUTLIER) cc_final: 0.5128 (t80) REVERT: M 366 ASN cc_start: 0.5464 (m-40) cc_final: 0.5227 (p0) REVERT: J 307 GLU cc_start: 0.5665 (pt0) cc_final: 0.5378 (pt0) REVERT: N 314 MET cc_start: 0.7252 (mmm) cc_final: 0.6881 (tmm) REVERT: N 387 GLU cc_start: 0.5228 (pp20) cc_final: 0.4932 (pt0) REVERT: 4 200 ARG cc_start: 0.6334 (mmm160) cc_final: 0.4825 (ttp80) REVERT: 4 261 ARG cc_start: 0.4616 (mtt-85) cc_final: 0.4213 (ttm110) REVERT: 4 273 ARG cc_start: 0.8005 (ttm170) cc_final: 0.7798 (ttm110) REVERT: O 152 PHE cc_start: 0.6939 (OUTLIER) cc_final: 0.6076 (t80) outliers start: 263 outliers final: 180 residues processed: 1120 average time/residue: 0.9694 time to fit residues: 1905.5366 Evaluate side-chains 1070 residues out of total 9568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 879 time to evaluate : 7.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 87 VAL Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 152 SER Chi-restraints excluded: chain p residue 62 LEU Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 108 ASP Chi-restraints excluded: chain p residue 131 ASP Chi-restraints excluded: chain p residue 143 THR Chi-restraints excluded: chain d residue 170 TRP Chi-restraints excluded: chain d residue 206 SER Chi-restraints excluded: chain d residue 216 MET Chi-restraints excluded: chain d residue 257 LYS Chi-restraints excluded: chain d residue 271 ASP Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 247 THR Chi-restraints excluded: chain r residue 19 ASP Chi-restraints excluded: chain r residue 41 LEU Chi-restraints excluded: chain r residue 82 SER Chi-restraints excluded: chain r residue 126 ASP Chi-restraints excluded: chain s residue 12 ASN Chi-restraints excluded: chain s residue 73 GLN Chi-restraints excluded: chain s residue 88 SER Chi-restraints excluded: chain t residue 150 ASP Chi-restraints excluded: chain t residue 186 ASP Chi-restraints excluded: chain c residue 62 THR Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 80 MET Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 83 ASP Chi-restraints excluded: chain m residue 125 LEU Chi-restraints excluded: chain y residue 39 VAL Chi-restraints excluded: chain y residue 42 VAL Chi-restraints excluded: chain y residue 50 PHE Chi-restraints excluded: chain y residue 66 ASP Chi-restraints excluded: chain D residue 30 CYS Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain z residue 70 THR Chi-restraints excluded: chain z residue 74 MET Chi-restraints excluded: chain z residue 102 THR Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain w residue 8 THR Chi-restraints excluded: chain w residue 9 VAL Chi-restraints excluded: chain w residue 71 ILE Chi-restraints excluded: chain w residue 96 ILE Chi-restraints excluded: chain w residue 98 VAL Chi-restraints excluded: chain w residue 117 LEU Chi-restraints excluded: chain b residue 32 ASP Chi-restraints excluded: chain b residue 175 VAL Chi-restraints excluded: chain e residue 25 THR Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 79 HIS Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 97 PHE Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain e residue 140 ASP Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 203 ASN Chi-restraints excluded: chain v residue 82 ASN Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain o residue 34 MET Chi-restraints excluded: chain o residue 96 VAL Chi-restraints excluded: chain o residue 126 VAL Chi-restraints excluded: chain g residue 20 THR Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 19 ASN Chi-restraints excluded: chain k residue 50 ILE Chi-restraints excluded: chain k residue 77 TYR Chi-restraints excluded: chain k residue 83 PHE Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain x residue 49 ASP Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain h residue 28 ASN Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 101 SER Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain S residue 32 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain l residue 53 ILE Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 137 ASP Chi-restraints excluded: chain U residue 144 CYS Chi-restraints excluded: chain V residue 5 MET Chi-restraints excluded: chain V residue 107 ASP Chi-restraints excluded: chain V residue 113 PHE Chi-restraints excluded: chain V residue 153 CYS Chi-restraints excluded: chain V residue 194 TYR Chi-restraints excluded: chain i residue 45 THR Chi-restraints excluded: chain i residue 52 THR Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 67 ASP Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain i residue 107 THR Chi-restraints excluded: chain i residue 131 ASP Chi-restraints excluded: chain j residue 112 VAL Chi-restraints excluded: chain j residue 115 ILE Chi-restraints excluded: chain j residue 125 VAL Chi-restraints excluded: chain G residue 59 CYS Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 627 LYS Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 142 HIS Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 216 TRP Chi-restraints excluded: chain H residue 319 ILE Chi-restraints excluded: chain H residue 352 ASN Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain L residue 200 TYR Chi-restraints excluded: chain L residue 288 TYR Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 371 LEU Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 229 VAL Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 163 ASP Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 273 GLU Chi-restraints excluded: chain J residue 288 CYS Chi-restraints excluded: chain J residue 357 MET Chi-restraints excluded: chain J residue 392 LEU Chi-restraints excluded: chain J residue 421 THR Chi-restraints excluded: chain J residue 445 VAL Chi-restraints excluded: chain J residue 555 MET Chi-restraints excluded: chain J residue 572 ASN Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 166 SER Chi-restraints excluded: chain N residue 170 VAL Chi-restraints excluded: chain N residue 182 MET Chi-restraints excluded: chain N residue 186 GLU Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 217 THR Chi-restraints excluded: chain 4 residue 225 ILE Chi-restraints excluded: chain 4 residue 278 TYR Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 83 ASP Chi-restraints excluded: chain O residue 152 PHE Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain O residue 167 LEU Chi-restraints excluded: chain Z residue 46 THR Chi-restraints excluded: chain Z residue 73 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1250 random chunks: chunk 406 optimal weight: 10.0000 chunk 1088 optimal weight: 5.9990 chunk 238 optimal weight: 8.9990 chunk 709 optimal weight: 50.0000 chunk 298 optimal weight: 10.0000 chunk 1209 optimal weight: 30.0000 chunk 1003 optimal weight: 10.0000 chunk 559 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 400 optimal weight: 20.0000 chunk 634 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 165 ASN e 79 HIS ** u 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 77 ASN ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 ASN ** C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN E 283 GLN ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 GLN ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 495 HIS M 362 ASN J 12 ASN N 300 GLN ** Z 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 128058 Z= 0.363 Angle : 0.706 15.971 181769 Z= 0.360 Chirality : 0.043 0.295 22023 Planarity : 0.005 0.096 16598 Dihedral : 21.508 179.967 39964 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.10 % Favored : 91.87 % Rotamer: Outliers : 3.60 % Allowed : 18.90 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.11 % Twisted Proline : 0.75 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.08), residues: 10761 helix: 0.14 (0.08), residues: 4253 sheet: -1.21 (0.13), residues: 1505 loop : -2.04 (0.08), residues: 5003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP B 482 HIS 0.010 0.002 HIS C 432 PHE 0.032 0.002 PHE u 16 TYR 0.029 0.002 TYR C 106 ARG 0.016 0.001 ARG C 501 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21522 Ramachandran restraints generated. 