Starting phenix.real_space_refine on Sun Mar 24 03:24:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raw_4785/03_2024/6raw_4785_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raw_4785/03_2024/6raw_4785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raw_4785/03_2024/6raw_4785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raw_4785/03_2024/6raw_4785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raw_4785/03_2024/6raw_4785_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raw_4785/03_2024/6raw_4785_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 54 5.49 5 S 233 5.16 5 C 24842 2.51 5 N 6960 2.21 5 O 7621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 ARG 177": "NH1" <-> "NH2" Residue "2 ARG 183": "NH1" <-> "NH2" Residue "2 ARG 189": "NH1" <-> "NH2" Residue "2 ARG 195": "NH1" <-> "NH2" Residue "2 ARG 201": "NH1" <-> "NH2" Residue "2 ARG 206": "NH1" <-> "NH2" Residue "2 GLU 260": "OE1" <-> "OE2" Residue "2 GLU 265": "OE1" <-> "OE2" Residue "2 GLU 278": "OE1" <-> "OE2" Residue "2 ARG 292": "NH1" <-> "NH2" Residue "2 ARG 369": "NH1" <-> "NH2" Residue "2 ARG 457": "NH1" <-> "NH2" Residue "2 ARG 461": "NH1" <-> "NH2" Residue "2 ARG 478": "NH1" <-> "NH2" Residue "2 GLU 522": "OE1" <-> "OE2" Residue "2 ARG 552": "NH1" <-> "NH2" Residue "2 ARG 621": "NH1" <-> "NH2" Residue "2 GLU 630": "OE1" <-> "OE2" Residue "2 ARG 698": "NH1" <-> "NH2" Residue "2 GLU 706": "OE1" <-> "OE2" Residue "2 ARG 709": "NH1" <-> "NH2" Residue "2 ARG 728": "NH1" <-> "NH2" Residue "2 GLU 752": "OE1" <-> "OE2" Residue "2 ARG 756": "NH1" <-> "NH2" Residue "2 ARG 760": "NH1" <-> "NH2" Residue "2 ARG 773": "NH1" <-> "NH2" Residue "2 GLU 777": "OE1" <-> "OE2" Residue "3 ARG 43": "NH1" <-> "NH2" Residue "3 ARG 53": "NH1" <-> "NH2" Residue "3 ARG 58": "NH1" <-> "NH2" Residue "3 ARG 75": "NH1" <-> "NH2" Residue "3 ARG 106": "NH1" <-> "NH2" Residue "3 GLU 125": "OE1" <-> "OE2" Residue "3 ARG 149": "NH1" <-> "NH2" Residue "3 ARG 225": "NH1" <-> "NH2" Residue "3 ARG 231": "NH1" <-> "NH2" Residue "3 ARG 239": "NH1" <-> "NH2" Residue "3 ARG 245": "NH1" <-> "NH2" Residue "3 ARG 254": "NH1" <-> "NH2" Residue "3 GLU 268": "OE1" <-> "OE2" Residue "3 ARG 275": "NH1" <-> "NH2" Residue "3 GLU 276": "OE1" <-> "OE2" Residue "3 GLU 321": "OE1" <-> "OE2" Residue "3 ARG 329": "NH1" <-> "NH2" Residue "3 ARG 351": "NH1" <-> "NH2" Residue "3 ARG 359": "NH1" <-> "NH2" Residue "3 ARG 366": "NH1" <-> "NH2" Residue "3 GLU 382": "OE1" <-> "OE2" Residue "3 GLU 385": "OE1" <-> "OE2" Residue "3 ARG 414": "NH1" <-> "NH2" Residue "3 GLU 422": "OE1" <-> "OE2" Residue "3 ARG 425": "NH1" <-> "NH2" Residue "3 ARG 453": "NH1" <-> "NH2" Residue "3 ARG 498": "NH1" <-> "NH2" Residue "3 ARG 550": "NH1" <-> "NH2" Residue "3 ARG 563": "NH1" <-> "NH2" Residue "3 GLU 578": "OE1" <-> "OE2" Residue "3 ARG 590": "NH1" <-> "NH2" Residue "3 GLU 598": "OE1" <-> "OE2" Residue "3 ARG 603": "NH1" <-> "NH2" Residue "3 ARG 610": "NH1" <-> "NH2" Residue "3 ARG 624": "NH1" <-> "NH2" Residue "4 ARG 174": "NH1" <-> "NH2" Residue "4 ARG 227": "NH1" <-> "NH2" Residue "4 ARG 251": "NH1" <-> "NH2" Residue "4 ARG 303": "NH1" <-> "NH2" Residue "4 ARG 324": "NH1" <-> "NH2" Residue "4 ARG 341": "NH1" <-> "NH2" Residue "4 ARG 346": "NH1" <-> "NH2" Residue "4 GLU 348": "OE1" <-> "OE2" Residue "4 ARG 425": "NH1" <-> "NH2" Residue "4 ARG 447": "NH1" <-> "NH2" Residue "4 ARG 463": "NH1" <-> "NH2" Residue "4 ARG 499": "NH1" <-> "NH2" Residue "4 ARG 503": "NH1" <-> "NH2" Residue "4 ARG 538": "NH1" <-> "NH2" Residue "4 GLU 554": "OE1" <-> "OE2" Residue "4 ARG 556": "NH1" <-> "NH2" Residue "4 ARG 629": "NH1" <-> "NH2" Residue "4 ARG 663": "NH1" <-> "NH2" Residue "4 ARG 676": "NH1" <-> "NH2" Residue "4 GLU 680": "OE1" <-> "OE2" Residue "4 ARG 690": "NH1" <-> "NH2" Residue "4 ARG 697": "NH1" <-> "NH2" Residue "4 ARG 711": "NH1" <-> "NH2" Residue "4 ARG 726": "NH1" <-> "NH2" Residue "4 ARG 734": "NH1" <-> "NH2" Residue "4 ARG 750": "NH1" <-> "NH2" Residue "4 GLU 761": "OE1" <-> "OE2" Residue "4 ARG 765": "NH1" <-> "NH2" Residue "5 ARG 39": "NH1" <-> "NH2" Residue "5 ARG 56": "NH1" <-> "NH2" Residue "5 ARG 62": "NH1" <-> "NH2" Residue "5 GLU 68": "OE1" <-> "OE2" Residue "5 GLU 70": "OE1" <-> "OE2" Residue "5 GLU 89": "OE1" <-> "OE2" Residue "5 ARG 99": "NH1" <-> "NH2" Residue "5 ARG 109": "NH1" <-> "NH2" Residue "5 GLU 114": "OE1" <-> "OE2" Residue "5 ARG 162": "NH1" <-> "NH2" Residue "5 GLU 250": "OE1" <-> "OE2" Residue "5 ARG 251": "NH1" <-> "NH2" Residue "5 ARG 267": "NH1" <-> "NH2" Residue "5 ARG 291": "NH1" <-> "NH2" Residue "5 ARG 307": "NH1" <-> "NH2" Residue "5 ARG 320": "NH1" <-> "NH2" Residue "5 ARG 321": "NH1" <-> "NH2" Residue "5 GLU 330": "OE1" <-> "OE2" Residue "5 ARG 331": "NH1" <-> "NH2" Residue "5 ARG 344": "NH1" <-> "NH2" Residue "5 ARG 359": "NH1" <-> "NH2" Residue "5 ARG 361": "NH1" <-> "NH2" Residue "5 ARG 368": "NH1" <-> "NH2" Residue "5 GLU 392": "OE1" <-> "OE2" Residue "5 ARG 422": "NH1" <-> "NH2" Residue "5 GLU 499": "OE1" <-> "OE2" Residue "5 ARG 584": "NH1" <-> "NH2" Residue "5 ARG 589": "NH1" <-> "NH2" Residue "5 GLU 596": "OE1" <-> "OE2" Residue "5 ARG 602": "NH1" <-> "NH2" Residue "5 GLU 620": "OE1" <-> "OE2" Residue "5 ARG 626": "NH1" <-> "NH2" Residue "6 ARG 20": "NH1" <-> "NH2" Residue "6 ARG 42": "NH1" <-> "NH2" Residue "6 ARG 52": "NH1" <-> "NH2" Residue "6 ARG 95": "NH1" <-> "NH2" Residue "6 ARG 114": "NH1" <-> "NH2" Residue "6 ARG 118": "NH1" <-> "NH2" Residue "6 ARG 130": "NH1" <-> "NH2" Residue "6 ARG 160": "NH1" <-> "NH2" Residue "6 ARG 175": "NH1" <-> "NH2" Residue "6 ARG 182": "NH1" <-> "NH2" Residue "6 ARG 184": "NH1" <-> "NH2" Residue "6 GLU 190": "OE1" <-> "OE2" Residue "6 ARG 201": "NH1" <-> "NH2" Residue "6 GLU 204": "OE1" <-> "OE2" Residue "6 ARG 211": "NH1" <-> "NH2" Residue "6 ARG 216": "NH1" <-> "NH2" Residue "6 GLU 219": "OE1" <-> "OE2" Residue "6 ARG 223": "NH1" <-> "NH2" Residue "6 ARG 257": "NH1" <-> "NH2" Residue "6 GLU 259": "OE1" <-> "OE2" Residue "6 ARG 287": "NH1" <-> "NH2" Residue "6 ARG 301": "NH1" <-> "NH2" Residue "6 ARG 336": "NH1" <-> "NH2" Residue "6 ARG 358": "NH1" <-> "NH2" Residue "6 ARG 379": "NH1" <-> "NH2" Residue "6 ARG 407": "NH1" <-> "NH2" Residue "6 GLU 430": "OE1" <-> "OE2" Residue "6 GLU 453": "OE1" <-> "OE2" Residue "6 ARG 460": "NH1" <-> "NH2" Residue "6 GLU 467": "OE1" <-> "OE2" Residue "6 ARG 478": "NH1" <-> "NH2" Residue "6 ARG 482": "NH1" <-> "NH2" Residue "6 ARG 504": "NH1" <-> "NH2" Residue "6 ARG 521": "NH1" <-> "NH2" Residue "6 ARG 542": "NH1" <-> "NH2" Residue "6 GLU 556": "OE1" <-> "OE2" Residue "6 ARG 557": "NH1" <-> "NH2" Residue "6 ARG 561": "NH1" <-> "NH2" Residue "6 ARG 594": "NH1" <-> "NH2" Residue "6 ARG 596": "NH1" <-> "NH2" Residue "6 ARG 607": "NH1" <-> "NH2" Residue "6 GLU 614": "OE1" <-> "OE2" Residue "6 ARG 631": "NH1" <-> "NH2" Residue "6 ARG 635": "NH1" <-> "NH2" Residue "6 PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 642": "NH1" <-> "NH2" Residue "7 ARG 3": "NH1" <-> "NH2" Residue "7 ARG 4": "NH1" <-> "NH2" Residue "7 ARG 10": "NH1" <-> "NH2" Residue "7 GLU 11": "OE1" <-> "OE2" Residue "7 GLU 19": "OE1" <-> "OE2" Residue "7 ARG 71": "NH1" <-> "NH2" Residue "7 ARG 72": "NH1" <-> "NH2" Residue "7 ARG 133": "NH1" <-> "NH2" Residue "7 GLU 144": "OE1" <-> "OE2" Residue "7 GLU 151": "OE1" <-> "OE2" Residue "7 ARG 186": "NH1" <-> "NH2" Residue "7 ARG 212": "NH1" <-> "NH2" Residue "7 ARG 219": "NH1" <-> "NH2" Residue "7 GLU 239": "OE1" <-> "OE2" Residue "7 ARG 258": "NH1" <-> "NH2" Residue "7 ARG 302": "NH1" <-> "NH2" Residue "7 ARG 365": "NH1" <-> "NH2" Residue "7 ARG 372": "NH1" <-> "NH2" Residue "7 ARG 396": "NH1" <-> "NH2" Residue "7 ARG 407": "NH1" <-> "NH2" Residue "7 GLU 426": "OE1" <-> "OE2" Residue "7 GLU 446": "OE1" <-> "OE2" Residue "7 ARG 494": "NH1" <-> "NH2" Residue "7 ARG 498": "NH1" <-> "NH2" Residue "7 ARG 499": "NH1" <-> "NH2" Residue "7 ARG 527": "NH1" <-> "NH2" Residue "7 ARG 532": "NH1" <-> "NH2" Residue "7 ARG 550": "NH1" <-> "NH2" Residue "7 ARG 561": "NH1" <-> "NH2" Residue "7 ARG 568": "NH1" <-> "NH2" Residue "7 ARG 590": "NH1" <-> "NH2" Residue "7 ARG 593": "NH1" <-> "NH2" Residue "7 ARG 611": "NH1" <-> "NH2" Residue "7 ARG 618": "NH1" <-> "NH2" Residue "7 ARG 620": "NH1" <-> "NH2" Residue "7 GLU 626": "OE1" <-> "OE2" Residue "7 GLU 632": "OE1" <-> "OE2" Residue "7 ARG 635": "NH1" <-> "NH2" Residue "7 GLU 638": "OE1" <-> "OE2" Residue "A ARG 7": "NH1" <-> "NH2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 60": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 197": "NH1" <-> "NH2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A ARG 481": "NH1" <-> "NH2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 494": "NH1" <-> "NH2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 565": "NH1" <-> "NH2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 20": "OE1" <-> "OE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H GLU 156": "OE1" <-> "OE2" Residue "H GLU 190": "OE1" <-> "OE2" Residue "L GLU 7": "OE1" <-> "OE2" Residue "L GLU 111": "OE1" <-> "OE2" Residue "L GLU 152": "OE1" <-> "OE2" Residue "M GLU 14": "OE1" <-> "OE2" Residue "M GLU 146": "OE1" <-> "OE2" Residue "N GLU 23": "OE1" <-> "OE2" Residue "N GLU 25": "OE1" <-> "OE2" Residue "N GLU 31": "OE1" <-> "OE2" Residue "N GLU 40": "OE1" <-> "OE2" Residue "N PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39710 Number of models: 1 Model: "" Number of chains: 18 Chain: "2" Number of atoms: 4769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4769 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 28, 'TRANS': 574} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "3" Number of atoms: 4551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4551 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 21, 'TRANS': 563} Chain breaks: 8 Chain: "4" Number of atoms: 4863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4863 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 26, 'TRANS': 581} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "5" Number of atoms: 4532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4532 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 551} Chain breaks: 7 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "6" Number of atoms: 4777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4777 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 583} Chain breaks: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "7" Number of atoms: 4923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4923 Classifications: {'peptide': 631} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 606} Unresolved chain links: 4 Chain breaks: 3 Unresolved chain link angles: 16 Unresolved chain link dihedrals: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 527 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "G" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 266 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 4362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4362 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 14, 'TRANS': 527} Chain breaks: 2 Chain: "H" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1583 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 9, 'TRANS': 185} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1395 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 14, 'TRANS': 156} Chain: "M" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1349 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1639 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ILE%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.27, per 1000 atoms: 0.51 Number of scatterers: 39710 At special positions: 0 Unit cell: (208.44, 183.6, 141.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 233 16.00 P 54 15.00 O 7621 8.00 N 6960 7.00 C 24842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS 5 192 " - pdb=" SG CYS 5 202 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 152 " - pdb=" SG CYS 6 179 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 187 " - pdb=" SG CYS 7 211 " distance=2.03 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.69 Conformation dependent library (CDL) restraints added in 7.0 seconds 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9258 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 158 helices and 27 sheets defined 31.1% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.04 Creating SS restraints... Processing helix chain '2' and resid 179 through 185 Processing helix chain '2' and resid 199 through 210 removed outlier: 4.191A pdb=" N ILE 2 204 " --> pdb=" O TYR 2 200 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ARG 2 205 " --> pdb=" O ARG 2 201 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN 2 210 " --> pdb=" O ARG 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 219 through 225 Processing helix chain '2' and resid 237 through 255 removed outlier: 4.095A pdb=" N VAL 2 247 " --> pdb=" O ILE 2 243 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER 2 254 " --> pdb=" O ASP 2 250 " (cutoff:3.500A) Processing helix chain '2' and resid 257 through 259 No H-bonds generated for 'chain '2' and resid 257 through 259' Processing helix chain '2' and resid 284 through 286 No H-bonds generated for 'chain '2' and resid 284 through 286' Processing helix chain '2' and resid 449 through 452 No H-bonds generated for 'chain '2' and resid 449 through 452' Processing helix chain '2' and resid 457 through 464 removed outlier: 3.767A pdb=" N ALA 2 464 " --> pdb=" O ARG 2 461 " (cutoff:3.500A) Processing helix chain '2' and resid 474 through 483 Processing helix chain '2' and resid 517 through 524 removed outlier: 4.154A pdb=" N THR 2 521 " --> pdb=" O PHE 2 517 " (cutoff:3.500A) Processing helix chain '2' and resid 561 through 563 No H-bonds generated for 'chain '2' and resid 561 through 563' Processing helix chain '2' and resid 579 through 582 No H-bonds generated for 'chain '2' and resid 579 through 582' Processing helix chain '2' and resid 588 through 591 No H-bonds generated for 'chain '2' and resid 588 through 591' Processing helix chain '2' and resid 636 through 639 No H-bonds generated for 'chain '2' and resid 636 through 639' Processing helix chain '2' and resid 654 through 668 Processing helix chain '2' and resid 694 through 706 removed outlier: 4.343A pdb=" N ARG 2 698 " --> pdb=" O GLN 2 694 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLN 2 699 " --> pdb=" O ASP 2 695 " (cutoff:3.500A) Processing helix chain '2' and resid 719 through 730 Processing helix chain '2' and resid 742 through 757 removed outlier: 3.781A pdb=" N VAL 2 747 " --> pdb=" O HIS 2 743 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE 2 748 " --> pdb=" O ILE 2 744 " (cutoff:3.500A) Processing helix chain '2' and resid 765 through 781 Processing helix chain '2' and resid 789 through 792 No H-bonds generated for 'chain '2' and resid 789 through 792' Processing helix chain '3' and resid 7 through 19 Processing helix chain '3' and resid 48 through 54 Processing helix chain '3' and resid 56 through 59 No H-bonds generated for 'chain '3' and resid 56 through 59' Processing helix chain '3' and resid 69 through 84 removed outlier: 3.792A pdb=" N THR 3 83 " --> pdb=" O GLU 3 79 " (cutoff:3.500A) Processing helix chain '3' and resid 86 through 88 No H-bonds generated for 'chain '3' and resid 86 through 88' Processing helix chain '3' and resid 202 through 204 No H-bonds generated for 'chain '3' and resid 202 through 204' Processing helix chain '3' and resid 220 through 222 No H-bonds generated for 'chain '3' and resid 220 through 222' Processing helix chain '3' and resid 277 through 286 removed outlier: 4.211A pdb=" N LYS 3 286 " --> pdb=" O LYS 3 282 " (cutoff:3.500A) Processing helix chain '3' and resid 291 through 298 Processing helix chain '3' and resid 309 through 317 removed outlier: 4.122A pdb=" N CYS 3 314 " --> pdb=" O GLN 3 310 " (cutoff:3.500A) Processing helix chain '3' and resid 394 through 396 No H-bonds generated for 'chain '3' and resid 394 through 396' Processing helix chain '3' and resid 414 through 422 Processing helix chain '3' and resid 470 through 473 No H-bonds generated for 'chain '3' and resid 470 through 473' Processing helix chain '3' and resid 489 through 499 Processing helix chain '3' and resid 560 through 564 Processing helix chain '3' and resid 567 through 571 Processing helix chain '3' and resid 581 through 594 Processing helix chain '3' and resid 611 through 622 Processing helix chain '3' and resid 633 through 640 Processing helix chain '4' and resid 161 through 173 Processing helix chain '4' and resid 178 through 181 No H-bonds generated for 'chain '4' and resid 178 through 181' Processing helix chain '4' and resid 195 through 204 Processing helix chain '4' and resid 217 through 219 No H-bonds generated for 'chain '4' and resid 217 through 219' Processing helix chain '4' and resid 223 through 230 Processing helix chain '4' and resid 233 through 251 removed outlier: 3.700A pdb=" N ILE 4 237 " --> pdb=" O PRO 4 233 " (cutoff:3.500A) Proline residue: 4 238 - end of helix removed outlier: 3.608A pdb=" N PHE 4 249 " --> pdb=" O ASN 4 245 " (cutoff:3.500A) Processing helix chain '4' and resid 379 through 381 No H-bonds generated for 'chain '4' and resid 379 through 381' Processing helix chain '4' and resid 445 through 455 removed outlier: 3.538A pdb=" N GLN 4 452 " --> pdb=" O GLU 4 449 " (cutoff:3.500A) Processing helix chain '4' and resid 458 through 467 removed outlier: 3.510A pdb=" N ARG 4 463 " --> pdb=" O ILE 4 460 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU 4 464 " --> pdb=" O TYR 4 461 " (cutoff:3.500A) Processing helix chain '4' and resid 476 through 486 removed outlier: 3.830A pdb=" N LYS 4 480 " --> pdb=" O ASP 4 476 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY 4 481 " --> pdb=" O ASP 4 477 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU 4 484 " --> pdb=" O LYS 4 480 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN 4 485 " --> pdb=" O GLY 4 481 " (cutoff:3.500A) Processing helix chain '4' and resid 518 through 526 Processing helix chain '4' and resid 565 through 568 Processing helix chain '4' and resid 589 through 595 Processing helix chain '4' and resid 658 through 674 removed outlier: 3.713A pdb=" N LYS 4 662 " --> pdb=" O ILE 4 659 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU 4 664 " --> pdb=" O ASP 4 661 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER 4 666 " --> pdb=" O ARG 4 663 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LEU 4 668 " --> pdb=" O ALA 4 665 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU 4 671 " --> pdb=" O LEU 4 668 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL 4 674 " --> pdb=" O LEU 4 671 " (cutoff:3.500A) Processing helix chain '4' and resid 688 through 697 removed outlier: 4.119A pdb=" N TYR 4 692 " --> pdb=" O VAL 4 688 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE 4 693 " --> pdb=" O LEU 4 689 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA 4 696 " --> pdb=" O TYR 4 692 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG 4 697 " --> pdb=" O ILE 4 693 " (cutoff:3.500A) Processing helix chain '4' and resid 710 through 720 removed outlier: 6.375A pdb=" N VAL 4 717 " --> pdb=" O ILE 4 713 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASP 4 718 " --> pdb=" O GLN 4 714 " (cutoff:3.500A) Processing helix chain '4' and resid 735 through 748 Processing helix chain '4' and resid 758 through 768 removed outlier: 3.578A pdb=" N GLU 4 762 " --> pdb=" O LEU 4 758 " (cutoff:3.500A) Processing helix chain '5' and resid 27 through 40 removed outlier: 3.824A pdb=" N LYS 5 32 " --> pdb=" O GLN 5 28 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N TYR 5 34 " --> pdb=" O VAL 5 30 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LYS 5 35 " --> pdb=" O LYS 5 31 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE 5 38 " --> pdb=" O TYR 5 34 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG 5 39 " --> pdb=" O LYS 5 35 " (cutoff:3.500A) Processing helix chain '5' and resid 51 through 60 removed outlier: 4.404A pdb=" N ASN 5 60 " --> pdb=" O ARG 5 56 " (cutoff:3.500A) Processing helix chain '5' and resid 72 through 74 No H-bonds generated for 'chain '5' and resid 72 through 74' Processing helix chain '5' and resid 79 through 83 Processing helix chain '5' and resid 87 through 106 removed outlier: 4.260A pdb=" N GLU 5 92 " --> pdb=" O THR 5 88 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU 5 95 " --> pdb=" O LEU 5 91 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU 5 104 " --> pdb=" O GLU 5 100 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE 5 105 " --> pdb=" O VAL 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 132 through 134 No H-bonds generated for 'chain '5' and resid 132 through 134' Processing helix chain '5' and resid 313 through 323 Processing helix chain '5' and resid 329 through 334 removed outlier: 4.281A pdb=" N GLN 5 334 " --> pdb=" O GLU 5 330 " (cutoff:3.500A) Processing helix chain '5' and resid 352 through 355 No H-bonds generated for 'chain '5' and resid 352 through 355' Processing helix chain '5' and resid 384 through 393 Processing helix chain '5' and resid 449 through 451 No H-bonds generated for 'chain '5' and resid 449 through 451' Processing helix chain '5' and resid 453 through 461 removed outlier: 3.788A pdb=" N MET 5 459 " --> pdb=" O ILE 5 455 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU 5 460 " --> pdb=" O HIS 5 456 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN 5 461 " --> pdb=" O GLU 5 457 " (cutoff:3.500A) Processing helix chain '5' and resid 490 through 495 removed outlier: 4.149A pdb=" N ASP 5 493 " --> pdb=" O GLY 5 490 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR 5 495 " --> pdb=" O TRP 5 492 " (cutoff:3.500A) Processing helix chain '5' and resid 523 through 536 removed outlier: 3.627A pdb=" N ILE 5 533 " --> pdb=" O LEU 5 529 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN 5 535 " --> pdb=" O LYS 5 531 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL 5 536 " --> pdb=" O HIS 5 532 " (cutoff:3.500A) Processing helix chain '5' and resid 555 through 567 removed outlier: 4.213A pdb=" N THR 5 567 " --> pdb=" O HIS 5 563 " (cutoff:3.500A) Processing helix chain '5' and resid 576 through 597 removed outlier: 3.921A pdb=" N LYS 5 580 " --> pdb=" O ALA 5 576 " (cutoff:3.500A) Processing helix chain '5' and resid 609 through 626 removed outlier: 4.404A pdb=" N ARG 5 617 " --> pdb=" O GLU 5 613 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE 5 618 " --> pdb=" O ALA 5 614 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER 5 619 " --> pdb=" O VAL 5 615 " (cutoff:3.500A) Processing helix chain '5' and resid 635 through 649 removed outlier: 4.109A pdb=" N GLU 5 638 " --> pdb=" O HIS 5 635 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN 5 644 " --> pdb=" O ARG 5 641 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU 5 648 " --> pdb=" O VAL 5 645 " (cutoff:3.500A) Processing helix chain '6' and resid 14 through 30 removed outlier: 3.546A pdb=" N VAL 6 17 " --> pdb=" O LYS 6 14 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN 6 22 " --> pdb=" O ILE 6 19 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU 6 30 " --> pdb=" O ASP 6 27 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 50 removed outlier: 4.379A pdb=" N SER 6 49 " --> pdb=" O ALA 6 45 " (cutoff:3.500A) Proline residue: 6 50 - end of helix Processing helix chain '6' and resid 60 through 64 Processing helix chain '6' and resid 70 through 73 No H-bonds generated for 'chain '6' and resid 70 through 73' Processing helix chain '6' and resid 77 through 94 Proline residue: 6 82 - end of helix removed outlier: 3.705A pdb=" N CYS 6 85 " --> pdb=" O TYR 6 81 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN 6 86 " --> pdb=" O PRO 6 82 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP 6 94 " --> pdb=" O ASN 6 90 " (cutoff:3.500A) Processing helix chain '6' and resid 325 through 332 removed outlier: 5.066A pdb=" N TYR 6 330 " --> pdb=" O HIS 6 327 " (cutoff:3.500A) Processing helix chain '6' and resid 338 through 345 removed outlier: 3.773A pdb=" N SER 6 345 " --> pdb=" O ASN 6 341 " (cutoff:3.500A) Processing helix chain '6' and resid 360 through 364 Processing helix chain '6' and resid 396 through 399 No H-bonds generated for 'chain '6' and resid 396 through 399' Processing helix chain '6' and resid 401 through 404 No H-bonds generated for 'chain '6' and resid 401 through 404' Processing helix chain '6' and resid 441 through 443 No H-bonds generated for 'chain '6' and resid 441 through 443' Processing helix chain '6' and resid 461 through 468 removed outlier: 3.987A pdb=" N GLU 6 467 " --> pdb=" O VAL 6 463 " (cutoff:3.500A) Processing helix chain '6' and resid 508 through 512 Processing helix chain '6' and resid 517 through 521 Processing helix chain '6' and resid 534 through 546 removed outlier: 3.936A pdb=" N ASP 6 546 " --> pdb=" O ARG 6 542 " (cutoff:3.500A) Processing helix chain '6' and resid 561 through 571 Processing helix chain '6' and resid 581 through 596 removed outlier: 5.777A pdb=" N VAL 6 587 " --> pdb=" O GLY 6 583 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLU 6 588 " --> pdb=" O HIS 6 584 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN 6 589 " --> pdb=" O MET 6 585 " (cutoff:3.500A) Processing helix chain '6' and resid 611 through 625 removed outlier: 3.542A pdb=" N ILE 6 617 " --> pdb=" O LEU 6 613 " (cutoff:3.500A) Processing helix chain '6' and resid 636 through 651 Processing helix chain '7' and resid 8 through 18 Processing helix chain '7' and resid 32 through 41 Processing helix chain '7' and resid 52 through 58 Processing helix chain '7' and resid 65 through 69 removed outlier: 3.987A pdb=" N ASN 7 69 " --> pdb=" O ALA 7 65 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 65 through 69' Processing helix chain '7' and resid 73 through 82 Processing helix chain '7' and resid 98 through 107 Processing helix chain '7' and resid 224 through 226 No H-bonds generated for 'chain '7' and resid 224 through 226' Processing helix chain '7' and resid 321 through 327 removed outlier: 4.344A pdb=" N GLU 7 325 " --> pdb=" O PRO 7 321 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N GLU 7 326 " --> pdb=" O GLU 7 322 " (cutoff:3.500A) Processing helix chain '7' and resid 334 through 337 No H-bonds generated for 'chain '7' and resid 334 through 337' Processing helix chain '7' and resid 348 through 359 removed outlier: 3.636A pdb=" N LYS 7 352 " --> pdb=" O LEU 7 348 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA 7 353 " --> pdb=" O ASP 7 349 " (cutoff:3.500A) Processing helix chain '7' and resid 366 through 368 No H-bonds generated for 'chain '7' and resid 366 through 368' Processing helix chain '7' and resid 387 through 397 removed outlier: 3.896A pdb=" N LEU 7 391 " --> pdb=" O LYS 7 387 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG 7 396 " --> pdb=" O GLY 7 392 " (cutoff:3.500A) Processing helix chain '7' and resid 411 through 414 No H-bonds generated for 'chain '7' and resid 411 through 414' Processing helix chain '7' and resid 433 through 436 No H-bonds generated for 'chain '7' and resid 433 through 436' Processing helix chain '7' and resid 453 through 459 Processing helix chain '7' and resid 509 through 514 Processing helix chain '7' and resid 530 through 542 removed outlier: 4.006A pdb=" N TYR 7 539 " --> pdb=" O LYS 7 535 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL 7 540 " --> pdb=" O HIS 7 536 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N HIS 7 541 " --> pdb=" O ILE 7 537 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER 7 542 " --> pdb=" O THR 7 538 " (cutoff:3.500A) Processing helix chain '7' and resid 556 through 568 removed outlier: 3.709A pdb=" N ARG 7 561 " --> pdb=" O ASN 7 557 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN 7 564 " --> pdb=" O ARG 7 560 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N CYS 7 566 " --> pdb=" O TYR 7 562 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS 7 567 " --> pdb=" O ILE 7 563 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ARG 7 568 " --> pdb=" O ASN 7 564 " (cutoff:3.500A) Processing helix chain '7' and resid 575 through 591 removed outlier: 3.697A pdb=" N ASP 7 579 " --> pdb=" O ASP 7 575 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TYR 7 580 " --> pdb=" O GLU 7 576 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL 7 582 " --> pdb=" O THR 7 578 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY 7 583 " --> pdb=" O ASP 7 579 " (cutoff:3.500A) Processing helix chain '7' and resid 603 through 618 removed outlier: 4.050A pdb=" N LEU 7 606 " --> pdb=" O ALA 7 603 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE 7 609 " --> pdb=" O LEU 7 606 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU 7 610 " --> pdb=" O LEU 7 607 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU 7 612 " --> pdb=" O ILE 7 609 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER 7 613 " --> pdb=" O LEU 7 610 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR 7 614 " --> pdb=" O ARG 7 611 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU 7 616 " --> pdb=" O SER 7 613 " (cutoff:3.500A) Processing helix chain '7' and resid 629 through 640 removed outlier: 4.324A pdb=" N ALA 7 633 " --> pdb=" O ASP 7 629 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG 7 635 " --> pdb=" O ALA 7 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 13 No H-bonds generated for 'chain 'A' and resid 11 through 13' Processing helix chain 'A' and resid 27 through 40 removed