10761 Oldfield, 0 Emsley, 10761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21522 Ramachandran restraints generated. 10761 Oldfield, 0 Emsley, 10761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1177 residues out of total 9568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 875 time to evaluate : 8.232 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: d 221 ASP cc_start: 0.7182 (p0) cc_final: 0.6856 (p0) REVERT: t 96 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.7959 (mt) REVERT: t 157 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7946 (mtmm) REVERT: c 89 GLU cc_start: 0.8033 (tp30) cc_final: 0.7616 (tp30) REVERT: T 36 MET cc_start: 0.7162 (ttp) cc_final: 0.6917 (ttp) REVERT: w 71 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6932 (mm) REVERT: o 51 ARG cc_start: 0.7206 (mmm-85) cc_final: 0.6248 (tpt-90) REVERT: k 15 VAL cc_start: 0.7628 (m) cc_final: 0.7402 (p) REVERT: k 83 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7101 (m-80) REVERT: x 88 MET cc_start: 0.7941 (mmt) cc_final: 0.7164 (mmt) REVERT: h 28 ASN cc_start: 0.5922 (OUTLIER) cc_final: 0.5437 (p0) REVERT: h 100 GLN cc_start: 0.7353 (mp-120) cc_final: 0.6928 (mp10) REVERT: G 64 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7188 (ttmm) REVERT: B 509 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.5872 (mt) REVERT: B 538 GLN cc_start: 0.1829 (OUTLIER) cc_final: 0.0745 (mm-40) REVERT: B 550 ARG cc_start: 0.6990 (mtp85) cc_final: 0.6424 (mmt-90) REVERT: B 561 MET cc_start: 0.3349 (mmt) cc_final: 0.2047 (ttp) REVERT: A 318 MET cc_start: 0.5460 (tmm) cc_final: 0.4826 (tmm) REVERT: C 582 TRP cc_start: 0.7278 (OUTLIER) cc_final: 0.6847 (t-100) REVERT: C 744 MET cc_start: 0.7019 (tmm) cc_final: 0.6781 (tmm) REVERT: E 283 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.7019 (pt0) REVERT: E 417 MET cc_start: 0.5082 (mmm) cc_final: 0.4832 (mmt) REVERT: F 110 ASN cc_start: 0.4125 (OUTLIER) cc_final: 0.2746 (t0) REVERT: F 192 ARG cc_start: 0.5332 (ptp-170) cc_final: 0.4830 (ttm110) REVERT: F 196 ASN cc_start: 0.3841 (OUTLIER) cc_final: 0.3450 (p0) REVERT: F 221 MET cc_start: 0.4927 (mmm) cc_final: 0.4340 (mtm) REVERT: K 121 LEU cc_start: 0.1176 (OUTLIER) cc_final: 0.0777 (tp) REVERT: K 125 MET cc_start: -0.2514 (mtp) cc_final: -0.4609 (tpt) REVERT: L 200 TYR cc_start: 0.1660 (OUTLIER) cc_final: 0.1458 (t80) REVERT: L 288 TYR cc_start: 0.2032 (OUTLIER) cc_final: 0.1287 (t80) REVERT: L 318 TYR cc_start: 0.5022 (OUTLIER) cc_final: 0.4412 (t80) REVERT: M 317 ARG cc_start: 0.6531 (tpt170) cc_final: 0.5701 (tpp80) REVERT: N 314 MET cc_start: 0.7294 (mmm) cc_final: 0.6872 (tmm) REVERT: 4 200 ARG cc_start: 0.6334 (mmm160) cc_final: 0.4812 (ttp80) REVERT: 4 261 ARG cc_start: 0.4654 (mtt-85) cc_final: 0.4212 (ttm110) REVERT: 4 273 ARG cc_start: 0.8013 (ttm170) cc_final: 0.7764 (ttm110) REVERT: O 152 PHE cc_start: 0.7060 (OUTLIER) cc_final: 0.6292 (t80) outliers start: 302 outliers final: 216 residues processed: 1088 average time/residue: 1.0352 time to fit residues: 1980.6460 Evaluate side-chains 1064 residues out of total 9568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 831 time to evaluate : 7.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 87 VAL Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 152 SER Chi-restraints excluded: chain a residue 210 ILE Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 108 ASP Chi-restraints excluded: chain p residue 131 ASP Chi-restraints excluded: chain p residue 143 THR Chi-restraints excluded: chain d residue 104 ASP Chi-restraints excluded: chain d residue 130 ILE Chi-restraints excluded: chain d residue 206 SER Chi-restraints excluded: chain d residue 216 MET Chi-restraints excluded: chain d residue 257 LYS Chi-restraints excluded: chain d residue 268 GLU Chi-restraints excluded: chain d residue 271 ASP Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 141 THR Chi-restraints excluded: chain q residue 247 THR Chi-restraints excluded: chain r residue 19 ASP Chi-restraints excluded: chain r residue 82 SER Chi-restraints excluded: chain r residue 126 ASP Chi-restraints excluded: chain s residue 12 ASN Chi-restraints excluded: chain s residue 45 ILE Chi-restraints excluded: chain s residue 88 SER Chi-restraints excluded: chain s residue 105 THR Chi-restraints excluded: chain t residue 96 LEU Chi-restraints excluded: chain t residue 130 THR Chi-restraints excluded: chain t residue 150 ASP Chi-restraints excluded: chain t residue 157 LYS Chi-restraints excluded: chain t residue 186 ASP Chi-restraints excluded: chain c residue 62 THR Chi-restraints excluded: chain n residue 80 MET Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain m residue 83 ASP Chi-restraints excluded: chain y residue 39 VAL Chi-restraints excluded: chain y residue 42 VAL Chi-restraints excluded: chain y residue 50 PHE Chi-restraints excluded: chain y residue 66 ASP Chi-restraints excluded: chain D residue 30 CYS Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain z residue 70 THR Chi-restraints excluded: chain z residue 74 MET Chi-restraints excluded: chain z residue 98 GLU Chi-restraints excluded: chain z residue 102 THR Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain w residue 8 THR Chi-restraints excluded: chain w residue 9 VAL Chi-restraints excluded: chain w residue 71 ILE Chi-restraints excluded: chain w residue 96 ILE Chi-restraints excluded: chain w residue 98 VAL Chi-restraints excluded: chain w residue 108 LEU Chi-restraints excluded: chain w residue 117 LEU Chi-restraints excluded: chain b residue 32 ASP Chi-restraints excluded: chain b residue 41 VAL Chi-restraints excluded: chain b residue 175 VAL Chi-restraints excluded: chain b residue 206 ASP Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 223 ILE Chi-restraints excluded: chain e residue 25 THR Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 97 PHE Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain e residue 140 ASP Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain u residue 68 TYR Chi-restraints excluded: chain u residue 93 THR Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 82 ASN Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain o residue 34 MET Chi-restraints excluded: chain o residue 84 ILE Chi-restraints excluded: chain o residue 96 VAL Chi-restraints excluded: chain o residue 101 THR Chi-restraints excluded: chain o residue 126 VAL Chi-restraints excluded: chain g residue 20 THR Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 