outlier: 4.019A pdb=" N ILE A 35 " --> pdb=" O CYS A 31 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 64 Processing helix chain 'A' and resid 83 through 86 No H-bonds generated for 'chain 'A' and resid 83 through 86' Processing helix chain 'A' and resid 184 through 200 removed outlier: 4.838A pdb=" N ARG A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 225 removed outlier: 3.917A pdb=" N LYS A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 removed outlier: 4.355A pdb=" N GLN A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 removed outlier: 4.740A pdb=" N GLU A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLN A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 318 through 331 removed outlier: 3.766A pdb=" N LYS A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 347 through 357 removed outlier: 5.818A pdb=" N PHE A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER A 355 " --> pdb=" O LYS A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 393 No H-bonds generated for 'chain 'A' and resid 390 through 393' Processing helix chain 'A' and resid 405 through 413 Processing helix chain 'A' and resid 423 through 447 removed outlier: 3.901A pdb=" N ALA A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE A 440 " --> pdb=" O HIS A 436 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 489 removed outlier: 3.707A pdb=" N PHE A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG A 485 " --> pdb=" O ARG A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 541 Processing helix chain 'A' and resid 564 through 569 Processing helix chain 'H' and resid 11 through 19 removed outlier: 4.280A pdb=" N LEU H 16 " --> pdb=" O PHE H 13 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU H 18 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 39 Processing helix chain 'H' and resid 41 through 43 No H-bonds generated for 'chain 'H' and resid 41 through 43' Processing helix chain 'H' and resid 45 through 48 No H-bonds generated for 'chain 'H' and resid 45 through 48' Processing helix chain 'H' and resid 61 through 97 Proline residue: H 65 - end of helix removed outlier: 5.021A pdb=" N GLU H 87 " --> pdb=" O TYR H 84 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG H 91 " --> pdb=" O ARG H 88 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE H 92 " --> pdb=" O CYS H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 132 removed outlier: 3.538A pdb=" N VAL H 116 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE H 119 " --> pdb=" O VAL H 116 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN H 120 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER H 132 " --> pdb=" O TYR H 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 12 removed outlier: 5.829A pdb=" N LYS L 12 " --> pdb=" O PHE L 8 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 53 Processing helix chain 'L' and resid 70 through 79 removed outlier: 5.236A pdb=" N LYS L 75 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU L 76 " --> pdb=" O GLU L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 100 removed outlier: 3.815A pdb=" N ALA L 96 " --> pdb=" O TYR L 92 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN L 97 " --> pdb=" O MET L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 105 No H-bonds generated for 'chain 'L' and resid 103 through 105' Processing helix chain 'L' and resid 112 through 130 removed outlier: 3.984A pdb=" N ILE L 123 " --> pdb=" O ASP L 119 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 153 through 155 No H-bonds generated for 'chain 'L' and resid 153 through 155' Processing helix chain 'L' and resid 160 through 170 removed outlier: 5.057A pdb=" N HIS L 166 " --> pdb=" O TYR L 162 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TYR L 170 " --> pdb=" O HIS L 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 61 removed outlier: 3.801A pdb=" N GLU M 61 " --> pdb=" O TYR M 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 58 through 61' Processing helix chain 'M' and resid 79 through 87 Processing helix chain 'M' and resid 105 through 112 Proline residue: M 110 - end of helix Processing helix chain 'M' and resid 117 through 131 removed outlier: 3.568A pdb=" N ARG M 128 " --> pdb=" O THR M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 171 removed outlier: 3.675A pdb=" N GLU M 169 " --> pdb=" O SER M 165 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 50 removed outlier: 4.048A pdb=" N ILE N 42 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR N 44 " --> pdb=" O GLU N 40 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ALA N 45 " --> pdb=" O ILE N 41 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU N 49 " --> pdb=" O ALA N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 79 removed outlier: 3.641A pdb=" N VAL N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER N 68 " --> pdb=" O GLU N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 114 Processing helix chain 'N' and resid 119 through 125 Processing helix chain 'N' and resid 135 through 154 removed outlier: 3.942A pdb=" N ASP N 149 " --> pdb=" O ALA N 145 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS N 154 " --> pdb=" O GLU N 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 220 through 222 No H-bonds generated for 'chain 'N' and resid 220 through 222' Processing sheet with id= A, first strand: chain '2' and resid 215 through 217 Processing sheet with id= B, first strand: chain '2' and resid 304 through 307 removed outlier: 3.695A pdb=" N ARG 2 356 " --> pdb=" O GLN 2 306 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '2' and resid 359 through 364 removed outlier: 3.830A pdb=" N GLN 2 359 " --> pdb=" O LEU 2 383 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU 2 383 " --> pdb=" O GLN 2 359 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 568 through 571 removed outlier: 6.531A pdb=" N THR 2 610 " --> pdb=" O CYS 2 569 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE 2 571 " --> pdb=" O THR 2 610 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE 2 612 " --> pdb=" O ILE 2 571 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain '2' and resid 593 through 595 removed outlier: 3.894A pdb=" N LEU 2 605 " --> pdb=" O ILE 2 594 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 197 through 199 removed outlier: 4.115A pdb=" N THR 3 197 " --> pdb=" O THR 3 129 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR 3 129 " --> pdb=" O THR 3 197 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN 3 199 " --> pdb=" O ILE 3 127 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL 3 235 " --> pdb=" O ASN 3 261 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN 3 261 " --> pdb=" O VAL 3 235 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 134 through 136 removed outlier: 3.516A pdb=" N ARG 3 135 " --> pdb=" O HIS 3 193 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLN 3 194 " --> pdb=" O CYS 3 218 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '3' and resid 237 through 239 Processing sheet with id= I, first strand: chain '4' and resid 304 through 306 removed outlier: 3.586A pdb=" N ALA 4 305 " --> pdb=" O VAL 4 318 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL 4 318 " --> pdb=" O ALA 4 305 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain '4' and resid 355 through 357 Processing sheet with id= K, first strand: chain '4' and resid 392 through 394 removed outlier: 3.870A pdb=" N THR 4 392 " --> pdb=" O ARG 4 425 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG 4 425 " --> pdb=" O THR 4 392 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS 4 423 " --> pdb=" O THR 4 394 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '4' and resid 397 through 400 Processing sheet with id= M, first strand: chain '4' and resid 509 through 511 removed outlier: 4.088A pdb=" N CYS 4 511 " --> pdb=" O PHE 4 650 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '4' and resid 550 through 552 removed outlier: 4.092A pdb=" N THR 4 550 " --> pdb=" O VAL 4 559 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL 4 559 " --> pdb=" O THR 4 550 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP 4 552 " --> pdb=" O GLN 4 557 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '4' and resid 599 through 601 Processing sheet with id= P, first strand: chain '5' and resid 146 through 149 removed outlier: 3.733A pdb=" N ILE 5 260 " --> pdb=" O ILE 5 146 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '5' and resid 223 through 225 Processing sheet with id= R, first strand: chain '5' and resid 262 through 264 removed outlier: 3.766A pdb=" N ILE 5 263 " --> pdb=" O ARG 5 291 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG 5 291 " --> pdb=" O ILE 5 263 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain '5' and resid 398 through 401 removed outlier: 7.052A pdb=" N VAL 5 438 " --> pdb=" O VAL 5 399 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N THR 5 401 " --> pdb=" O VAL 5 438 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N CYS 5 440 " --> pdb=" O THR 5 401 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain '6' and resid 198 through 202 removed outlier: 3.768A pdb=" N GLN 6 198 " --> pdb=" O LEU 6 222 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU 6 222 " --> pdb=" O GLN 6 198 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE 6 220 " --> pdb=" O ILE 6 200 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '7' and resid 162 through 164 removed outlier: 6.256A pdb=" N VAL 7 276 " --> pdb=" O ALA 7 300 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA 7 300 " --> pdb=" O VAL 7 276 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU 7 278 " --> pdb=" O LEU 7 298 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LEU 7 298 " --> pdb=" O LEU 7 278 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain '7' and resid 166 through 168 Processing sheet with id= W, first strand: chain '7' and resid 174 through 176 Processing sheet with id= X, first strand: chain '7' and resid 401 through 404 removed outlier: 7.825A pdb=" N VAL 7 441 " --> pdb=" O GLN 7 402 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N THR 7 404 " --> pdb=" O VAL 7 441 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N CYS 7 443 " --> pdb=" O THR 7 404 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER 7 483 " --> pdb=" O CYS 7 442 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ILE 7 444 " --> pdb=" O SER 7 483 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU 7 485 " --> pdb=" O ILE 7 444 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'A' and resid 18 through 20 removed outlier: 6.793A pdb=" N TYR A 71 " --> pdb=" O ILE A 19 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'A' and resid 284 through 289 removed outlier: 3.960A pdb=" N THR A 284 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 375 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 14 through 18 827 hydrogen bonds defined for protein. 2067 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.72 Time building geometry restraints manager: 16.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10412 1.33 - 1.46: 8327 1.46 - 1.58: 21255 1.58 - 1.70: 104 1.70 - 1.83: 368 Bond restraints: 40466 Sorted by residual: bond pdb=" C4 ATP 2 902 " pdb=" C5 ATP 2 902 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 6.99e+01 bond pdb=" C4 ATP 3 901 " pdb=" C5 ATP 3 901 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.93e+01 bond pdb=" C4 ATP 2 901 " pdb=" C5 ATP 2 901 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.61e+01 bond pdb=" C5 ATP 3 901 " pdb=" C6 ATP 3 901 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.69e+01 bond pdb=" C5 ATP 2 902 " pdb=" C6 ATP 2 902 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.51e+01 ... (remaining 40461 not shown) Histogram of bond angle deviations from ideal: 97.73 - 106.53: 1465 106.53 - 115.33: 24218 115.33 - 124.13: 27860 124.13 - 132.93: 1239 132.93 - 141.73: 40 Bond angle restraints: 54822 Sorted by residual: angle pdb=" PB ATP 2 901 " pdb=" O3B ATP 2 901 " pdb=" PG ATP 2 901 " ideal model delta sigma weight residual 139.87 115.22 24.65 1.00e+00 1.00e+00 6.08e+02 angle pdb=" PA ATP 2 902 " pdb=" O3A ATP 2 902 " pdb=" PB ATP 2 902 " ideal model delta sigma weight residual 136.83 112.42 24.41 1.00e+00 1.00e+00 5.96e+02 angle pdb=" PB ATP 2 902 " pdb=" O3B ATP 2 902 " pdb=" PG ATP 2 902 " ideal model delta sigma weight residual 139.87 116.50 23.37 1.00e+00 1.00e+00 5.46e+02 angle pdb=" PA ATP 2 901 " pdb=" O3A ATP 2 901 " pdb=" PB ATP 2 901 " ideal model delta sigma weight residual 136.83 115.56 21.27 1.00e+00 1.00e+00 4.52e+02 angle pdb=" PB ATP 3 901 " pdb=" O3B ATP 3 901 " pdb=" PG ATP 3 901 " ideal model delta sigma weight residual 139.87 119.39 20.48 1.00e+00 1.00e+00 4.19e+02 ... (remaining 54817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.68: 22799 26.68 - 53.35: 1722 53.35 - 80.03: 204 80.03 - 106.71: 44 106.71 - 133.38: 4 Dihedral angle restraints: 24773 sinusoidal: 10523 harmonic: 14250 Sorted by residual: dihedral pdb=" CD ARG 4 734 " pdb=" NE ARG 4 734 " pdb=" CZ ARG 4 734 " pdb=" NH1 ARG 4 734 " ideal model delta sinusoidal sigma weight residual 0.00 110.84 -110.84 1 1.00e+01 1.00e-02 1.30e+02 dihedral pdb=" CA THR 6 609 " pdb=" C THR 6 609 " pdb=" N VAL 6 610 " pdb=" CA VAL 6 610 " ideal model delta harmonic sigma weight residual -180.00 -126.77 -53.23 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CA THR A 490 " pdb=" C THR A 490 " pdb=" N SER A 491 " pdb=" CA SER A 491 " ideal model delta harmonic sigma weight residual 180.00 134.32 45.68 0 5.00e+00 4.00e-02 8.35e+01 ... (remaining 24770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.428: 6159 0.428 - 0.856: 9 0.856 - 1.284: 0 1.284 - 1.712: 15 1.712 - 2.140: 10 Chirality restraints: 6193 Sorted by residual: chirality pdb=" CB THR 6 609 " pdb=" CA THR 6 609 " pdb=" OG1 THR 6 609 " pdb=" CG2 THR 6 609 " both_signs ideal model delta sigma weight residual False 2.55 0.41 2.14 2.00e-01 2.50e+01 1.14e+02 chirality pdb=" CB ILE 3 484 " pdb=" CA ILE 3 484 " pdb=" CG1 ILE 3 484 " pdb=" CG2 ILE 3 484 " both_signs ideal model delta sigma weight residual False 2.64 0.72 1.93 2.00e-01 2.50e+01 9.28e+01 chirality pdb=" CG LEU 5 529 " pdb=" CB LEU 5 529 " pdb=" CD1 LEU 5 529 " pdb=" CD2 LEU 5 529 " both_signs ideal model delta sigma weight residual False -2.59 -0.67 -1.92 2.00e-01 2.50e+01 9.22e+01 ... (remaining 6190 not shown) Planarity restraints: 6950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 7 604 " -0.381 9.50e-02 1.11e+02 1.98e-01 1.42e+02 pdb=" NE ARG 7 604 " 0.092 2.00e-02 2.50e+03 pdb=" CZ ARG 7 604 " -0.188 2.00e-02 2.50e+03 pdb=" NH1 ARG 7 604 " 0.065 2.00e-02 2.50e+03 pdb=" NH2 ARG 7 604 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 4 734 " -0.530 9.50e-02 1.11e+02 2.55e-01 1.41e+02 pdb=" NE ARG 4 734 " 0.098 2.00e-02 2.50e+03 pdb=" CZ ARG 4 734 " -0.172 2.00e-02 2.50e+03 pdb=" NH1 ARG 4 734 " 0.049 2.00e-02 2.50e+03 pdb=" NH2 ARG 4 734 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 2 641 " 0.319 9.50e-02 1.11e+02 1.72e-01 1.29e+02 pdb=" NE ARG 2 641 " -0.086 2.00e-02 2.50e+03 pdb=" CZ ARG 2 641 " 0.183 2.00e-02 2.50e+03 pdb=" NH1 ARG 2 641 " -0.064 2.00e-02 2.50e+03 pdb=" NH2 ARG 2 641 " -0.046 2.00e-02 2.50e+03 ... (remaining 6947 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 5 1.94 - 2.68: 1678 2.68 - 3.42: 58499 3.42 - 4.16: 90909 4.16 - 4.90: 152251 Nonbonded interactions: 303342 Sorted by model distance: nonbonded pdb=" O HIS 6 466 " pdb=" NH2 ARG 6 521 " model vdw 1.198 2.520 nonbonded pdb=" OD2 ASP 7 382 " pdb=" CE LYS 7 387 " model vdw 1.537 3.440 nonbonded pdb=" OD2 ASP 7 382 " pdb=" NZ LYS 7 387 " model vdw 1.621 2.520 nonbonded pdb=" CG ASP 7 382 " pdb=" CE LYS 7 387 " model vdw 1.829 3.670 nonbonded pdb=" CD1 LEU 2 541 " pdb=" CA ALA 6 479 " model vdw 1.931 3.890 ... (remaining 303337 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=1.00 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: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 13.890 Check model and map are aligned: 0.610 Set scattering table: 0.370 Process input model: 100.880 Find NCS groups from input model: 2.550 Set up NCS constraints: 0.180 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4826 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 : 0.007 0.116 40466 Z= 0.437 Angle : 1.287 24.651 54822 Z= 0.719 Chirality : 0.126 2.140 6193 Planarity : 0.010 0.385 6950 Dihedral : 18.381 133.383 15506 Min Nonbonded Distance : 1.198 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.31 % Allowed : 18.92 % Favored : 80.77 % Rotamer: Outliers : 6.37 % Allowed : 12.88 % Favored : 80.74 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.80 % 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: -5.55 (0.09), residues: 4789 helix: -3.21 (0.09), residues: 1515 sheet: -4.49 (0.17), residues: 370 loop : -4.07 (0.10), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP M 170 HIS 0.037 0.003 HIS M 98 PHE 0.082 0.004 PHE 5 41 TYR 0.055 0.003 TYR 3 454 ARG 0.193 0.003 ARG 7 604 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1055 time to evaluate : 4.568 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 TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 250 ASP cc_start: 0.7210 (t0) cc_final: 0.6646 (t0) REVERT: 2 271 SER cc_start: 0.6369 (OUTLIER) cc_final: 0.5884 (m) REVERT: 2 281 THR cc_start: 0.6576 (p) cc_final: 0.6202 (m) REVERT: 2 314 CYS cc_start: -0.2554 (OUTLIER) cc_final: -0.3421 (t) REVERT: 2 350 MET cc_start: 0.3764 (mmt) cc_final: 0.2237 (ptp) REVERT: 2 355 TYR cc_start: 0.6305 (m-80) cc_final: 0.5782 (m-80) REVERT: 2 643 ASP cc_start: 0.5992 (OUTLIER) cc_final: 0.5522 (m-30) REVERT: 2 657 ASP cc_start: 0.6133 (m-30) cc_final: 0.5815 (m-30) REVERT: 2 723 MET cc_start: 0.3865 (mmt) cc_final: 0.3215 (mmp) REVERT: 2 761 GLU cc_start: 0.6628 (tt0) cc_final: 0.6351 (tm-30) REVERT: 3 8 PHE cc_start: 0.5864 (p90) cc_final: 0.5166 (m-80) REVERT: 3 13 GLN cc_start: 0.7535 (mt0) cc_final: 0.7334 (mt0) REVERT: 3 118 LEU cc_start: 0.6565 (tp) cc_final: 0.6273 (tp) REVERT: 3 124 VAL cc_start: 0.5017 (OUTLIER) cc_final: 0.4768 (m) REVERT: 3 214 VAL cc_start: 0.1192 (OUTLIER) cc_final: 0.0638 (m) REVERT: 3 234 ILE cc_start: 0.6395 (tp) cc_final: 0.6062 (tp) REVERT: 3 278 ILE cc_start: 0.6712 (tt) cc_final: 0.6414 (mt) REVERT: 3 402 CYS cc_start: 0.5983 (OUTLIER) cc_final: 0.5666 (p) REVERT: 3 461 MET cc_start: 0.6914 (tpp) cc_final: 0.6631 (tpt) REVERT: 3 462 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: 3 610 ARG cc_start: 0.6856 (mtp180) cc_final: 0.6180 (mtt180) REVERT: 4 200 LEU cc_start: 0.4764 (OUTLIER) cc_final: 0.2997 (mt) REVERT: 4 201 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7566 (mt-10) REVERT: 4 242 MET cc_start: 0.3188 (tpp) cc_final: 0.2241 (ptt) REVERT: 4 483 LEU cc_start: 0.6828 (mp) cc_final: 0.6530 (mp) REVERT: 4 551 LYS cc_start: 0.5421 (tptp) cc_final: 0.4171 (mtpt) REVERT: 4 653 LEU cc_start: 0.4647 (OUTLIER) cc_final: 0.4335 (tt) REVERT: 4 693 ILE cc_start: 0.8224 (mt) cc_final: 0.7034 (mt) REVERT: 5 120 GLN cc_start: 0.4728 (pt0) cc_final: 0.4381 (tt0) REVERT: 5 435 ASP cc_start: 0.6414 (p0) cc_final: 0.6144 (p0) REVERT: 5 620 GLU cc_start: 0.5878 (OUTLIER) cc_final: 0.5390 (mm-30) REVERT: 6 55 LEU cc_start: 0.5262 (OUTLIER) cc_final: 0.4941 (tt) REVERT: 6 80 ILE cc_start: 0.6650 (mt) cc_final: 0.6267 (mt) REVERT: 6 113 THR cc_start: 0.6189 (m) cc_final: 0.5877 (m) REVERT: 6 114 ARG cc_start: 0.5892 (mpt-90) cc_final: 0.5241 (tmt170) REVERT: 6 151 MET cc_start: 0.1530 (ppp) cc_final: 0.0495 (tmm) REVERT: 6 194 PHE cc_start: 0.5209 (OUTLIER) cc_final: 0.3923 (m-80) REVERT: 6 332 MET cc_start: 0.7283 (mtt) cc_final: 0.7072 (mtp) REVERT: 6 365 PHE cc_start: 0.5565 (OUTLIER) cc_final: 0.5309 (t80) REVERT: 6 519 MET cc_start: 0.4377 (ptt) cc_final: 0.3997 (ptp) REVERT: 6 533 ASN cc_start: 0.7394 (OUTLIER) cc_final: 0.6701 (p0) REVERT: 6 632 VAL cc_start: 0.1905 (OUTLIER) cc_final: 0.1591 (m) REVERT: 7 160 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6340 (tp) REVERT: 7 302 ARG cc_start: 0.5511 (tpp-160) cc_final: 0.5142 (tpp-160) REVERT: 7 308 LYS cc_start: 0.2352 (OUTLIER) cc_final: 0.1829 (mttm) REVERT: 7 365 ARG cc_start: 0.5236 (mmm-85) cc_final: 0.2576 (ptp90) REVERT: 7 402 GLN cc_start: 0.5018 (mm110) cc_final: 0.4501 (mt0) REVERT: 7 450 MET cc_start: 0.5584 (tpt) cc_final: 0.5309 (tpt) REVERT: 7 468 SER cc_start: 0.6276 (m) cc_final: 0.5984 (p) REVERT: 7 489 ASN cc_start: 0.6720 (OUTLIER) cc_final: 0.6505 (p0) REVERT: 7 528 ASP cc_start: 0.6757 (m-30) cc_final: 0.6549 (m-30) REVERT: 7 627 LYS cc_start: 0.6554 (tptp) cc_final: 0.6335 (tttt) REVERT: A 45 MET cc_start: 0.2991 (mpp) cc_final: 0.2171 (mtt) REVERT: A 83 ILE cc_start: 0.4913 (pt) cc_final: 0.4712 (pt) REVERT: A 86 LEU cc_start: 0.7884 (tp) cc_final: 0.7297 (mm) REVERT: A 93 VAL cc_start: 0.6680 (t) cc_final: 0.6428 (m) REVERT: A 166 ASP cc_start: 0.0999 (OUTLIER) cc_final: -0.1309 (t0) REVERT: A 258 LEU cc_start: -0.0448 (OUTLIER) cc_final: -0.0999 (pp) REVERT: A 405 THR cc_start: 0.3852 (OUTLIER) cc_final: 0.3520 (p) REVERT: A 564 THR cc_start: 0.5486 (OUTLIER) cc_final: 0.5281 (m) REVERT: H 40 GLU cc_start: 0.7942 (tt0) cc_final: 0.7612 (mm-30) REVERT: H 76 ARG cc_start: 0.2466 (tpt170) cc_final: 0.0564 (ptm-80) REVERT: H 80 CYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6570 (p) REVERT: H 86 TYR cc_start: 0.6247 (OUTLIER) cc_final: 0.4548 (t80) REVERT: H 130 MET cc_start: 0.5076 (mtm) cc_final: 0.4791 (ptp) REVERT: L 8 PHE cc_start: 0.2450 (m-80) cc_final: 0.2118 (m-80) REVERT: L 99 VAL cc_start: 0.3690 (t) cc_final: 0.3429 (t) REVERT: L 109 ARG cc_start: 0.7373 (mtt180) cc_final: 0.6961 (mtp180) REVERT: L 114 ARG cc_start: 0.6136 (OUTLIER) cc_final: 0.3582 (mmt90) REVERT: L 154 HIS cc_start: 0.2369 (p90) cc_final: 0.2052 (p90) REVERT: L 171 GLN cc_start: 0.5772 (OUTLIER) cc_final: 0.5570 (mp10) REVERT: M 56 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6589 (tt) REVERT: N 142 GLN cc_start: 0.4592 (mp-120) cc_final: 0.4283 (mm-40) outliers start: 272 outliers final: 73 residues processed: 1274 average time/residue: 0.5718 time to fit residues: 1140.2596 Evaluate side-chains 750 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 650 time to evaluate : 4.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 258 THR Chi-restraints excluded: chain 2 residue 271 SER Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 424 ILE Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 524 VAL Chi-restraints excluded: chain 2 residue 532 THR Chi-restraints excluded: chain 2 residue 574 PHE Chi-restraints excluded: chain 2 residue 590 GLU Chi-restraints excluded: chain 2 residue 603 THR Chi-restraints excluded: chain 2 residue 610 THR Chi-restraints excluded: chain 2 residue 643 ASP Chi-restraints excluded: chain 2 residue 742 ARG Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 214 VAL Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 402 CYS Chi-restraints excluded: chain 3 residue 462 GLU Chi-restraints excluded: chain 3 residue 478 PHE Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 4 residue 200 LEU Chi-restraints excluded: chain 4 residue 296 SER Chi-restraints excluded: chain 4 residue 316 THR Chi-restraints excluded: chain 4 residue 411 VAL Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 550 THR Chi-restraints excluded: chain 4 residue 605 ILE Chi-restraints excluded: chain 4 residue 613 THR Chi-restraints excluded: chain 4 residue 653 LEU Chi-restraints excluded: chain 5 residue 258 VAL Chi-restraints excluded: chain 5 residue 376 LEU Chi-restraints excluded: chain 5 residue 505 PRO Chi-restraints excluded: chain 5 residue 529 LEU Chi-restraints excluded: chain 5 residue 574 SER Chi-restraints excluded: chain 5 residue 620 GLU Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 55 LEU Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 230 VAL Chi-restraints excluded: chain 6 residue 245 VAL Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 365 PHE Chi-restraints excluded: chain 6 residue 425 VAL Chi-restraints excluded: chain 6 residue 426 VAL Chi-restraints excluded: chain 6 residue 533 ASN Chi-restraints excluded: chain 6 residue 579 SER Chi-restraints excluded: chain 6 residue 609 THR Chi-restraints excluded: chain 6 residue 632 VAL Chi-restraints excluded: chain 6 residue 644 LEU Chi-restraints excluded: chain 7 residue 25 ASP Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain 7 residue 160 LEU Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 173 VAL Chi-restraints excluded: chain 7 residue 198 LEU Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 269 ASP Chi-restraints excluded: chain 7 residue 308 LYS Chi-restraints excluded: chain 7 residue 336 LEU Chi-restraints excluded: chain 7 residue 387 LYS Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 466 THR Chi-restraints excluded: chain 7 residue 484 ILE Chi-restraints excluded: chain 7 residue 489 ASN Chi-restraints excluded: chain 7 residue 546 GLN Chi-restraints excluded: chain 7 residue 558 LEU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 CYS Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 112 CYS Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 114 ARG Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 171 GLN Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 411 optimal weight: 0.8980 chunk 369 optimal weight: 5.9990 chunk 204 optimal weight: 0.3980 chunk 126 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 197 optimal weight: 0.4980 chunk 381 optimal weight: 0.4980 chunk 147 optimal weight: 4.9990 chunk 232 optimal weight: 0.5980 chunk 284 optimal weight: 1.9990 chunk 442 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 289 GLN ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 591 GLN 2 656 GLN 2 694 GLN 2 699 GLN ** 2 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 13 GLN 3 65 ASN ** 3 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 448 ASN 3 495 HIS 3 553 HIS 3 586 ASN 4 182 GLN ** 4 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 501 ASN ** 4 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 570 ASN 4 637 GLN 4 735 GLN 4 746 HIS ** 5 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 90 HIS 5 120 GLN 5 233 GLN ** 5 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 420 GLN ** 5 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 353 ASN 6 400 GLN 6 584 HIS ** 7 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 69 ASN ** 7 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 402 GLN 7 479 ASN 7 496 ASN ** 7 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 453 HIS A 467 HIS H 175 HIS H 181 GLN H 199 HIS ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 ASN N 36 GLN N 117 GLN N 153 HIS N 180 HIS N 214 GLN N 224 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5203 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 40466 Z= 0.252 Angle : 0.847 16.761 54822 Z= 0.426 Chirality : 0.049 0.337 6193 Planarity : 0.007 0.082 6950 Dihedral : 13.551 119.832 6037 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.40 % Favored : 87.60 % Rotamer: Outliers : 4.36 % Allowed : 19.21 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.50 (0.10), residues: 4789 helix: -2.04 (0.12), residues: 1566 sheet: -3.73 (0.18), residues: 490 loop : -3.58 (0.10), residues: 2733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP M 170 HIS 0.011 0.001 HIS 2 586 PHE 0.022 0.002 PHE M 17 TYR 0.030 0.002 TYR 3 454 ARG 0.012 0.001 ARG M 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 775 time to evaluate : 4.