19 ASN Chi-restraints excluded: chain k residue 77 TYR Chi-restraints excluded: chain k residue 83 PHE Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain x residue 49 ASP Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain h residue 28 ASN Chi-restraints excluded: chain h residue 35 VAL Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 97 ILE Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain S residue 32 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain l residue 53 ILE Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 137 ASP Chi-restraints excluded: chain U residue 144 CYS Chi-restraints excluded: chain V residue 5 MET Chi-restraints excluded: chain V residue 107 ASP Chi-restraints excluded: chain V residue 113 PHE Chi-restraints excluded: chain V residue 154 VAL Chi-restraints excluded: chain V residue 194 TYR Chi-restraints excluded: chain i residue 45 THR Chi-restraints excluded: chain i residue 52 THR Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 67 ASP Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain i residue 107 THR Chi-restraints excluded: chain i residue 131 ASP Chi-restraints excluded: chain j residue 112 VAL Chi-restraints excluded: chain j residue 115 ILE Chi-restraints excluded: chain j residue 125 VAL Chi-restraints excluded: chain G residue 59 CYS Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 582 TRP Chi-restraints excluded: chain C residue 627 LYS Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain F residue 110 ASN Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 142 HIS Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 319 ILE Chi-restraints excluded: chain H residue 352 ASN Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 124 ASN Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain L residue 200 TYR Chi-restraints excluded: chain L residue 288 TYR Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 321 PHE Chi-restraints excluded: chain L residue 371 LEU Chi-restraints excluded: chain L residue 432 HIS Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 229 VAL Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 163 ASP Chi-restraints excluded: chain J residue 184 VAL Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 273 GLU Chi-restraints excluded: chain J residue 288 CYS Chi-restraints excluded: chain J residue 357 MET Chi-restraints excluded: chain J residue 392 LEU Chi-restraints excluded: chain J residue 421 THR Chi-restraints excluded: chain J residue 445 VAL Chi-restraints excluded: chain J residue 555 MET Chi-restraints excluded: chain J residue 572 ASN Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 166 SER Chi-restraints excluded: chain N residue 170 VAL Chi-restraints excluded: chain N residue 182 MET Chi-restraints excluded: chain N residue 186 GLU Chi-restraints excluded: chain N residue 234 VAL Chi-restraints excluded: chain N residue 399 TRP Chi-restraints excluded: chain N residue 503 GLU Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain 4 residue 203 VAL Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 217 THR Chi-restraints excluded: chain 4 residue 225 ILE Chi-restraints excluded: chain 4 residue 254 ASN Chi-restraints excluded: chain 4 residue 278 TYR Chi-restraints excluded: chain 4 residue 305 CYS Chi-restraints excluded: chain O residue 20 MET Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain O residue 83 ASP Chi-restraints excluded: chain O residue 152 PHE Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain O residue 167 LEU Chi-restraints excluded: chain O residue 229 ILE Chi-restraints excluded: chain Z residue 46 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1250 random chunks: chunk 1166 optimal weight: 30.0000 chunk 136 optimal weight: 3.9990 chunk 689 optimal weight: 0.0170 chunk 883 optimal weight: 6.9990 chunk 684 optimal weight: 30.0000 chunk 1018 optimal weight: 1.9990 chunk 675 optimal weight: 0.0980 chunk 1204 optimal weight: 2.9990 chunk 753 optimal weight: 20.0000 chunk 734 optimal weight: 8.9990 chunk 556 optimal weight: 6.9990 overall best weight: 1.8224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 58 HIS ** z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 36 GLN ** u 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 92 HIS ** h 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 77 ASN ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 16 ASN ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 ASN ** C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 ASN ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 322 GLN ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 495 HIS ** J 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 310 ASN N 300 GLN ** Z 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 128058 Z= 0.153 Angle : 0.589 16.003 181769 Z= 0.300 Chirality : 0.038 0.254 22023 Planarity : 0.004 0.090 16598 Dihedral : 21.361 179.470 39964 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.04 % Favored : 93.94 % Rotamer: Outliers : 2.49 % Allowed : 20.39 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.11 % Twisted Proline : 0.75 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.08), residues: 10761 helix: 0.56 (0.08), residues: 4256 sheet: -1.07 (0.13), residues: 1547 loop : -1.85 (0.09), residues: 4958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 482 HIS 0.009 0.001 HIS C 432 PHE 0.030 0.001 PHE s 72 TYR 0.022 0.001 TYR C 106 ARG 0.014 0.000 ARG R 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21522 Ramachandran restraints generated. 10761 Oldfield, 0 Emsley, 10761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21522 Ramachandran restraints generated. 10761 Oldfield, 0 Emsley, 10761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1190 residues out of total 9568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 981 time to evaluate : 8.048 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: p 79 VAL cc_start: 0.9270 (OUTLIER) cc_final: 0.9036 (p) REVERT: d 221 ASP cc_start: 0.6963 (p0) cc_final: 0.6597 (p0) REVERT: d 271 ASP cc_start: 0.6601 (OUTLIER) cc_final: 0.6321 (p0) REVERT: T 36 MET cc_start: 0.7030 (ttp) cc_final: 0.6820 (ttp) REVERT: w 71 ILE cc_start: 0.6746 (OUTLIER) cc_final: 0.6489 (mm) REVERT: b 38 GLU cc_start: 0.6475 (tp30) cc_final: 0.5967 (tm-30) REVERT: e 38 TYR cc_start: 0.6086 (m-80) cc_final: 0.5844 (m-80) REVERT: o 37 TYR cc_start: 0.7004 (m-80) cc_final: 0.6588 (m-80) REVERT: o 51 ARG cc_start: 0.7171 (mmm-85) cc_final: 0.6252 (tpt170) REVERT: g 107 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6870 (mt-10) REVERT: k 83 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.6954 (m-80) REVERT: x 88 MET cc_start: 0.7878 (mmt) cc_final: 0.6988 (mmt) REVERT: h 28 ASN cc_start: 0.5795 (OUTLIER) cc_final: 0.5470 (p0) REVERT: h 100 GLN cc_start: 0.7141 (mp-120) cc_final: 0.6805 (mp10) REVERT: S 18 LEU cc_start: 0.7403 (mm) cc_final: 0.6952 (mt) REVERT: S 33 GLU cc_start: 0.4306 (OUTLIER) cc_final: 0.3749 (tt0) REVERT: V 42 MET cc_start: 0.4942 (ptp) cc_final: 0.4510 (ptt) REVERT: G 30 GLU cc_start: 0.5976 (tm-30) cc_final: 0.5684 (tm-30) REVERT: G 64 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.7057 (ttmm) REVERT: B 502 GLN cc_start: 0.3560 (pp30) cc_final: 0.2901 (pt0) REVERT: B 550 ARG