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 250 ASP cc_start: 0.7340 (t0) cc_final: 0.6663 (t0) REVERT: 2 255 ILE cc_start: 0.6065 (mt) cc_final: 0.5782 (mt) REVERT: 2 277 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.6084 (pt0) REVERT: 2 314 CYS cc_start: -0.0723 (OUTLIER) cc_final: -0.1302 (t) REVERT: 2 350 MET cc_start: 0.3789 (mmt) cc_final: 0.2449 (ptp) REVERT: 2 355 TYR cc_start: 0.6629 (m-80) cc_final: 0.6170 (m-80) REVERT: 2 362 THR cc_start: 0.6191 (p) cc_final: 0.5982 (p) REVERT: 2 531 THR cc_start: 0.2980 (t) cc_final: 0.1969 (m) REVERT: 2 589 MET cc_start: 0.3859 (mmp) cc_final: 0.3298 (mmp) REVERT: 2 723 MET cc_start: 0.4108 (mmt) cc_final: 0.2108 (ptt) REVERT: 2 792 ARG cc_start: 0.7225 (mtm-85) cc_final: 0.6917 (mtm-85) REVERT: 3 8 PHE cc_start: 0.5879 (p90) cc_final: 0.5373 (m-80) REVERT: 3 14 ARG cc_start: 0.8230 (tpp80) cc_final: 0.7925 (mmt-90) REVERT: 3 278 ILE cc_start: 0.6977 (tt) cc_final: 0.6573 (mp) REVERT: 3 441 CYS cc_start: 0.5070 (p) cc_final: 0.4778 (p) REVERT: 4 242 MET cc_start: 0.2438 (tpp) cc_final: 0.1243 (ptt) REVERT: 4 247 MET cc_start: 0.7651 (ttp) cc_final: 0.6097 (tpt) REVERT: 4 664 LEU cc_start: 0.7645 (pp) cc_final: 0.6760 (mt) REVERT: 4 675 THR cc_start: 0.2224 (OUTLIER) cc_final: 0.1897 (p) REVERT: 4 700 LEU cc_start: 0.5029 (mp) cc_final: 0.4633 (mm) REVERT: 4 771 LEU cc_start: 0.5835 (mt) cc_final: 0.4964 (pp) REVERT: 5 51 ARG cc_start: 0.3993 (mtp85) cc_final: 0.2603 (mtp85) REVERT: 5 210 MET cc_start: 0.6773 (mtp) cc_final: 0.6367 (mtp) REVERT: 5 252 VAL cc_start: 0.7418 (OUTLIER) cc_final: 0.7210 (t) REVERT: 5 416 MET cc_start: 0.6399 (ptm) cc_final: 0.6129 (ptp) REVERT: 5 508 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8149 (tt) REVERT: 5 620 GLU cc_start: 0.6259 (mm-30) cc_final: 0.5916 (mm-30) REVERT: 6 151 MET cc_start: 0.1265 (ppp) cc_final: 0.0191 (tmm) REVERT: 6 168 PHE cc_start: 0.5479 (m-80) cc_final: 0.5227 (m-80) REVERT: 6 170 ASN cc_start: 0.5693 (m-40) cc_final: 0.5184 (p0) REVERT: 6 194 PHE cc_start: 0.5387 (OUTLIER) cc_final: 0.4218 (m-80) REVERT: 6 337 ASN cc_start: 0.6997 (m110) cc_final: 0.6772 (m110) REVERT: 6 519 MET cc_start: 0.4982 (ptt) cc_final: 0.4587 (ptp) REVERT: 6 548 HIS cc_start: 0.4866 (m-70) cc_final: 0.4494 (m90) REVERT: 6 630 ASN cc_start: 0.2616 (OUTLIER) cc_final: 0.2233 (m-40) REVERT: 7 31 PHE cc_start: 0.6448 (m-80) cc_final: 0.6156 (m-80) REVERT: 7 160 LEU cc_start: 0.7508 (tp) cc_final: 0.7291 (tp) REVERT: 7 365 ARG cc_start: 0.5504 (mmm-85) cc_final: 0.2767 (ptp90) REVERT: 7 380 MET cc_start: 0.6389 (tpt) cc_final: 0.6118 (tpt) REVERT: 7 397 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6667 (mm) REVERT: 7 458 ILE cc_start: 0.6930 (tp) cc_final: 0.6663 (mm) REVERT: 7 598 MET cc_start: 0.6748 (mmt) cc_final: 0.6371 (mmp) REVERT: 7 612 LEU cc_start: 0.3647 (pp) cc_final: 0.2999 (mt) REVERT: 7 627 LYS cc_start: 0.6653 (tptp) cc_final: 0.6328 (tttm) REVERT: A 45 MET cc_start: 0.3239 (mpp) cc_final: 0.2664 (mtt) REVERT: A 166 ASP cc_start: 0.0744 (OUTLIER) cc_final: -0.1554 (t0) REVERT: A 230 MET cc_start: 0.2176 (mtt) cc_final: 0.1966 (mtt) REVERT: A 268 LEU cc_start: 0.0115 (OUTLIER) cc_final: -0.0141 (pp) REVERT: A 303 MET cc_start: 0.6917 (mtt) cc_final: 0.6674 (mtt) REVERT: A 342 TYR cc_start: 0.6168 (t80) cc_final: 0.5521 (t80) REVERT: A 541 LYS cc_start: 0.8239 (tptt) cc_final: 0.7532 (tmtt) REVERT: H 64 TRP cc_start: 0.7293 (OUTLIER) cc_final: 0.7042 (m100) REVERT: H 70 ARG cc_start: 0.8235 (tmm160) cc_final: 0.7899 (tmm160) REVERT: H 76 ARG cc_start: 0.3618 (tpt170) cc_final: 0.1370 (ptm160) REVERT: H 86 TYR cc_start: 0.6580 (OUTLIER) cc_final: 0.5245 (t80) REVERT: L 7 GLU cc_start: 0.5370 (mp0) cc_final: 0.4257 (mt-10) REVERT: L 56 GLN cc_start: 0.7335 (mp10) cc_final: 0.6848 (pp30) REVERT: L 73 GLU cc_start: 0.5992 (pt0) cc_final: 0.5723 (mm-30) REVERT: L 100 MET cc_start: 0.8124 (mpp) cc_final: 0.7694 (mpp) REVERT: L 109 ARG cc_start: 0.7250 (mtt180) cc_final: 0.6958 (mtp180) REVERT: L 114 ARG cc_start: 0.6484 (OUTLIER) cc_final: 0.4206 (mmt90) REVERT: L 154 HIS cc_start: 0.2310 (p90) cc_final: 0.1961 (p90) REVERT: N 73 MET cc_start: 0.7000 (mmt) cc_final: 0.6681 (mmm) outliers start: 186 outliers final: 97 residues processed: 914 average time/residue: 0.5268 time to fit residues: 769.2466 Evaluate side-chains 749 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 639 time to evaluate : 4.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 207 MET Chi-restraints excluded: chain 2 residue 277 GLU Chi-restraints excluded: chain 2 residue 293 THR Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 361 ILE Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 448 THR Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 520 TYR Chi-restraints excluded: chain 2 residue 524 VAL Chi-restraints excluded: chain 2 residue 574 PHE Chi-restraints excluded: chain 2 residue 584 SER Chi-restraints excluded: chain 2 residue 616 ASN Chi-restraints excluded: chain 2 residue 697 LEU Chi-restraints excluded: chain 3 residue 20 LEU Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 214 VAL Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 313 LEU Chi-restraints excluded: chain 3 residue 315 LEU Chi-restraints excluded: chain 3 residue 356 THR Chi-restraints excluded: chain 3 residue 394 VAL Chi-restraints excluded: chain 3 residue 448 ASN Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 316 THR Chi-restraints excluded: chain 4 residue 347 SER Chi-restraints excluded: chain 4 residue 350 THR Chi-restraints excluded: chain 4 residue 363 ASP Chi-restraints excluded: chain 4 residue 396 ILE Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 671 LEU Chi-restraints excluded: chain 4 residue 675 THR Chi-restraints excluded: chain 4 residue 752 SER Chi-restraints excluded: chain 5 residue 123 LEU Chi-restraints excluded: chain 5 residue 144 VAL Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 371 ASP Chi-restraints excluded: chain 5 residue 376 LEU Chi-restraints excluded: chain 5 residue 377 LEU Chi-restraints excluded: chain 5 residue 507 ILE Chi-restraints excluded: chain 5 residue 508 LEU Chi-restraints excluded: chain 5 residue 580 LYS Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 245 VAL Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 356 VAL Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 450 CYS Chi-restraints excluded: chain 6 residue 630 ASN Chi-restraints excluded: chain 7 residue 6 TYR Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 72 ARG Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain 7 residue 149 ILE Chi-restraints excluded: chain 7 residue 173 VAL Chi-restraints excluded: chain 7 residue 191 THR Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 295 GLU Chi-restraints excluded: chain 7 residue 336 LEU Chi-restraints excluded: chain 7 residue 362 VAL Chi-restraints excluded: chain 7 residue 374 ASN Chi-restraints excluded: chain 7 residue 397 LEU Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 466 THR Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain H residue 7 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 64 TRP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 112 CYS Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 114 ARG Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 245 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 368 optimal weight: 2.9990 chunk 301 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 443 optimal weight: 1.9990 chunk 478 optimal weight: 6.9990 chunk 394 optimal weight: 5.9990 chunk 439 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 355 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 352 GLN 2 364 GLN ** 2 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 199 GLN ** 3 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 310 GLN 3 418 HIS 3 467 GLN 3 495 HIS 3 622 HIS 4 192 ASN 4 193 GLN 4 223 GLN ** 4 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 378 HIS ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 735 GLN 4 767 HIS ** 5 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 84 ASN 5 239 HIS ** 5 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 256 ASN 5 373 ASN ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 537 HIS ** 5 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 644 GLN 6 101 GLN 6 231 GLN ** 6 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 341 ASN 6 353 ASN 6 472 GLN 6 550 ASN 6 636 HIS 7 45 GLN 7 69 ASN ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 543 HIS A 13 GLN A 65 HIS A 66 GLN A 101 HIS ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN A 495 GLN ** H 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 HIS M 9 ASN M 81 HIS N 48 ASN ** N 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 208 GLN N 224 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5869 moved from start: 0.6581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 40466 Z= 0.373 Angle : 0.937 18.794 54822 Z= 0.478 Chirality : 0.052 0.365 6193 Planarity : 0.007 0.090 6950 Dihedral : 13.173 129.070 5921 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.14 % Favored : 84.78 % Rotamer: Outliers : 6.93 % Allowed : 20.85 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.10), residues: 4789 helix: -1.88 (0.12), residues: 1531 sheet: -3.11 (0.20), residues: 516 loop : -3.45 (0.10), residues: 2742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP A 297 HIS 0.050 0.003 HIS A 453 PHE 0.034 0.003 PHE 3 253 TYR 0.035 0.003 TYR N 104 ARG 0.010 0.001 ARG 3 329 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1089 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 793 time to evaluate : 4.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 240 MET cc_start: 0.6279 (mmm) cc_final: 0.5964 (mmm) REVERT: 2 250 ASP cc_start: 0.7652 (t0) cc_final: 0.7143 (t0) REVERT: 2 275 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6894 (pp) REVERT: 2 314 CYS cc_start: -0.0815 (OUTLIER) cc_final: -0.1259 (t) REVERT: 2 350 MET cc_start: 0.3970 (mmt) cc_final: 0.3071 (ptp) REVERT: 2 415 GLN cc_start: 0.5610 (OUTLIER) cc_final: 0.5251 (mm-40) REVERT: 2 450 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7363 (mp10) REVERT: 2 458 ILE cc_start: 0.4283 (OUTLIER) cc_final: 0.4081 (pp) REVERT: 2 610 THR cc_start: 0.5038 (OUTLIER) cc_final: 0.4341 (m) REVERT: 2 723 MET cc_start: 0.5189 (mmt) cc_final: 0.3489 (ptt) REVERT: 3 8 PHE cc_start: 0.5706 (p90) cc_final: 0.5157 (m-80) REVERT: 3 14 ARG cc_start: 0.8371 (tpp80) cc_final: 0.7997 (mmt-90) REVERT: 3 16 TYR cc_start: 0.4849 (m-80) cc_final: 0.4526 (m-10) REVERT: 3 238 TYR cc_start: 0.7650 (t80) cc_final: 0.7298 (m-80) REVERT: 3 277 ASP cc_start: 0.8245 (m-30) cc_final: 0.7983 (m-30) REVERT: 3 323 ILE cc_start: 0.6568 (mm) cc_final: 0.6356 (mm) REVERT: 3 355 ASN cc_start: 0.8177 (p0) cc_final: 0.7743 (m110) REVERT: 3 590 ARG cc_start: 0.5770 (tpp-160) cc_final: 0.5533 (tpt170) REVERT: 4 173 MET cc_start: 0.5665 (mmm) cc_final: 0.5363 (mmm) REVERT: 4 242 MET cc_start: 0.2451 (tpp) cc_final: 0.0881 (ptt) REVERT: 4 247 MET cc_start: 0.7839 (ttp) cc_final: 0.6383 (tpt) REVERT: 4 397 TYR cc_start: 0.2229 (OUTLIER) cc_final: 0.0879 (m-10) REVERT: 4 415 TYR cc_start: 0.4801 (m-10) cc_final: 0.4335 (m-80) REVERT: 4 463 ARG cc_start: 0.6070 (mtt180) cc_final: 0.5476 (ttt-90) REVERT: 4 556 ARG cc_start: 0.5627 (OUTLIER) cc_final: 0.5173 (ttt-90) REVERT: 4 580 LYS cc_start: 0.7941 (mmmm) cc_final: 0.7647 (ttmt) REVERT: 4 664 LEU cc_start: 0.8153 (pp) cc_final: 0.7270 (mt) REVERT: 4 697 ARG cc_start: 0.9207 (mmm160) cc_final: 0.8255 (mtt180) REVERT: 4 700 LEU cc_start: 0.6342 (mp) cc_final: 0.5966 (mm) REVERT: 4 736 LEU cc_start: 0.4857 (OUTLIER) cc_final: 0.4417 (pp) REVERT: 4 758 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7993 (mt) REVERT: 5 56 ARG cc_start: 0.6429 (ptt-90) cc_final: 0.6136 (ptt-90) REVERT: 5 88 THR cc_start: 0.7825 (OUTLIER) cc_final: 0.7453 (m) REVERT: 5 120 GLN cc_start: 0.6028 (OUTLIER) cc_final: 0.5685 (tt0) REVERT: 5 123 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6250 (mp) REVERT: 5 339 SER cc_start: 0.7723 (p) cc_final: 0.7300 (t) REVERT: 5 345 ASP cc_start: 0.6944 (m-30) cc_final: 0.6672 (p0) REVERT: 5 361 ARG cc_start: 0.8384 (ptm160) cc_final: 0.7887 (ttt90) REVERT: 5 416 MET cc_start: 0.7092 (ptm) cc_final: 0.6772 (ptp) REVERT: 5 447 MET cc_start: 0.7256 (ptm) cc_final: 0.6932 (ptt) REVERT: 5 499 GLU cc_start: 0.6246 (mm-30) cc_final: 0.5985 (mm-30) REVERT: 5 500 ASN cc_start: 0.7364 (t0) cc_final: 0.7124 (m-40) REVERT: 5 508 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8511 (tt) REVERT: 6 152 CYS cc_start: 0.3753 (OUTLIER) cc_final: 0.3455 (p) REVERT: 6 167 LYS cc_start: 0.5989 (OUTLIER) cc_final: 0.5195 (ttpt) REVERT: 6 170 ASN cc_start: 0.5746 (m-40) cc_final: 0.5221 (p0) REVERT: 6 186 MET cc_start: 0.5026 (tpt) cc_final: 0.4775 (mtt) REVERT: 6 194 PHE cc_start: 0.6088 (OUTLIER) cc_final: 0.4699 (m-80) REVERT: 6 337 ASN cc_start: 0.6887 (m110) cc_final: 0.6483 (m110) REVERT: 6 382 ILE cc_start: 0.7763 (pt) cc_final: 0.7222 (pt) REVERT: 6 445 ASP cc_start: 0.6887 (m-30) cc_final: 0.6157 (t0) REVERT: 6 469 MET cc_start: 0.6607 (ptm) cc_final: 0.5256 (ptp) REVERT: 6 639 GLU cc_start: 0.6767 (tp30) cc_final: 0.6474 (tp30) REVERT: 7 21 CYS cc_start: 0.5850 (m) cc_final: 0.5650 (m) REVERT: 7 48 ILE cc_start: 0.2554 (OUTLIER) cc_final: 0.2169 (pt) REVERT: 7 281 MET cc_start: 0.5435 (mpp) cc_final: 0.4748 (tmm) REVERT: 7 402 GLN cc_start: 0.6475 (mt0) cc_final: 0.6026 (mt0) REVERT: 7 468 SER cc_start: 0.6061 (m) cc_final: 0.5670 (p) REVERT: 7 562 TYR cc_start: 0.4194 (m-80) cc_final: 0.3681 (m-80) REVERT: 7 627 LYS cc_start: 0.6576 (tptp) cc_final: 0.6167 (tttm) REVERT: A 101 HIS cc_start: 0.6067 (OUTLIER) cc_final: 0.5324 (p-80) REVERT: A 166 ASP cc_start: 0.0311 (OUTLIER) cc_final: -0.2065 (t0) REVERT: A 230 MET cc_start: 0.4366 (mtt) cc_final: 0.4045 (mtt) REVERT: A 303 MET cc_start: 0.7920 (mtt) cc_final: 0.7624 (mtt) REVERT: A 304 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.5475 (ttp80) REVERT: A 342 TYR cc_start: 0.6739 (t80) cc_final: 0.6230 (t80) REVERT: A 364 TYR cc_start: 0.5260 (m-80) cc_final: 0.4676 (m-80) REVERT: A 405 THR cc_start: 0.5283 (OUTLIER) cc_final: 0.5069 (m) REVERT: A 533 LYS cc_start: 0.7245 (ttmt) cc_final: 0.6955 (mtpp) REVERT: H 64 TRP cc_start: 0.7620 (m100) cc_final: 0.7305 (m100) REVERT: H 76 ARG cc_start: 0.4765 (tpt170) cc_final: 0.2856 (ptm-80) REVERT: L 27 HIS cc_start: 0.4143 (OUTLIER) cc_final: 0.3856 (t70) REVERT: L 64 GLU cc_start: 0.7679 (mp0) cc_final: 0.7475 (tp30) REVERT: L 100 MET cc_start: 0.8035 (mpp) cc_final: 0.7606 (mpp) REVERT: L 114 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.4878 (mmm-85) REVERT: L 171 GLN cc_start: 0.5469 (OUTLIER) cc_final: 0.5169 (tp40) REVERT: M 108 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7969 (tt) REVERT: M 122 PHE cc_start: 0.6907 (t80) cc_final: 0.6611 (t80) REVERT: N 94 LEU cc_start: 0.7358 (tt) cc_final: 0.6228 (tt) outliers start: 296 outliers final: 158 residues processed: 1018 average time/residue: 0.5122 time to fit residues: 841.8500 Evaluate side-chains 840 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 656 time to evaluate : 4.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 204 ILE Chi-restraints excluded: chain 2 residue 207 MET Chi-restraints excluded: chain 2 residue 275 LEU Chi-restraints excluded: chain 2 residue 282 PHE Chi-restraints excluded: chain 2 residue 293 THR Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 361 ILE Chi-restraints excluded: chain 2 residue 363 LEU Chi-restraints excluded: chain 2 residue 375 ILE Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 GLN Chi-restraints excluded: chain 2 residue 419 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 448 THR Chi-restraints excluded: chain 2 residue 450 GLN Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 458 ILE Chi-restraints excluded: chain 2 residue 462 VAL Chi-restraints excluded: chain 2 residue 463 VAL Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 509 ASP Chi-restraints excluded: chain 2 residue 520 TYR Chi-restraints excluded: chain 2 residue 532 THR Chi-restraints excluded: chain 2 residue 574 PHE Chi-restraints excluded: chain 2 residue 584 SER Chi-restraints excluded: chain 2 residue 590 GLU Chi-restraints excluded: chain 2 residue 610 THR Chi-restraints excluded: chain 2 residue 612 ILE Chi-restraints excluded: chain 2 residue 616 ASN Chi-restraints excluded: chain 2 residue 647 VAL Chi-restraints excluded: chain 2 residue 741 VAL Chi-restraints excluded: chain 2 residue 750 MET Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 122 VAL Chi-restraints excluded: chain 3 residue 214 VAL Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 284 LEU Chi-restraints excluded: chain 3 residue 293 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 310 GLN Chi-restraints excluded: chain 3 residue 333 ASP Chi-restraints excluded: chain 3 residue 343 SER Chi-restraints excluded: chain 3 residue 356 THR Chi-restraints excluded: chain 3 residue 394 VAL Chi-restraints excluded: chain 3 residue 397 ASP Chi-restraints excluded: chain 4 residue 154 VAL Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 4 residue 189 ILE Chi-restraints excluded: chain 4 residue 244 ILE Chi-restraints excluded: chain 4 residue 296 SER Chi-restraints excluded: chain 4 residue 316 THR Chi-restraints excluded: chain 4 residue 338 HIS Chi-restraints excluded: chain 4 residue 347 SER Chi-restraints excluded: chain 4 residue 350 THR Chi-restraints excluded: chain 4 residue 363 ASP Chi-restraints excluded: chain 4 residue 374 LEU Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 396 ILE Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 424 PHE Chi-restraints excluded: chain 4 residue 448 VAL Chi-restraints excluded: chain 4 residue 535 THR Chi-restraints excluded: chain 4 residue 556 ARG Chi-restraints excluded: chain 4 residue 562 THR Chi-restraints excluded: chain 4 residue 626 TRP Chi-restraints excluded: chain 4 residue 661 ASP Chi-restraints excluded: chain 4 residue 671 LEU Chi-restraints excluded: chain 4 residue 689 LEU Chi-restraints excluded: chain 4 residue 736 LEU Chi-restraints excluded: chain 4 residue 752 SER Chi-restraints excluded: chain 4 residue 758 LEU Chi-restraints excluded: chain 4 residue 764 TRP Chi-restraints excluded: chain 5 residue 52 ASP Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 88 THR Chi-restraints excluded: chain 5 residue 120 GLN Chi-restraints excluded: chain 5 residue 123 LEU Chi-restraints excluded: chain 5 residue 130 THR Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 144 VAL Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 371 ASP Chi-restraints excluded: chain 5 residue 376 LEU Chi-restraints excluded: chain 5 residue 394 VAL Chi-restraints excluded: chain 5 residue 421 THR Chi-restraints excluded: chain 5 residue 507 ILE Chi-restraints excluded: chain 5 residue 508 LEU Chi-restraints excluded: chain 5 residue 556 SER Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 121 THR Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 152 CYS Chi-restraints excluded: chain 6 residue 167 LYS Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 339 TYR Chi-restraints excluded: chain 6 residue 356 VAL Chi-restraints excluded: chain 6 residue 381 ASP Chi-restraints excluded: chain 6 residue 387 VAL Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 450 CYS Chi-restraints excluded: chain 6 residue 508 LEU Chi-restraints excluded: chain 6 residue 512 ILE Chi-restraints excluded: chain 6 residue 529 VAL Chi-restraints excluded: chain 6 residue 625 LYS Chi-restraints excluded: chain 7 residue 6 TYR Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 7 residue 72 ARG Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain 7 residue 149 ILE Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 173 VAL Chi-restraints excluded: chain 7 residue 191 THR Chi-restraints excluded: chain 7 residue 195 VAL Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 224 THR Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 295 GLU Chi-restraints excluded: chain 7 residue 362 VAL Chi-restraints excluded: chain 7 residue 374 ASN Chi-restraints excluded: chain 7 residue 394 ILE Chi-restraints excluded: chain 7 residue 397 LEU Chi-restraints excluded: chain 7 residue 401 SER Chi-restraints excluded: chain 7 residue 466 THR Chi-restraints excluded: chain 7 residue 484 ILE Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain H residue 7 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 112 CYS Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 27 HIS Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 114 ARG Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain L residue 171 GLN Chi-restraints excluded: chain M residue 15 ASP Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 437 optimal weight: 0.6980 chunk 333 optimal weight: 10.0000 chunk 229 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 211 optimal weight: 0.9980 chunk 297 optimal weight: 4.9990 chunk 444 optimal weight: 0.9990 chunk 470 optimal weight: 0.0870 chunk 232 optimal weight: 0.5980 chunk 421 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 534 GLN 2 754 HIS ** 3 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 353 GLN ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 485 GLN ** 4 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 527 ASN 4 627 ASN 5 57 ASN 5 241 GLN ** 5 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 541 ASN 6 198 GLN ** 6 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 155 GLN 7 453 GLN A 421 HIS A 453 HIS ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 153 HIS N 224 GLN N 226 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5816 moved from start: 0.7143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 40466 Z= 0.202 Angle : 0.746 16.638 54822 Z= 0.374 Chirality : 0.046 0.280 6193 Planarity : 0.005 0.080 6950 Dihedral : 12.342 123.882 5911 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 5.46 % Allowed : 23.92 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.74 (0.11), residues: 4789 helix: -1.40 (0.13), residues: 1548 sheet: -2.91 (0.20), residues: 552 loop : -3.18 (0.11), residues: 2689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 297 HIS 0.021 0.001 HIS A 101 PHE 0.028 0.002 PHE A 440 TYR 0.021 0.002 TYR 3 454 ARG 0.007 0.001 ARG 6 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 730 time to evaluate : 4.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. REVERT: 2 250 ASP cc_start: 0.7536 (t0) cc_final: 0.7036 (t0) REVERT: 2 294 LEU cc_start: 0.7852 (pt) cc_final: 0.7452 (tt) REVERT: 2 350 MET cc_start: 0.4542 (mmt) cc_final: 0.3297 (ptm) REVERT: 2 351 GLU cc_start: 0.6527 (pm20) cc_final: 0.6185 (pm20) REVERT: 2 379 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7566 (tptp) REVERT: 2 397 LEU cc_start: 0.8114 (mp) cc_final: 0.7766 (mp) REVERT: 2 723 MET cc_start: 0.5461 (mmt) cc_final: 0.4045 (ptt) REVERT: 3 8 PHE cc_start: 0.5102 (p90) cc_final: 0.4641 (m-80) REVERT: 3 14 ARG cc_start: 0.8338 (tpp80) cc_final: 0.8034 (mmt180) REVERT: 3 214 VAL cc_start: 0.4584 (OUTLIER) cc_final: 0.4111 (t) REVERT: 3 277 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7897 (m-30) REVERT: 3 355 ASN cc_start: 0.7944 (p0) cc_final: 0.7617 (m-40) REVERT: 3 637 HIS cc_start: 0.6766 (m-70) cc_final: 0.5955 (t-170) REVERT: 4 189 ILE cc_start: 0.4217 (tt) cc_final: 0.3579 (mp) REVERT: 4 242 MET cc_start: 0.2115 (tpp) cc_final: 0.0851 (ptt) REVERT: 4 247 MET cc_start: 0.7954 (ttp) cc_final: 0.6551 (tpt) REVERT: 4 397 TYR cc_start: 0.2091 (OUTLIER) cc_final: 0.0798 (m-10) REVERT: 4 463 ARG cc_start: 0.5988 (mtt180) cc_final: 0.5150 (ttt-90) REVERT: 4 576 ASP cc_start: 0.6265 (m-30) cc_final: 0.5053 (t0) REVERT: 4 594 GLU cc_start: 0.6828 (tm-30) cc_final: 0.6427 (tm-30) REVERT: 4 664 LEU cc_start: 0.8079 (pp) cc_final: 0.7340 (mt) REVERT: 4 697 ARG cc_start: 0.9058 (mmm160) cc_final: 0.8506 (ttt180) REVERT: 4 700 LEU cc_start: 0.6437 (mp) cc_final: 0.6106 (mm) REVERT: 5 220 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6827 (tp40) REVERT: 5 361 ARG cc_start: 0.8311 (ptm160) cc_final: 0.7799 (ttt90) REVERT: 5 384 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6890 (mtmt) REVERT: 5 447 MET cc_start: 0.7075 (ptm) cc_final: 0.6825 (ptt) REVERT: 5 499 GLU cc_start: 0.6185 (mm-30) cc_final: 0.5931 (mm-30) REVERT: 6 59 PHE cc_start: 0.4720 (OUTLIER) cc_final: 0.4514 (t80) REVERT: 6 151 MET cc_start: 0.1370 (ppp) cc_final: -0.0595 (tmm) REVERT: 6 160 ARG cc_start: 0.6442 (mmp80) cc_final: 0.6209 (mmp80) REVERT: 6 170 ASN cc_start: 0.5667 (m-40) cc_final: 0.5204 (p0) REVERT: 6 186 MET cc_start: 0.4981 (tpt) cc_final: 0.4697 (mtt) REVERT: 6 194 PHE cc_start: 0.6119 (OUTLIER) cc_final: 0.4822 (m-80) REVERT: 6 299 THR cc_start: -0.1479 (OUTLIER) cc_final: -0.1816 (m) REVERT: 6 382 ILE cc_start: 0.8323 (pt) cc_final: 0.8100 (pt) REVERT: 6 445 ASP cc_start: 0.6883 (m-30) cc_final: 0.6075 (t0) REVERT: 6 469 MET cc_start: 0.6810 (ptm) cc_final: 0.5308 (ptp) REVERT: 6 519 MET cc_start: 0.6127 (ptt) cc_final: 0.5573 (ptp) REVERT: 6 580 GLN cc_start: 0.6139 (mt0) cc_final: 0.5905 (mt0) REVERT: 6 639 GLU cc_start: 0.6784 (tp30) cc_final: 0.6413 (tp30) REVERT: 7 48 ILE cc_start: 0.2397 (OUTLIER) cc_final: 0.1973 (pt) REVERT: 7 177 MET cc_start: 0.7251 (tmm) cc_final: 0.7045 (tmm) REVERT: 7 238 GLN cc_start: 0.6801 (OUTLIER) cc_final: 0.6504 (tm-30) REVERT: 7 281 MET cc_start: 0.5550 (mpp) cc_final: 0.4918 (tmm) REVERT: 7 299 GLN cc_start: 0.7082 (tp-100) cc_final: 0.6555 (tp-100) REVERT: 7 397 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6889 (mm) REVERT: 7 552 LYS cc_start: 0.5232 (mppt) cc_final: 0.5025 (tptt) REVERT: 7 562 TYR cc_start: 0.4042 (m-80) cc_final: 0.3694 (m-80) REVERT: 7 627 LYS cc_start: 0.6656 (tptp) cc_final: 0.6270 (tttm) REVERT: A 303 MET cc_start: 0.7734 (mtt) cc_final: 0.7299 (mtt) REVERT: A 304 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.5276 (ttp80) REVERT: A 312 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.6070 (mp10) REVERT: A 321 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7108 (mm-30) REVERT: A 342 TYR cc_start: 0.6418 (t80) cc_final: 0.5975 (t80) REVERT: A 405 THR cc_start: 0.5596 (OUTLIER) cc_final: 0.5392 (m) REVERT: A 533 LYS cc_start: 0.7152 (ttmt) cc_final: 0.6830 (mtpp) REVERT: A 541 LYS cc_start: 0.8369 (tptt) cc_final: 0.7651 (tmmt) REVERT: H 76 ARG cc_start: 0.4625 (tpt170) cc_final: 0.3042 (ptm-80) REVERT: L 56 GLN cc_start: 0.7844 (mp10) cc_final: 0.7401 (mp10) REVERT: L 114 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.5052 (mmm-85) REVERT: M 127 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7606 (mm110) REVERT: N 153 HIS cc_start: 0.7511 (OUTLIER) cc_final: 0.7197 (m170) outliers start: 233 outliers final: 133 residues processed: 900 average time/residue: 0.5514 time to fit residues: 802.5654 Evaluate side-chains 805 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 655 time to evaluate : 4.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 184 PHE Chi-restraints excluded: chain 2 residue 277 GLU Chi-restraints excluded: chain 2 residue 282 PHE Chi-restraints excluded: chain 2 residue 293 THR Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 375 ILE Chi-restraints excluded: chain 2 residue 379 LYS Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 402 ILE Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 462 VAL Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 520 TYR Chi-restraints excluded: chain 2 residue 524 VAL Chi-restraints excluded: chain 2 residue 574 PHE Chi-restraints excluded: chain 2 residue 584 SER Chi-restraints excluded: chain 2 residue 616 ASN Chi-restraints excluded: chain 2 residue 697 LEU Chi-restraints excluded: chain 2 residue 698 ARG Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 214 VAL Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 277 ASP Chi-restraints excluded: chain 3 residue 284 LEU Chi-restraints excluded: chain 3 residue 293 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 315 LEU Chi-restraints excluded: chain 3 residue 371 VAL Chi-restraints excluded: chain 3 residue 394 VAL Chi-restraints excluded: chain 3 residue 420 VAL Chi-restraints excluded: chain 3 residue 443 VAL Chi-restraints excluded: chain 3 residue 448 ASN Chi-restraints excluded: chain 3 residue 557 LEU Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 296 SER Chi-restraints excluded: chain 4 residue 316 THR Chi-restraints excluded: chain 4 residue 347 SER Chi-restraints excluded: chain 4 residue 350 THR Chi-restraints excluded: chain 4 residue 363 ASP Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 396 ILE Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 424 PHE Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 671 LEU Chi-restraints excluded: chain 4 residue 752 SER Chi-restraints excluded: chain 4 residue 764 TRP Chi-restraints excluded: chain 5 residue 52 ASP Chi-restraints excluded: chain 5 residue 123 LEU Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 241 GLN Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 371 ASP Chi-restraints excluded: chain 5 residue 377 LEU Chi-restraints excluded: chain 5 residue 384 LYS Chi-restraints excluded: chain 5 residue 394 VAL Chi-restraints excluded: chain 5 residue 421 THR Chi-restraints excluded: chain 5 residue 529 LEU Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 59 PHE Chi-restraints excluded: chain 6 residue 132 SER Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 166 PHE Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 356 VAL Chi-restraints excluded: chain 6 residue 381 ASP Chi-restraints excluded: chain 6 residue 387 VAL Chi-restraints excluded: chain 6 residue 531 GLU Chi-restraints excluded: chain 6 residue 630 ASN Chi-restraints excluded: chain 6 residue 644 LEU Chi-restraints excluded: chain 7 residue 6 TYR Chi-restraints excluded: chain 7 residue 25 ASP Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 72 ARG Chi-restraints excluded: chain 7 residue 149 ILE Chi-restraints excluded: chain 7 residue 155 GLN Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 173 VAL Chi-restraints excluded: chain 7 residue 191 THR Chi-restraints excluded: chain 7 residue 195 VAL Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 224 THR Chi-restraints excluded: chain 7 residue 238 GLN Chi-restraints excluded: chain 7 residue 362 VAL Chi-restraints excluded: chain 7 residue 397 LEU Chi-restraints excluded: chain 7 residue 458 ILE Chi-restraints excluded: chain 7 residue 555 ASP Chi-restraints excluded: chain 7 residue 625 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 505 CYS Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 114 ARG Chi-restraints excluded: chain L residue 135 PHE Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain L residue 153 ILE Chi-restraints excluded: chain M residue 15 ASP Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 115 PHE Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 211 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 392 optimal weight: 0.7980 chunk 267 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 350 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 401 optimal weight: 3.9990 chunk 325 optimal weight: 0.0870 chunk 0 optimal weight: 7.9990 chunk 240 optimal weight: 0.0060 chunk 422 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 overall best weight: 0.5174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 329 ASN ** 2 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 57 ASN 5 521 HIS 6 134 GLN 6 198 GLN 6 203 GLN ** 6 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 466 HIS 7 69 ASN ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 546 GLN H 120 ASN ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 118 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 moved from start: 0.7580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 40466 Z= 0.187 Angle : 0.709 16.763 54822 Z= 0.352 Chirality : 0.045 0.254 6193 Planarity : 0.005 0.080 6950 Dihedral : 11.899 124.939 5902 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 5.36 % Allowed : 25.16 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.45 (0.11), residues: 4789 helix: -1.12 (0.13), residues: 1518 sheet: -2.54 (0.20), residues: 555 loop : -3.07 (0.11), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 170 HIS 0.034 0.001 HIS N 153 PHE 0.042 0.002 PHE L 84 TYR 0.025 0.001 TYR H 84 ARG 0.006 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 708 time to evaluate : 4.