cc_start: 0.6841 (mtp85) cc_final: 0.6551 (mmt-90) REVERT: B 561 MET cc_start: 0.3612 (mmt) cc_final: 0.2063 (ttp) REVERT: A 318 MET cc_start: 0.5583 (tmm) cc_final: 0.4864 (tmm) REVERT: E 417 MET cc_start: 0.5107 (mmm) cc_final: 0.4875 (mmt) REVERT: F 221 MET cc_start: 0.4724 (mmm) cc_final: 0.4003 (mtm) REVERT: F 286 VAL cc_start: 0.3338 (t) cc_final: 0.2925 (t) REVERT: H 104 MET cc_start: 0.5679 (tmm) cc_final: 0.2448 (tpp) REVERT: K 125 MET cc_start: -0.2814 (mtp) cc_final: -0.4800 (tpt) REVERT: L 268 MET cc_start: 0.2079 (tmm) cc_final: 0.1818 (tmm) REVERT: L 288 TYR cc_start: 0.1960 (OUTLIER) cc_final: 0.1407 (t80) REVERT: L 318 TYR cc_start: 0.4877 (OUTLIER) cc_final: 0.4507 (t80) REVERT: N 314 MET cc_start: 0.7179 (mmm) cc_final: 0.6894 (tmm) REVERT: N 330 MET cc_start: 0.3848 (mpp) cc_final: 0.3321 (mpp) REVERT: 4 200 ARG cc_start: 0.6447 (mmm160) cc_final: 0.4842 (ttp80) REVERT: 4 261 ARG cc_start: 0.4986 (mtt-85) cc_final: 0.4305 (ttm110) REVERT: O 152 PHE cc_start: 0.7000 (OUTLIER) cc_final: 0.6323 (t80) outliers start: 209 outliers final: 136 residues processed: 1119 average time/residue: 0.9925 time to fit residues: 1950.1330 Evaluate side-chains 1027 residues out of total 9568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 881 time to evaluate : 7.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 152 SER Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 143 THR Chi-restraints excluded: chain d residue 170 TRP Chi-restraints excluded: chain d residue 216 MET Chi-restraints excluded: chain d residue 268 GLU Chi-restraints excluded: chain d residue 271 ASP Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 42 LEU Chi-restraints excluded: chain q residue 247 THR Chi-restraints excluded: chain r residue 19 ASP Chi-restraints excluded: chain r residue 126 ASP Chi-restraints excluded: chain s residue 88 SER Chi-restraints excluded: chain t residue 150 ASP Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 62 THR Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain y residue 39 VAL Chi-restraints excluded: chain y residue 42 VAL Chi-restraints excluded: chain y residue 50 PHE Chi-restraints excluded: chain y residue 66 ASP Chi-restraints excluded: chain D residue 30 CYS Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain z residue 70 THR Chi-restraints excluded: chain z residue 102 THR Chi-restraints excluded: chain w residue 9 VAL Chi-restraints excluded: chain w residue 71 ILE Chi-restraints excluded: chain w residue 96 ILE Chi-restraints excluded: chain w residue 98 VAL Chi-restraints excluded: chain w residue 108 LEU Chi-restraints excluded: chain w residue 117 LEU Chi-restraints excluded: chain b residue 41 VAL Chi-restraints excluded: chain b residue 175 VAL Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 97 PHE Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain e residue 140 ASP Chi-restraints excluded: chain v residue 82 ASN Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain o residue 34 MET Chi-restraints excluded: chain o residue 101 THR Chi-restraints excluded: chain o residue 126 VAL Chi-restraints excluded: chain g residue 101 ASP Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 83 PHE Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain x residue 49 ASP Chi-restraints excluded: chain x residue 93 SER Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain h residue 28 ASN Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 101 SER Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain S residue 32 VAL Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain V residue 5 MET Chi-restraints excluded: chain V residue 107 ASP Chi-restraints excluded: chain V residue 113 PHE Chi-restraints excluded: chain V residue 194 TYR Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain i residue 107 THR Chi-restraints excluded: chain j residue 112 VAL Chi-restraints excluded: chain j residue 115 ILE Chi-restraints excluded: chain j residue 125 VAL Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 59 CYS Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 627 LYS Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 142 HIS Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain K residue 124 ASN Chi-restraints excluded: chain L residue 288 TYR Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 321 PHE Chi-restraints excluded: chain L residue 432 HIS Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 229 VAL Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 163 ASP Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 421 THR Chi-restraints excluded: chain J residue 555 MET Chi-restraints excluded: chain J residue 572 ASN Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 166 SER Chi-restraints excluded: chain N residue 234 VAL Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 217 THR Chi-restraints excluded: chain 4 residue 225 ILE Chi-restraints excluded: chain 4 residue 254 ASN Chi-restraints excluded: chain 4 residue 305 CYS Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 152 PHE Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain O residue 167 LEU Chi-restraints excluded: chain Z residue 73 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1250 random chunks: chunk 745 optimal weight: 7.9990 chunk 481 optimal weight: 0.3980 chunk 719 optimal weight: 50.0000 chunk 362 optimal weight: 50.0000 chunk 236 optimal weight: 6.9990 chunk 233 optimal weight: 8.9990 chunk 765 optimal weight: 6.9990 chunk 820 optimal weight: 9.9990 chunk 595 optimal weight: 20.0000 chunk 112 optimal weight: 30.0000 chunk 947 optimal weight: 20.0000 overall best weight: 6.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 42 ASN ** u 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 101 ASN ** x 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN j 77 ASN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN A 274 ASN ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 ASN ** C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 495 HIS J 12 ASN J 74 ASN ** Z 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 128058 Z= 0.307 Angle : 0.662 16.371 181769 Z= 0.335 Chirality : 0.042 0.274 22023 Planarity : 0.005 0.106 16598 Dihedral : 21.352 179.392 39964 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.56 % Favored : 92.42 % Rotamer: Outliers : 2.76 % Allowed : 20.65 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.11 % Twisted Proline : 0.75 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.08), residues: 10761 helix: 0.48 (0.08), residues: 4262 sheet: -1.08 (0.13), residues: 1552 loop : -1.90 (0.09), residues: 4947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 482 HIS 0.008 0.001 HIS C 432 PHE 0.024 0.002 PHE l 14 TYR 0.030 0.002 TYR G 35 ARG 0.021 0.001 ARG A 469 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21522 Ramachandran restraints generated. 10761 Oldfield, 0 Emsley, 10761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21522 Ramachandran restraints generated. 