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. REVERT: 2 250 ASP cc_start: 0.7466 (t0) cc_final: 0.6975 (t0) REVERT: 2 294 LEU cc_start: 0.7808 (pt) cc_final: 0.7484 (tt) REVERT: 2 350 MET cc_start: 0.4510 (mmt) cc_final: 0.3347 (ptp) REVERT: 2 351 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6333 (pm20) REVERT: 2 379 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7526 (tptp) REVERT: 2 397 LEU cc_start: 0.8332 (mp) cc_final: 0.7959 (mp) REVERT: 2 398 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6761 (mt-10) REVERT: 2 645 LEU cc_start: 0.5894 (tt) cc_final: 0.4815 (mp) REVERT: 2 662 LYS cc_start: 0.7040 (mttt) cc_final: 0.6840 (mttt) REVERT: 2 707 ASN cc_start: 0.7450 (m-40) cc_final: 0.7214 (m-40) REVERT: 2 723 MET cc_start: 0.5451 (mmt) cc_final: 0.4203 (ttp) REVERT: 3 8 PHE cc_start: 0.5016 (p90) cc_final: 0.4548 (m-80) REVERT: 3 14 ARG cc_start: 0.8316 (tpp80) cc_final: 0.8053 (mmt180) REVERT: 3 19 PHE cc_start: 0.6171 (t80) cc_final: 0.5878 (t80) REVERT: 3 121 MET cc_start: 0.5734 (ttp) cc_final: 0.5431 (ttt) REVERT: 3 177 ASP cc_start: 0.5509 (OUTLIER) cc_final: 0.3191 (m-30) REVERT: 3 203 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7212 (pm20) REVERT: 3 277 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7843 (m-30) REVERT: 3 355 ASN cc_start: 0.7735 (p0) cc_final: 0.7405 (m-40) REVERT: 3 637 HIS cc_start: 0.6822 (m-70) cc_final: 0.5987 (t-170) REVERT: 4 189 ILE cc_start: 0.3863 (tt) cc_final: 0.3235 (mp) REVERT: 4 242 MET cc_start: 0.2075 (tpp) cc_final: 0.0804 (ptt) REVERT: 4 353 GLN cc_start: 0.6129 (tm130) cc_final: 0.5895 (tm-30) REVERT: 4 364 MET cc_start: 0.5912 (tpp) cc_final: 0.5675 (tpp) REVERT: 4 397 TYR cc_start: 0.2155 (OUTLIER) cc_final: 0.0767 (m-10) REVERT: 4 463 ARG cc_start: 0.6080 (mtt180) cc_final: 0.5326 (ttt-90) REVERT: 4 521 MET cc_start: 0.7691 (ttp) cc_final: 0.7298 (ptm) REVERT: 4 532 SER cc_start: 0.7976 (t) cc_final: 0.7403 (p) REVERT: 4 556 ARG cc_start: 0.5492 (OUTLIER) cc_final: 0.5127 (ttt-90) REVERT: 4 576 ASP cc_start: 0.5963 (m-30) cc_final: 0.5394 (t0) REVERT: 4 594 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6604 (tm-30) REVERT: 4 664 LEU cc_start: 0.8087 (pp) cc_final: 0.7273 (mt) REVERT: 4 697 ARG cc_start: 0.9017 (mmm160) cc_final: 0.8540 (ttt180) REVERT: 4 700 LEU cc_start: 0.6659 (mp) cc_final: 0.6404 (mm) REVERT: 5 246 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.7058 (ttm170) REVERT: 5 259 LEU cc_start: 0.7759 (mt) cc_final: 0.7520 (mt) REVERT: 5 361 ARG cc_start: 0.8355 (ptm160) cc_final: 0.7913 (ttt90) REVERT: 5 384 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6884 (mtmt) REVERT: 5 447 MET cc_start: 0.7209 (ptm) cc_final: 0.6974 (ptm) REVERT: 5 523 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7445 (mm-30) REVERT: 6 160 ARG cc_start: 0.6369 (mmp80) cc_final: 0.6156 (mmp80) REVERT: 6 167 LYS cc_start: 0.5861 (OUTLIER) cc_final: 0.5066 (ttpt) REVERT: 6 170 ASN cc_start: 0.5436 (m-40) cc_final: 0.4940 (p0) REVERT: 6 194 PHE cc_start: 0.5907 (OUTLIER) cc_final: 0.4841 (m-80) REVERT: 6 299 THR cc_start: -0.1567 (OUTLIER) cc_final: -0.1819 (m) REVERT: 6 382 ILE cc_start: 0.8478 (pt) cc_final: 0.8208 (pt) REVERT: 6 445 ASP cc_start: 0.6970 (m-30) cc_final: 0.6129 (t0) REVERT: 6 469 MET cc_start: 0.7016 (ptm) cc_final: 0.6132 (ptp) REVERT: 6 519 MET cc_start: 0.6152 (ptt) cc_final: 0.5597 (ptp) REVERT: 6 621 GLU cc_start: 0.4718 (pp20) cc_final: 0.3839 (pt0) REVERT: 6 623 MET cc_start: 0.6816 (ptp) cc_final: 0.6609 (mpp) REVERT: 6 630 ASN cc_start: 0.3273 (OUTLIER) cc_final: 0.2976 (m110) REVERT: 7 48 ILE cc_start: 0.2307 (OUTLIER) cc_final: 0.1914 (pt) REVERT: 7 229 PHE cc_start: 0.5957 (m-10) cc_final: 0.5467 (m-10) REVERT: 7 238 GLN cc_start: 0.6828 (OUTLIER) cc_final: 0.6553 (tm-30) REVERT: 7 281 MET cc_start: 0.5256 (mpp) cc_final: 0.4896 (tmm) REVERT: 7 299 GLN cc_start: 0.7061 (tp-100) cc_final: 0.6550 (tp-100) REVERT: 7 365 ARG cc_start: 0.6232 (mmt90) cc_final: 0.5784 (mmt90) REVERT: 7 397 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6853 (mm) REVERT: 7 402 GLN cc_start: 0.6668 (mt0) cc_final: 0.6404 (mt0) REVERT: 7 459 HIS cc_start: 0.7299 (m-70) cc_final: 0.6782 (m-70) REVERT: 7 552 LYS cc_start: 0.5319 (mppt) cc_final: 0.5102 (tptt) REVERT: 7 627 LYS cc_start: 0.6689 (tptp) cc_final: 0.6186 (tttm) REVERT: A 166 ASP cc_start: 0.0571 (OUTLIER) cc_final: -0.1658 (t0) REVERT: A 303 MET cc_start: 0.7649 (mtt) cc_final: 0.7180 (mtt) REVERT: A 304 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6976 (ttp80) REVERT: A 312 GLN cc_start: 0.6991 (OUTLIER) cc_final: 0.6120 (mp10) REVERT: A 342 TYR cc_start: 0.6385 (t80) cc_final: 0.5995 (t80) REVERT: A 533 LYS cc_start: 0.7106 (ttmt) cc_final: 0.6861 (mtpp) REVERT: A 541 LYS cc_start: 0.8226 (tptt) cc_final: 0.7609 (tmmt) REVERT: H 19 LEU cc_start: 0.1750 (OUTLIER) cc_final: 0.1500 (tp) REVERT: H 76 ARG cc_start: 0.4690 (tpt170) cc_final: 0.3147 (ptm-80) REVERT: H 131 CYS cc_start: 0.4979 (m) cc_final: 0.4358 (p) REVERT: L 56 GLN cc_start: 0.7866 (mp10) cc_final: 0.7405 (mp10) REVERT: L 69 ASP cc_start: 0.7409 (p0) cc_final: 0.7203 (p0) REVERT: L 114 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.5231 (mmm-85) REVERT: L 169 ARG cc_start: 0.3385 (ppt170) cc_final: 0.3147 (ppt170) REVERT: N 178 MET cc_start: 0.6694 (tpp) cc_final: 0.5140 (ptt) outliers start: 229 outliers final: 148 residues processed: 872 average time/residue: 0.5059 time to fit residues: 711.7782 Evaluate side-chains 822 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 652 time to evaluate : 4.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 184 PHE Chi-restraints excluded: chain 2 residue 277 GLU Chi-restraints excluded: chain 2 residue 282 PHE Chi-restraints excluded: chain 2 residue 293 THR Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 329 ASN Chi-restraints excluded: chain 2 residue 351 GLU Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 375 ILE Chi-restraints excluded: chain 2 residue 379 LYS Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 398 GLU Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 402 ILE Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 520 TYR Chi-restraints excluded: chain 2 residue 524 VAL Chi-restraints excluded: chain 2 residue 574 PHE Chi-restraints excluded: chain 2 residue 584 SER Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 616 ASN Chi-restraints excluded: chain 2 residue 647 VAL Chi-restraints excluded: chain 2 residue 697 LEU Chi-restraints excluded: chain 2 residue 698 ARG Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 114 THR Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 177 ASP Chi-restraints excluded: chain 3 residue 203 GLU Chi-restraints excluded: chain 3 residue 223 VAL Chi-restraints excluded: chain 3 residue 234 ILE Chi-restraints excluded: chain 3 residue 238 TYR Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 277 ASP Chi-restraints excluded: chain 3 residue 284 LEU Chi-restraints excluded: chain 3 residue 290 ILE Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 315 LEU Chi-restraints excluded: chain 3 residue 371 VAL Chi-restraints excluded: chain 3 residue 394 VAL Chi-restraints excluded: chain 3 residue 420 VAL Chi-restraints excluded: chain 3 residue 443 VAL Chi-restraints excluded: chain 3 residue 448 ASN Chi-restraints excluded: chain 3 residue 479 VAL Chi-restraints excluded: chain 3 residue 488 VAL Chi-restraints excluded: chain 4 residue 154 VAL Chi-restraints excluded: chain 4 residue 200 LEU Chi-restraints excluded: chain 4 residue 296 SER Chi-restraints excluded: chain 4 residue 316 THR Chi-restraints excluded: chain 4 residue 347 SER Chi-restraints excluded: chain 4 residue 363 ASP Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 396 ILE Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 424 PHE Chi-restraints excluded: chain 4 residue 556 ARG Chi-restraints excluded: chain 4 residue 562 THR Chi-restraints excluded: chain 4 residue 573 CYS Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 686 MET Chi-restraints excluded: chain 4 residue 689 LEU Chi-restraints excluded: chain 4 residue 752 SER Chi-restraints excluded: chain 4 residue 764 TRP Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 52 ASP Chi-restraints excluded: chain 5 residue 123 LEU Chi-restraints excluded: chain 5 residue 130 THR Chi-restraints excluded: chain 5 residue 144 VAL Chi-restraints excluded: chain 5 residue 154 SER Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 221 THR Chi-restraints excluded: chain 5 residue 246 ARG Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 314 ASP Chi-restraints excluded: chain 5 residue 371 ASP Chi-restraints excluded: chain 5 residue 377 LEU Chi-restraints excluded: chain 5 residue 384 LYS Chi-restraints excluded: chain 5 residue 421 THR Chi-restraints excluded: chain 5 residue 506 THR Chi-restraints excluded: chain 5 residue 556 SER Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 56 GLU Chi-restraints excluded: chain 6 residue 57 VAL Chi-restraints excluded: chain 6 residue 132 SER Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 167 LYS Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 426 VAL Chi-restraints excluded: chain 6 residue 448 ILE Chi-restraints excluded: chain 6 residue 529 VAL Chi-restraints excluded: chain 6 residue 531 GLU Chi-restraints excluded: chain 6 residue 630 ASN Chi-restraints excluded: chain 6 residue 644 LEU Chi-restraints excluded: chain 7 residue 6 TYR Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 72 ARG Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain 7 residue 149 ILE Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 173 VAL Chi-restraints excluded: chain 7 residue 195 VAL Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 238 GLN Chi-restraints excluded: chain 7 residue 295 GLU Chi-restraints excluded: chain 7 residue 302 ARG Chi-restraints excluded: chain 7 residue 329 GLN Chi-restraints excluded: chain 7 residue 362 VAL Chi-restraints excluded: chain 7 residue 374 ASN Chi-restraints excluded: chain 7 residue 397 LEU Chi-restraints excluded: chain 7 residue 458 ILE Chi-restraints excluded: chain 7 residue 484 ILE Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 528 ASP Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 625 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 23 ASN Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 114 ARG Chi-restraints excluded: chain L residue 135 PHE Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain M residue 15 ASP Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 115 PHE Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 211 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 158 optimal weight: 0.5980 chunk 423 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 471 optimal weight: 0.7980 chunk 391 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 247 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 233 GLN 3 335 ASN ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 494 HIS ** 4 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 57 ASN 6 134 GLN 6 198 GLN 6 203 GLN ** 6 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 353 ASN ** 6 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 645 ASN 7 105 HIS ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 546 GLN A 264 HIS ** H 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 118 HIS N 153 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5883 moved from start: 0.8149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 40466 Z= 0.205 Angle : 0.706 17.770 54822 Z= 0.352 Chirality : 0.045 0.263 6193 Planarity : 0.005 0.078 6950 Dihedral : 11.617 122.906 5900 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 6.18 % Allowed : 24.81 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.40 (0.11), residues: 4789 helix: -1.04 (0.13), residues: 1551 sheet: -2.46 (0.20), residues: 563 loop : -3.09 (0.11), residues: 2675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 170 HIS 0.015 0.001 HIS N 153 PHE 0.024 0.002 PHE L 84 TYR 0.019 0.001 TYR H 84 ARG 0.008 0.001 ARG M 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 713 time to evaluate : 4.