10761 Oldfield, 0 Emsley, 10761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 9568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 884 time to evaluate : 7.980 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: d 221 ASP cc_start: 0.7159 (p0) cc_final: 0.6791 (p0) REVERT: d 271 ASP cc_start: 0.6768 (OUTLIER) cc_final: 0.6552 (p0) REVERT: T 36 MET cc_start: 0.7148 (ttp) cc_final: 0.6943 (ttp) REVERT: w 71 ILE cc_start: 0.7108 (OUTLIER) cc_final: 0.6873 (mm) REVERT: o 37 TYR cc_start: 0.7084 (m-80) cc_final: 0.6615 (m-80) REVERT: o 51 ARG cc_start: 0.7336 (mmm-85) cc_final: 0.6399 (tpt170) REVERT: g 107 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6893 (mt-10) REVERT: k 83 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.7038 (m-80) REVERT: x 88 MET cc_start: 0.7932 (mmt) cc_final: 0.7067 (mmt) REVERT: h 28 ASN cc_start: 0.5808 (OUTLIER) cc_final: 0.5426 (p0) REVERT: h 100 GLN cc_start: 0.7219 (mp-120) cc_final: 0.6804 (mp10) REVERT: S 33 GLU cc_start: 0.4549 (OUTLIER) cc_final: 0.3963 (tt0) REVERT: V 42 MET cc_start: 0.5008 (ptp) cc_final: 0.4644 (ptt) REVERT: G 30 GLU cc_start: 0.5923 (tm-30) cc_final: 0.5479 (tm-30) REVERT: B 561 MET cc_start: 0.3897 (mmt) cc_final: 0.2348 (ttp) REVERT: A 318 MET cc_start: 0.5622 (tmm) cc_final: 0.4924 (tmm) REVERT: C 806 THR cc_start: 0.6195 (t) cc_final: 0.5976 (t) REVERT: E 50 MET cc_start: 0.3351 (mmm) cc_final: 0.2823 (mmm) REVERT: E 417 MET cc_start: 0.5179 (mmm) cc_final: 0.4951 (mmt) REVERT: F 192 ARG cc_start: 0.5504 (ptp-170) cc_final: 0.4821 (ttm110) REVERT: F 221 MET cc_start: 0.4851 (mmm) cc_final: 0.4221 (mtm) REVERT: F 253 MET cc_start: 0.4533 (tmm) cc_final: 0.3480 (mmm) REVERT: H 101 MET cc_start: 0.5640 (tmm) cc_final: 0.4556 (ttt) REVERT: H 104 MET cc_start: 0.5575 (OUTLIER) cc_final: 0.2456 (tpp) REVERT: K 125 MET cc_start: -0.2737 (mtp) cc_final: -0.4773 (tpt) REVERT: L 288 TYR cc_start: 0.1783 (OUTLIER) cc_final: 0.1159 (t80) REVERT: L 318 TYR cc_start: 0.5052 (OUTLIER) cc_final: 0.4579 (t80) REVERT: L 371 LEU cc_start: 0.3857 (OUTLIER) cc_final: 0.3609 (tt) REVERT: L 483 GLU cc_start: 0.0936 (OUTLIER) cc_final: 0.0478 (mm-30) REVERT: N 314 MET cc_start: 0.7327 (mmm) cc_final: 0.6926 (tmm) REVERT: N 330 MET cc_start: 0.3886 (mpp) cc_final: 0.3446 (mpp) REVERT: 4 200 ARG cc_start: 0.6351 (mmm160) cc_final: 0.4836 (ttp80) REVERT: 4 261 ARG cc_start: 0.4976 (mtt-85) cc_final: 0.4317 (ttm110) REVERT: O 152 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.6372 (t80) REVERT: Z 79 TYR cc_start: 0.5249 (OUTLIER) cc_final: 0.4653 (t80) outliers start: 231 outliers final: 180 residues processed: 1051 average time/residue: 0.9849 time to fit residues: 1823.6826 Evaluate side-chains 1044 residues out of total 9568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 852 time to evaluate : 7.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 152 SER Chi-restraints excluded: chain a residue 193 HIS Chi-restraints excluded: chain a residue 210 ILE Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 131 ASP Chi-restraints excluded: chain p residue 143 THR Chi-restraints excluded: chain d residue 170 TRP Chi-restraints excluded: chain d residue 216 MET Chi-restraints excluded: chain d residue 268 GLU Chi-restraints excluded: chain d residue 271 ASP Chi-restraints excluded: chain d residue 273 LEU Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 42 LEU Chi-restraints excluded: chain q residue 247 THR Chi-restraints excluded: chain r residue 19 ASP Chi-restraints excluded: chain r residue 82 SER Chi-restraints excluded: chain r residue 126 ASP Chi-restraints excluded: chain s residue 12 ASN Chi-restraints excluded: chain s residue 88 SER Chi-restraints excluded: chain t residue 150 ASP Chi-restraints excluded: chain t residue 186 ASP Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 62 THR Chi-restraints excluded: chain n residue 85 THR Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain n residue 147 LYS Chi-restraints excluded: chain y residue 39 VAL Chi-restraints excluded: chain y residue 42 VAL Chi-restraints excluded: chain y residue 50 PHE Chi-restraints excluded: chain y residue 66 ASP Chi-restraints excluded: chain D residue 30 CYS Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain z residue 70 THR Chi-restraints excluded: chain z residue 102 THR Chi-restraints excluded: chain w residue 8 THR Chi-restraints excluded: chain w residue 9 VAL Chi-restraints excluded: chain w residue 71 ILE Chi-restraints excluded: chain w residue 96 ILE Chi-restraints excluded: chain w residue 98 VAL Chi-restraints excluded: chain w residue 117 LEU Chi-restraints excluded: chain b residue 32 ASP Chi-restraints excluded: chain b residue 41 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 175 VAL Chi-restraints excluded: chain b residue 188 ILE Chi-restraints excluded: chain b residue 206 ASP Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 97 PHE Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain e residue 140 ASP Chi-restraints excluded: chain u residue 68 TYR Chi-restraints excluded: chain v residue 82 ASN Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain o residue 34 MET Chi-restraints excluded: chain o residue 101 THR Chi-restraints excluded: chain o residue 126 VAL Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 77 TYR Chi-restraints excluded: chain k residue 83 PHE Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain x residue 49 ASP Chi-restraints excluded: chain x residue 93 SER Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain h residue 28 ASN Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 97 ILE Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 101 SER Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain S residue 32 VAL Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 137 ASP Chi-restraints excluded: chain U residue 144 CYS Chi-restraints excluded: chain V residue 5 MET Chi-restraints excluded: chain V residue 107 ASP Chi-restraints excluded: chain V residue 113 PHE Chi-restraints excluded: chain V residue 194 TYR Chi-restraints excluded: chain i residue 45 THR Chi-restraints excluded: chain i residue 52 THR Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain i residue 107 THR Chi-restraints excluded: chain j residue 112 VAL Chi-restraints excluded: chain j residue 115 ILE Chi-restraints excluded: chain j residue 125 VAL Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 59 CYS Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 627 LYS Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 142 HIS Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 216 TRP Chi-restraints excluded: chain H residue 322 GLN Chi-restraints excluded: chain K residue 124 ASN Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 288 TYR Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 321 PHE Chi-restraints excluded: chain L residue 371 LEU Chi-restraints excluded: chain L residue 432 HIS Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 229 VAL Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 163 ASP Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 273 GLU Chi-restraints excluded: chain J residue 288 CYS Chi-restraints excluded: chain J residue 357 MET Chi-restraints excluded: chain J residue 421 THR Chi-restraints excluded: chain J residue 445 VAL Chi-restraints excluded: chain J residue 555 MET Chi-restraints excluded: chain J residue 572 ASN Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 170 VAL Chi-restraints excluded: chain N residue 234 VAL Chi-restraints excluded: chain N residue 306 PHE Chi-restraints excluded: chain N residue 503 GLU Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain 4 residue 203 VAL Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 217 THR Chi-restraints excluded: chain 4 residue 225 ILE Chi-restraints excluded: chain 4 residue 254 ASN Chi-restraints excluded: chain 4 residue 278 TYR Chi-restraints excluded: chain 4 residue 305 CYS Chi-restraints excluded: chain O residue 20 MET Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain O residue 83 ASP Chi-restraints excluded: chain O residue 152 PHE Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain O residue 167 LEU Chi-restraints excluded: chain Z residue 35 ILE Chi-restraints excluded: chain Z residue 46 THR Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 79 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1250 random chunks: chunk 1095 optimal weight: 6.9990 chunk 1154 optimal weight: 30.0000 chunk 1053 optimal weight: 9.9990 chunk 1122 optimal weight: 0.7980 chunk 1153 optimal weight: 30.0000 chunk 675 optimal weight: 40.0000 chunk 489 optimal weight: 8.9990 chunk 881 optimal weight: 5.9990 chunk 344 optimal weight: 10.0000 chunk 1014 optimal weight: 0.9980 chunk 1061 optimal weight: 20.0000 overall best weight: 4.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 224 ASN ** s 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 ASN ** z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 77 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 225 HIS L 495 HIS ** J 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 322 ASN ** Z 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 128058 Z= 0.242 Angle : 0.633 16.255 181769 Z= 0.321 Chirality : 0.040 0.270 22023 Planarity : 0.004 0.089 16598 Dihedral : 21.332 179.887 39964 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.80 % Favored : 93.17 % Rotamer: Outliers : 2.70 % Allowed : 20.92 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.11 % Twisted Proline : 0.75 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.08), residues: 10761 helix: 0.56 (0.08), residues: 4264 sheet: -1.10 (0.13), residues: 1563 loop : -1.86 (0.09), residues: 4934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 482 HIS 0.009 0.001 HIS C 432 PHE 0.026 0.002 PHE s 72 TYR 0.026 0.002 TYR G 35 ARG 0.014 0.000 ARG m 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21522 Ramachandran restraints generated. 10761 Oldfield, 0 Emsley, 10761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21522 Ramachandran restraints generated. 10761 Oldfield, 0 Emsley, 10761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 9568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 873 time to evaluate : 8.024 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: d 221 ASP cc_start: 0.7077 (p0) cc_final: 0.6710 (p0) REVERT: d 271 ASP cc_start: 0.6698 (OUTLIER) cc_final: 0.6279 (p0) REVERT: T 36 MET cc_start: 0.7096 (ttp) cc_final: 0.6859 (ttp) REVERT: w 71 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6844 (mm) REVERT: b 189 MET cc_start: 0.7029 (ppp) cc_final: 0.6809 (mtm) REVERT: o 37 TYR cc_start: 0.6973 (m-80) cc_final: 0.6566 (m-80) REVERT: o 51 ARG cc_start: 0.7330 (mmm-85) cc_final: 0.6394 (tpt170) REVERT: k 83 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.6985 (m-80) REVERT: x 88 MET cc_start: 0.7918 (mmt) cc_final: 0.7053 (mmt) REVERT: h 28 ASN cc_start: 0.5796 (OUTLIER) cc_final: 0.5394 (p0) REVERT: h 100 GLN cc_start: 0.7023 (mp-120) cc_final: 0.6645 (mp10) REVERT: S 33 GLU cc_start: 0.4524 (OUTLIER) cc_final: 0.3952 (tt0) REVERT: V 42 MET cc_start: 0.5100 (ptp) cc_final: 0.4592 (ptt) REVERT: B 538 GLN cc_start: 0.1704 (OUTLIER) cc_final: 0.0849 (mp10) REVERT: B 561 MET cc_start: 0.3614 (mmt) cc_final: 0.2275 (ttp) REVERT: A 318 MET cc_start: 0.5668 (tmm) cc_final: 0.4989 (tmm) REVERT: C 806 THR cc_start: 0.6078 (t) cc_final: 0.5853 (t) REVERT: E 50 MET cc_start: 0.3342 (mmm) cc_final: 0.2827 (mmm) REVERT: E 55 MET cc_start: 0.4824 (mmp) cc_final: 0.4585 (mmp) REVERT: F 110 ASN cc_start: 0.3974 (OUTLIER) cc_final: 0.2755 (t0) REVERT: F 192 ARG cc_start: 0.5484 (ptp-170) cc_final: 0.4799 (ttm110) REVERT: F 221 MET cc_start: 0.4625 (mmm) cc_final: 0.4323 (mpp) REVERT: F 253 MET cc_start: 0.4695 (tmm) cc_final: 0.3559 (mmm) REVERT: H 101 MET cc_start: 0.5454 (tmm) cc_final: 0.4318 (ttm) REVERT: H 104 MET cc_start: 0.5582 (OUTLIER) cc_final: 0.2526 (tpp) REVERT: H 247 MET cc_start: -0.1181 (mtt) cc_final: -0.2133 (mtt) REVERT: K 125 MET cc_start: -0.2710 (mtp) cc_final: -0.4770 (tpt) REVERT: L 288 TYR cc_start: 0.1986 (OUTLIER) cc_final: 0.1459 (t80) REVERT: L 318 TYR cc_start: 0.5091 (OUTLIER) cc_final: 0.4591 (t80) REVERT: L 371 LEU cc_start: 0.3876 (OUTLIER) cc_final: 0.3652 (tt) REVERT: M 317 ARG cc_start: 0.6723 (tpt170) cc_final: 0.6436 (tpt170) REVERT: N 314 MET cc_start: 0.7266 (mmm) cc_final: 0.6917 (tmm) REVERT: N 330 MET cc_start: 0.3871 (mpp) cc_final: 0.3429 (mpp) REVERT: 4 200 ARG cc_start: 0.6342 (mmm160) cc_final: 0.4850 (ttp80) REVERT: 4 261 ARG cc_start: 0.4915 (mtt-85) cc_final: 0.4276 (ttm110) REVERT: O 152 PHE cc_start: 0.7051 (OUTLIER) cc_final: 0.6410 (t80) outliers start: 226 outliers final: 182 residues processed: 1039 average time/residue: 0.9709 time to fit residues: 1776.9514 Evaluate side-chains 1054 residues out of total 9568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 860 time to evaluate : 7.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 87 VAL Chi-restraints excluded: chain a residue 152 SER Chi-restraints excluded: chain a residue 210 ILE Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 143 THR Chi-restraints excluded: chain d residue 97 PHE Chi-restraints excluded: chain d residue 170 TRP Chi-restraints excluded: chain d residue 216 MET Chi-restraints excluded: chain d residue 257 LYS Chi-restraints excluded: chain d residue 268 GLU Chi-restraints excluded: chain d residue 271 ASP Chi-restraints excluded: chain d residue 273 LEU Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 42 LEU Chi-restraints excluded: chain q residue 247 THR Chi-restraints excluded: chain r residue 19 ASP Chi-restraints excluded: chain r residue 82 SER Chi-restraints excluded: chain r residue 126 ASP Chi-restraints excluded: chain s residue 88 SER Chi-restraints excluded: chain t residue 150 ASP Chi-restraints excluded: chain t residue 186 ASP Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 62 THR Chi-restraints excluded: chain n residue 85 THR Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain n residue 147 LYS Chi-restraints excluded: chain y residue 39 VAL Chi-restraints excluded: chain y residue 42 VAL Chi-restraints excluded: chain y residue 50 PHE Chi-restraints excluded: chain y residue 66 ASP Chi-restraints excluded: chain y residue 81 LYS Chi-restraints excluded: chain D residue 5 ASN Chi-restraints excluded: chain D residue 30 CYS Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain z residue 70 THR Chi-restraints excluded: chain z residue 102 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain w residue 8 THR Chi-restraints excluded: chain w residue 9 VAL Chi-restraints excluded: chain w residue 71 ILE Chi-restraints excluded: chain w residue 96 ILE Chi-restraints excluded: chain w residue 98 VAL Chi-restraints excluded: chain w residue 117 LEU Chi-restraints excluded: chain b residue 41 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 175 VAL Chi-restraints excluded: chain b residue 188 ILE Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain e residue 28 VAL Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 97 PHE Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain e residue 140 ASP Chi-restraints excluded: chain u residue 68 TYR Chi-restraints excluded: chain v residue 82 ASN Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain o residue 34 MET Chi-restraints excluded: chain o residue 101 THR Chi-restraints excluded: chain o residue 126 VAL Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 83 PHE Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain x residue 49 ASP Chi-restraints excluded: chain x residue 93 SER Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain h residue 28 ASN Chi-restraints excluded: chain h residue 35 VAL Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 97 ILE Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 101 SER Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain S residue 32 VAL Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 137 ASP Chi-restraints excluded: chain U residue 144 CYS Chi-restraints excluded: chain V residue 5 MET Chi-restraints excluded: chain V residue 107 ASP Chi-restraints excluded: chain V residue 113 PHE Chi-restraints excluded: chain V residue 154 VAL Chi-restraints excluded: chain V residue 194 TYR Chi-restraints excluded: chain i residue 45 THR Chi-restraints excluded: chain i residue 52 THR Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain i residue 107 THR Chi-restraints excluded: chain j residue 112 VAL Chi-restraints excluded: chain j residue 115 ILE Chi-restraints excluded: chain j residue 125 VAL Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 59 CYS Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 627 LYS Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain F residue 110 ASN Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 142 HIS Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 216 TRP Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 322 GLN Chi-restraints excluded: chain K residue 124 ASN Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 288 TYR Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 321 PHE Chi-restraints excluded: chain L residue 371 LEU Chi-restraints excluded: chain L residue 432 HIS Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 229 VAL Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 163 ASP Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 357 MET Chi-restraints excluded: chain J residue 421 THR Chi-restraints excluded: chain J residue 445 VAL Chi-restraints excluded: chain J residue 555 MET Chi-restraints excluded: chain J residue 572 ASN Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 166 SER Chi-restraints excluded: chain N residue 170 VAL Chi-restraints excluded: chain N residue 234 VAL Chi-restraints excluded: chain N residue 306 PHE Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain 4 residue 203 VAL Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 217 THR Chi-restraints excluded: chain 4 residue 225 ILE Chi-restraints excluded: chain 4 residue 254 ASN Chi-restraints excluded: chain 4 residue 278 TYR Chi-restraints excluded: chain 4 residue 305 CYS Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain O residue 83 ASP Chi-restraints excluded: chain O residue 152 PHE Chi-restraints excluded: chain O residue 167 LEU Chi-restraints excluded: chain O residue 229 ILE Chi-restraints excluded: chain Z residue 46 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1250 random chunks: chunk 1118 optimal weight: 3.9990 chunk 737 optimal weight: 1.9990 chunk 1187 optimal weight: 30.0000 chunk 724 optimal weight: 0.9990 chunk 563 optimal weight: 8.9990 chunk 825 optimal weight: 30.0000 chunk 1245 optimal weight: 7.9990 chunk 1146 optimal weight: 10.0000 chunk 991 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 765 optimal weight: 9.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 ASN z 19 GLN ** z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 77 ASN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 495 HIS ** J 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 322 ASN ** Z 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 128058 Z= 0.185 Angle : 0.604 16.207 181769 Z= 0.306 Chirality : 0.039 0.276 22023 Planarity : 0.004 0.091 16598 Dihedral : 21.260 179.409 39964 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.81 % Favored : 93.16 % Rotamer: Outliers : 2.36 % Allowed : 21.44 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.11 % Twisted Proline : 0.75 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.08), residues: 10761 helix: 0.72 (0.08), residues: 4266 sheet: -1.05 (0.13), residues: 1543 loop : -1.78 (0.09), residues: 4952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 482 HIS 0.008 0.001 HIS C 432 PHE 0.026 0.001 PHE s 72 TYR 0.027 0.001 TYR G 35 ARG 0.015 0.000 ARG A 469 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21522 Ramachandran restraints generated. 10761 Oldfield, 0 Emsley, 10761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21522 Ramachandran restraints generated. 10761 Oldfield, 0 Emsley, 10761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 9568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 906 time to evaluate : 7.928 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: d 221 ASP cc_start: 0.7049 (p0) cc_final: 0.6670 (p0) REVERT: d 271 ASP cc_start: 0.6572 (OUTLIER) cc_final: 0.6250 (p0) REVERT: z 74 MET cc_start: 0.7272 (mtm) cc_final: 0.6866 (mtm) REVERT: u 69 TRP cc_start: 0.5867 (m-90) cc_final: 0.5661 (m-90) REVERT: o 37 TYR cc_start: 0.6931 (m-80) cc_final: 0.6604 (m-80) REVERT: o 51 ARG cc_start: 0.7314 (mmm-85) cc_final: 0.6409 (tpt170) REVERT: k 83 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.6869 (m-80) REVERT: x 88 MET cc_start: 0.7897 (mmt) cc_final: 0.6970 (mmt) REVERT: h 28 ASN cc_start: 0.5795 (OUTLIER) cc_final: 0.5443 (p0) REVERT: h 100 GLN cc_start: 0.6873 (mp-120) cc_final: 0.6564 (mp10) REVERT: P 85 ARG cc_start: 0.8176 (mtp-110) cc_final: 0.7850 (mtp-110) REVERT: S 33 GLU cc_start: 0.4164 (OUTLIER) cc_final: 0.3605 (tt0) REVERT: V 42 MET cc_start: 0.5062 (ptp) cc_final: 0.4580 (ptt) REVERT: B 538 GLN cc_start: 0.1633 (OUTLIER) cc_final: 0.0820 (mp10) REVERT: B 561 MET cc_start: 0.3564 (mmt) cc_final: 0.2216 (ttp) REVERT: A 318 MET cc_start: 0.5645 (tmm) cc_final: 0.5021 (tmm) REVERT: C 806 THR cc_start: 0.6023 (t) cc_final: 0.5782 (t) REVERT: E 50 MET cc_start: 0.3459 (mmm) cc_final: 0.2901 (mmm) REVERT: F 110 ASN cc_start: 0.3863 (OUTLIER) cc_final: 0.2640 (t0) REVERT: F 221 MET cc_start: 0.4499 (mmm) cc_final: 0.4204 (mpp) REVERT: F 253 MET cc_start: 0.4781 (tmm) cc_final: 0.3348 (mmm) REVERT: F 286 VAL cc_start: 0.3415 (t) cc_final: 0.3007 (t) REVERT: H 101 MET cc_start: 0.5337 (tmm) cc_final: 0.4246 (ttm) REVERT: H 104 MET cc_start: 0.5615 (OUTLIER) cc_final: 0.2534 (tpp) REVERT: K 125 MET cc_start: -0.2680 (mtp) cc_final: -0.4802 (tpt) REVERT: L 268 MET cc_start: 0.1789 (tmm) cc_final: 0.1236 (tmm) REVERT: L 288 TYR cc_start: 0.1943 (OUTLIER) cc_final: 0.1486 (t80) REVERT: L 318 TYR cc_start: 0.4998 (OUTLIER) cc_final: 0.4471 (t80) REVERT: M 317 ARG cc_start: 0.6717 (tpt170) cc_final: 0.5768 (tpp80) REVERT: N 314 MET cc_start: 0.7272 (mmm) cc_final: 0.6915 (tmm) REVERT: 4 200 ARG cc_start: 0.6348 (mmm160) cc_final: 0.4813 (ttp80) REVERT: 4 232 GLN cc_start: 0.6819 (tm-30) cc_final: 0.6529 (tp40) REVERT: 4 261 ARG cc_start: 0.4890 (mtt-85) cc_final: 0.3988 (ttm110) REVERT: O 152 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.6377 (t80) outliers start: 198 outliers final: 164 residues processed: 1046 average time/residue: 1.0437 time to fit residues: 1928.1793 Evaluate side-chains 1037 residues out of total 9568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 863 time to evaluate : 7.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 87 VAL Chi-restraints excluded: chain a residue 152 SER Chi-restraints excluded: chain a residue 210 ILE Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 143 THR Chi-restraints excluded: chain d residue 170 TRP Chi-restraints excluded: chain d residue 216 MET Chi-restraints excluded: chain d residue 257 LYS Chi-restraints excluded: chain d residue 271 ASP Chi-restraints excluded: chain d residue 273 LEU Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 42 LEU Chi-restraints excluded: chain q residue 247 THR Chi-restraints excluded: chain r residue 19 ASP Chi-restraints excluded: chain r residue 82 SER Chi-restraints excluded: chain r residue 126 ASP Chi-restraints excluded: chain s residue 88 SER Chi-restraints excluded: chain t residue 150 ASP Chi-restraints excluded: chain t residue 186 ASP Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 62 THR Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain y residue 39 VAL Chi-restraints excluded: chain y residue 42 VAL Chi-restraints excluded: chain y residue 50 PHE Chi-restraints excluded: chain y residue 66 ASP Chi-restraints excluded: chain D residue 5 ASN Chi-restraints excluded: chain D residue 30 CYS Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain z residue 70 THR Chi-restraints excluded: chain z residue 102 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain w residue 8 THR Chi-restraints excluded: chain w residue 9 VAL Chi-restraints excluded: chain w residue 96 ILE Chi-restraints excluded: chain w residue 98 VAL Chi-restraints excluded: chain w residue 117 LEU Chi-restraints excluded: chain b residue 41 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 175 VAL Chi-restraints excluded: chain b residue 188 ILE Chi-restraints excluded: chain e residue 28 VAL Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 97 PHE Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain e residue 140 ASP Chi-restraints excluded: chain v residue 82 ASN Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain o residue 34 MET Chi-restraints excluded: chain o residue 101 THR Chi-restraints excluded: chain o residue 126 VAL Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 83 PHE Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain x residue 49 ASP Chi-restraints excluded: chain x residue 93 SER Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain h residue 28 ASN Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 97 ILE Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 101 SER Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain S residue 32 VAL Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain l residue 53 ILE Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 144 CYS Chi-restraints excluded: chain V residue 5 MET Chi-restraints excluded: chain V residue 107 ASP Chi-restraints excluded: chain V residue 113 PHE Chi-restraints excluded: chain V residue 154 VAL Chi-restraints excluded: chain V residue 194 TYR Chi-restraints excluded: chain i residue 45 THR Chi-restraints excluded: chain i residue 52 THR Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain i residue 107 THR Chi-restraints excluded: chain j residue 112 VAL Chi-restraints excluded: chain j residue 115 ILE Chi-restraints excluded: chain j residue 125 VAL Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 627 LYS Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain F residue 110 ASN Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 142 HIS Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 216 TRP Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 322 GLN Chi-restraints excluded: chain K residue 124 ASN Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 288 TYR Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 321 PHE Chi-restraints excluded: chain L residue 432 HIS Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 229 VAL Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 163 ASP Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 421 THR Chi-restraints excluded: chain J residue 445 VAL Chi-restraints excluded: chain J residue 555 MET Chi-restraints excluded: chain J residue 572 ASN Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 234 VAL Chi-restraints excluded: chain N residue 306 PHE Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 217 THR Chi-restraints excluded: chain 4 residue 225 ILE Chi-restraints excluded: chain 4 residue 254 ASN Chi-restraints excluded: chain 4 residue 268 GLU Chi-restraints excluded: chain 4 residue 278 TYR Chi-restraints excluded: chain 4 residue 305 CYS Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain O residue 83 ASP Chi-restraints excluded: chain O residue 152 PHE Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain O residue 167 LEU Chi-restraints excluded: chain Y residue 83 TYR Chi-restraints excluded: chain Z residue 46 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1250 random chunks: chunk 608 optimal weight: 7.9990 chunk 787 optimal weight: 20.0000 chunk 1056 optimal weight: 3.9990 chunk 303 optimal weight: 10.0000 chunk 914 optimal weight: 5.9990 chunk 146 optimal weight: 20.0000 chunk 275 optimal weight: 10.0000 chunk 993 optimal weight: 6.9990 chunk 415 optimal weight: 10.0000 chunk 1019 optimal weight: 20.0000 chunk 125 optimal weight: 10.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: r 186 GLN ** s 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 495 HIS ** M 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 ASN N 320 ASN N 322 ASN ** Z 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.094574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.069727 restraints weight = 513535.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.070350 restraints weight = 226836.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.069938 restraints weight = 160591.917| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 128058 Z= 0.332 Angle : 0.688 16.049 181769 Z= 0.347 Chirality : 0.042 0.272 22023 Planarity : 0.005 0.087 16598 Dihedral : 21.306 179.182 39964 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.78 % Favored : 92.19 % Rotamer: Outliers : 2.51 % Allowed : 21.52 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.11 % Twisted Proline : 0.75 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.08), residues: 10761 helix: 0.54 (0.08), residues: 4266 sheet: -1.11 (0.13), residues: 1564 loop : -1.88 (0.09), residues: 4931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 482 HIS 0.008 0.001 HIS C 432 PHE 0.023 0.002 PHE H 82 TYR 0.024 0.002 TYR G 35 ARG 0.014 0.001 ARG m 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28499.20 seconds wall clock time: 499 minutes 25.56 seconds (29965.56 seconds total)