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. REVERT: 2 239 GLN cc_start: 0.7438 (mp10) cc_final: 0.5915 (mt0) REVERT: 2 250 ASP cc_start: 0.7570 (t0) cc_final: 0.7102 (t0) REVERT: 2 253 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6739 (mp) REVERT: 2 350 MET cc_start: 0.4650 (mmt) cc_final: 0.3436 (ptp) REVERT: 2 379 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7490 (tptp) REVERT: 2 398 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6831 (mt-10) REVERT: 2 645 LEU cc_start: 0.5677 (tt) cc_final: 0.4575 (mp) REVERT: 2 662 LYS cc_start: 0.7181 (mttt) cc_final: 0.6885 (mtmt) REVERT: 2 707 ASN cc_start: 0.7474 (m-40) cc_final: 0.7180 (m-40) REVERT: 2 723 MET cc_start: 0.5555 (mmt) cc_final: 0.4313 (ttp) REVERT: 3 8 PHE cc_start: 0.5007 (p90) cc_final: 0.4454 (m-80) REVERT: 3 14 ARG cc_start: 0.8306 (tpp80) cc_final: 0.8064 (mmt180) REVERT: 3 19 PHE cc_start: 0.5968 (t80) cc_final: 0.5695 (t80) REVERT: 3 121 MET cc_start: 0.5764 (OUTLIER) cc_final: 0.5496 (ttt) REVERT: 3 203 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7499 (pt0) REVERT: 3 277 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7918 (m-30) REVERT: 3 393 MET cc_start: 0.5524 (tpt) cc_final: 0.4569 (tpt) REVERT: 3 412 ILE cc_start: 0.7715 (pt) cc_final: 0.7200 (tt) REVERT: 3 467 GLN cc_start: 0.7311 (mt0) cc_final: 0.6754 (mp10) REVERT: 3 468 ASP cc_start: 0.8665 (t70) cc_final: 0.8307 (t0) REVERT: 3 637 HIS cc_start: 0.6992 (m-70) cc_final: 0.6083 (t-170) REVERT: 4 189 ILE cc_start: 0.3661 (tt) cc_final: 0.3063 (mp) REVERT: 4 221 PHE cc_start: 0.5078 (OUTLIER) cc_final: 0.4140 (t80) REVERT: 4 242 MET cc_start: 0.2262 (tpp) cc_final: 0.0875 (ptt) REVERT: 4 248 PHE cc_start: 0.6851 (OUTLIER) cc_final: 0.6355 (m-10) REVERT: 4 463 ARG cc_start: 0.6184 (mtt180) cc_final: 0.5512 (ttt-90) REVERT: 4 532 SER cc_start: 0.8391 (t) cc_final: 0.7904 (p) REVERT: 4 556 ARG cc_start: 0.5664 (OUTLIER) cc_final: 0.5082 (ttt-90) REVERT: 4 576 ASP cc_start: 0.6261 (m-30) cc_final: 0.5389 (t0) REVERT: 4 594 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6631 (tm-30) REVERT: 4 697 ARG cc_start: 0.9007 (mmm160) cc_final: 0.8440 (ttt180) REVERT: 4 772 LYS cc_start: 0.0841 (tptt) cc_final: 0.0170 (tppt) REVERT: 5 220 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.6758 (tp40) REVERT: 5 259 LEU cc_start: 0.7705 (mt) cc_final: 0.7469 (mt) REVERT: 5 293 VAL cc_start: 0.8186 (t) cc_final: 0.7878 (m) REVERT: 5 348 LYS cc_start: 0.4262 (OUTLIER) cc_final: 0.3921 (tppt) REVERT: 5 361 ARG cc_start: 0.8335 (ptm160) cc_final: 0.7975 (ttt90) REVERT: 5 384 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.7027 (mtmt) REVERT: 5 508 LEU cc_start: 0.8506 (tt) cc_final: 0.8296 (tt) REVERT: 6 167 LYS cc_start: 0.6185 (OUTLIER) cc_final: 0.5401 (ttpt) REVERT: 6 170 ASN cc_start: 0.5480 (m-40) cc_final: 0.4850 (p0) REVERT: 6 194 PHE cc_start: 0.6145 (OUTLIER) cc_final: 0.5090 (m-80) REVERT: 6 299 THR cc_start: -0.1456 (OUTLIER) cc_final: -0.1760 (m) REVERT: 6 382 ILE cc_start: 0.8395 (pt) cc_final: 0.8173 (pt) REVERT: 6 445 ASP cc_start: 0.7087 (m-30) cc_final: 0.6370 (t0) REVERT: 6 461 ASP cc_start: 0.5672 (OUTLIER) cc_final: 0.5345 (t0) REVERT: 6 469 MET cc_start: 0.7084 (ptm) cc_final: 0.6217 (ptp) REVERT: 6 519 MET cc_start: 0.6645 (ptt) cc_final: 0.6170 (ptp) REVERT: 6 621 GLU cc_start: 0.4797 (pp20) cc_final: 0.3839 (pt0) REVERT: 6 630 ASN cc_start: 0.3562 (OUTLIER) cc_final: 0.3155 (m110) REVERT: 7 3 ARG cc_start: 0.4382 (ttp80) cc_final: 0.3717 (mpt180) REVERT: 7 48 ILE cc_start: 0.2338 (OUTLIER) cc_final: 0.1917 (pt) REVERT: 7 177 MET cc_start: 0.7684 (tmm) cc_final: 0.7358 (tmm) REVERT: 7 229 PHE cc_start: 0.6056 (m-10) cc_final: 0.5754 (m-10) REVERT: 7 238 GLN cc_start: 0.6793 (OUTLIER) cc_final: 0.6430 (tm-30) REVERT: 7 299 GLN cc_start: 0.7140 (tp-100) cc_final: 0.6682 (tp-100) REVERT: 7 365 ARG cc_start: 0.6223 (mmt90) cc_final: 0.5780 (mmt90) REVERT: 7 397 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6817 (mm) REVERT: 7 402 GLN cc_start: 0.6766 (mt0) cc_final: 0.6478 (mt0) REVERT: 7 427 MET cc_start: 0.2170 (mmm) cc_final: 0.1009 (mmm) REVERT: 7 459 HIS cc_start: 0.7185 (m-70) cc_final: 0.6377 (m-70) REVERT: 7 552 LYS cc_start: 0.5343 (mppt) cc_final: 0.5107 (tptt) REVERT: 7 556 MET cc_start: 0.4872 (pmm) cc_final: 0.4172 (ppp) REVERT: 7 627 LYS cc_start: 0.6576 (tptp) cc_final: 0.6035 (tttm) REVERT: A 6 LEU cc_start: 0.3487 (OUTLIER) cc_final: 0.2451 (pp) REVERT: A 101 HIS cc_start: 0.6437 (OUTLIER) cc_final: 0.5680 (p90) REVERT: A 166 ASP cc_start: 0.0422 (OUTLIER) cc_final: -0.1764 (t0) REVERT: A 230 MET cc_start: 0.5787 (mmm) cc_final: 0.5380 (mtt) REVERT: A 284 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8560 (p) REVERT: A 303 MET cc_start: 0.7641 (mtt) cc_final: 0.7113 (mtt) REVERT: A 312 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.5896 (mp10) REVERT: A 533 LYS cc_start: 0.7212 (ttmt) cc_final: 0.6855 (mmmt) REVERT: A 541 LYS cc_start: 0.8234 (tptt) cc_final: 0.7633 (tmmt) REVERT: A 567 LEU cc_start: 0.6595 (OUTLIER) cc_final: 0.6369 (mm) REVERT: H 19 LEU cc_start: 0.1852 (OUTLIER) cc_final: 0.1647 (tp) REVERT: H 39 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6664 (tm-30) REVERT: H 76 ARG cc_start: 0.4820 (tpt170) cc_final: 0.3348 (ptm-80) REVERT: H 131 CYS cc_start: 0.4699 (m) cc_final: 0.4147 (p) REVERT: H 198 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6719 (tt) REVERT: L 56 GLN cc_start: 0.7965 (mp10) cc_final: 0.7689 (mp10) REVERT: L 100 MET cc_start: 0.7678 (mmt) cc_final: 0.7319 (mmm) REVERT: M 34 MET cc_start: 0.6089 (mmp) cc_final: 0.5610 (mmp) REVERT: N 147 ASN cc_start: 0.6782 (t160) cc_final: 0.6298 (t0) outliers start: 264 outliers final: 177 residues processed: 905 average time/residue: 0.5106 time to fit residues: 751.2842 Evaluate side-chains 863 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 658 time to evaluate : 4.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 184 PHE Chi-restraints excluded: chain 2 residue 253 LEU Chi-restraints excluded: chain 2 residue 277 GLU Chi-restraints excluded: chain 2 residue 282 PHE Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 375 ILE Chi-restraints excluded: chain 2 residue 379 LYS Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 398 GLU Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 402 ILE Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 462 VAL Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 520 TYR Chi-restraints excluded: chain 2 residue 524 VAL Chi-restraints excluded: chain 2 residue 532 THR Chi-restraints excluded: chain 2 residue 574 PHE Chi-restraints excluded: chain 2 residue 584 SER Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 616 ASN Chi-restraints excluded: chain 2 residue 647 VAL Chi-restraints excluded: chain 2 residue 698 ARG Chi-restraints excluded: chain 2 residue 785 PHE Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 121 MET Chi-restraints excluded: chain 3 residue 122 VAL Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 203 GLU Chi-restraints excluded: chain 3 residue 234 ILE Chi-restraints excluded: chain 3 residue 238 TYR Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 277 ASP Chi-restraints excluded: chain 3 residue 290 ILE Chi-restraints excluded: chain 3 residue 293 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 315 LEU Chi-restraints excluded: chain 3 residue 333 ASP Chi-restraints excluded: chain 3 residue 343 SER Chi-restraints excluded: chain 3 residue 371 VAL Chi-restraints excluded: chain 3 residue 394 VAL Chi-restraints excluded: chain 3 residue 420 VAL Chi-restraints excluded: chain 3 residue 443 VAL Chi-restraints excluded: chain 3 residue 448 ASN Chi-restraints excluded: chain 3 residue 479 VAL Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 488 VAL Chi-restraints excluded: chain 3 residue 557 LEU Chi-restraints excluded: chain 4 residue 154 VAL Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 221 PHE Chi-restraints excluded: chain 4 residue 248 PHE Chi-restraints excluded: chain 4 residue 296 SER Chi-restraints excluded: chain 4 residue 316 THR Chi-restraints excluded: chain 4 residue 338 HIS Chi-restraints excluded: chain 4 residue 347 SER Chi-restraints excluded: chain 4 residue 350 THR Chi-restraints excluded: chain 4 residue 363 ASP Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 396 ILE Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 424 PHE Chi-restraints excluded: chain 4 residue 556 ARG Chi-restraints excluded: chain 4 residue 573 CYS Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 593 MET Chi-restraints excluded: chain 4 residue 626 TRP Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 671 LEU Chi-restraints excluded: chain 4 residue 686 MET Chi-restraints excluded: chain 4 residue 689 LEU Chi-restraints excluded: chain 4 residue 752 SER Chi-restraints excluded: chain 4 residue 764 TRP Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 52 ASP Chi-restraints excluded: chain 5 residue 123 LEU Chi-restraints excluded: chain 5 residue 130 THR Chi-restraints excluded: chain 5 residue 144 VAL Chi-restraints excluded: chain 5 residue 154 SER Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 253 VAL Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 314 ASP Chi-restraints excluded: chain 5 residue 348 LYS Chi-restraints excluded: chain 5 residue 371 ASP Chi-restraints excluded: chain 5 residue 377 LEU Chi-restraints excluded: chain 5 residue 384 LYS Chi-restraints excluded: chain 5 residue 421 THR Chi-restraints excluded: chain 5 residue 486 ASN Chi-restraints excluded: chain 5 residue 529 LEU Chi-restraints excluded: chain 5 residue 556 SER Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 590 SER Chi-restraints excluded: chain 5 residue 608 THR Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 56 GLU Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 132 SER Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 166 PHE Chi-restraints excluded: chain 6 residue 167 LYS Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 204 GLU Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 381 ASP Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 426 VAL Chi-restraints excluded: chain 6 residue 448 ILE Chi-restraints excluded: chain 6 residue 461 ASP Chi-restraints excluded: chain 6 residue 529 VAL Chi-restraints excluded: chain 6 residue 531 GLU Chi-restraints excluded: chain 6 residue 630 ASN Chi-restraints excluded: chain 6 residue 644 LEU Chi-restraints excluded: chain 7 residue 6 TYR Chi-restraints excluded: chain 7 residue 25 ASP Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 72 ARG Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain 7 residue 149 ILE Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 195 VAL Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 238 GLN Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 262 THR Chi-restraints excluded: chain 7 residue 295 GLU Chi-restraints excluded: chain 7 residue 329 GLN Chi-restraints excluded: chain 7 residue 344 ILE Chi-restraints excluded: chain 7 residue 358 LEU Chi-restraints excluded: chain 7 residue 362 VAL Chi-restraints excluded: chain 7 residue 382 ASP Chi-restraints excluded: chain 7 residue 397 LEU Chi-restraints excluded: chain 7 residue 436 LEU Chi-restraints excluded: chain 7 residue 458 ILE Chi-restraints excluded: chain 7 residue 484 ILE Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 555 ASP Chi-restraints excluded: chain 7 residue 601 THR Chi-restraints excluded: chain 7 residue 625 VAL Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 135 PHE Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain L residue 153 ILE Chi-restraints excluded: chain M residue 15 ASP Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 115 HIS Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 115 PHE Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 211 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 454 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 268 optimal weight: 0.9980 chunk 344 optimal weight: 2.9990 chunk 266 optimal weight: 0.7980 chunk 396 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 469 optimal weight: 1.9990 chunk 293 optimal weight: 5.9990 chunk 286 optimal weight: 3.9990 chunk 216 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 267 HIS ** 2 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 754 HIS 3 310 GLN 3 335 ASN ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 644 GLN 6 203 GLN ** 6 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 589 ASN ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 301 HIS A 264 HIS ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 ASN ** L 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 97 GLN L 147 ASN M 53 ASN M 131 HIS N 118 HIS N 142 GLN N 147 ASN N 162 ASN N 224 GLN N 226 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 moved from start: 0.8887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 40466 Z= 0.281 Angle : 0.779 18.023 54822 Z= 0.391 Chirality : 0.047 0.270 6193 Planarity : 0.006 0.083 6950 Dihedral : 11.717 115.165 5894 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.59 % Favored : 86.41 % Rotamer: Outliers : 6.30 % Allowed : 25.74 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.11), residues: 4789 helix: -1.19 (0.13), residues: 1535 sheet: -2.53 (0.20), residues: 571 loop : -3.12 (0.11), residues: 2683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 297 HIS 0.009 0.001 HIS H 71 PHE 0.052 0.002 PHE L 84 TYR 0.023 0.002 TYR A 391 ARG 0.012 0.001 ARG 6 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 683 time to evaluate : 4.800 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: 2 250 ASP cc_start: 0.7760 (t0) cc_final: 0.7252 (t0) REVERT: 2 253 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6951 (mp) REVERT: 2 294 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7560 (tt) REVERT: 2 329 ASN cc_start: 0.4098 (m-40) cc_final: 0.3794 (t0) REVERT: 2 350 MET cc_start: 0.4638 (mmt) cc_final: 0.3546 (ptp) REVERT: 2 351 GLU cc_start: 0.6436 (pm20) cc_final: 0.6039 (mt-10) REVERT: 2 379 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7500 (tptp) REVERT: 2 398 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6996 (mt-10) REVERT: 2 645 LEU cc_start: 0.5788 (tt) cc_final: 0.4725 (mp) REVERT: 2 662 LYS cc_start: 0.7709 (mttt) cc_final: 0.7301 (mtmt) REVERT: 2 723 MET cc_start: 0.5572 (mmt) cc_final: 0.4125 (tmm) REVERT: 2 727 LEU cc_start: 0.5868 (OUTLIER) cc_final: 0.5579 (mp) REVERT: 2 797 LYS cc_start: 0.4713 (OUTLIER) cc_final: 0.3799 (tmtt) REVERT: 3 8 PHE cc_start: 0.4930 (p90) cc_final: 0.4333 (m-80) REVERT: 3 14 ARG cc_start: 0.8377 (tpp80) cc_final: 0.8053 (mmt-90) REVERT: 3 277 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7943 (m-30) REVERT: 3 462 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7295 (tp30) REVERT: 3 468 ASP cc_start: 0.8629 (t70) cc_final: 0.8325 (t0) REVERT: 3 590 ARG cc_start: 0.6188 (tpp-160) cc_final: 0.5829 (tpt170) REVERT: 3 617 ARG cc_start: 0.4750 (mpp80) cc_final: 0.4474 (mtt90) REVERT: 3 637 HIS cc_start: 0.7219 (m-70) cc_final: 0.6301 (t-170) REVERT: 4 221 PHE cc_start: 0.5180 (OUTLIER) cc_final: 0.4403 (t80) REVERT: 4 242 MET cc_start: 0.2263 (tpp) cc_final: 0.0980 (ptt) REVERT: 4 248 PHE cc_start: 0.6657 (OUTLIER) cc_final: 0.6427 (m-10) REVERT: 4 463 ARG cc_start: 0.6146 (mtt180) cc_final: 0.5580 (ttt-90) REVERT: 4 521 MET cc_start: 0.7942 (ttp) cc_final: 0.7565 (ptm) REVERT: 4 532 SER cc_start: 0.8688 (t) cc_final: 0.8440 (p) REVERT: 4 556 ARG cc_start: 0.6038 (OUTLIER) cc_final: 0.5223 (ttt-90) REVERT: 4 697 ARG cc_start: 0.9049 (mmm160) cc_final: 0.8644 (ttt180) REVERT: 5 126 ASN cc_start: 0.7226 (m-40) cc_final: 0.7018 (m-40) REVERT: 5 259 LEU cc_start: 0.7970 (mt) cc_final: 0.7730 (mt) REVERT: 5 308 TYR cc_start: 0.4534 (OUTLIER) cc_final: 0.4129 (m-10) REVERT: 5 361 ARG cc_start: 0.8272 (ptm160) cc_final: 0.7715 (ttt90) REVERT: 5 384 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6977 (mtmt) REVERT: 6 90 ASN cc_start: 0.7432 (t0) cc_final: 0.6831 (t0) REVERT: 6 95 ARG cc_start: 0.3595 (mtm-85) cc_final: 0.2184 (mtm110) REVERT: 6 167 LYS cc_start: 0.6178 (OUTLIER) cc_final: 0.5241 (ttpt) REVERT: 6 170 ASN cc_start: 0.5532 (m-40) cc_final: 0.4804 (p0) REVERT: 6 299 THR cc_start: -0.1180 (OUTLIER) cc_final: -0.1431 (m) REVERT: 6 382 ILE cc_start: 0.8398 (pt) cc_final: 0.8177 (pt) REVERT: 6 469 MET cc_start: 0.7142 (ptm) cc_final: 0.6738 (ptp) REVERT: 6 519 MET cc_start: 0.7152 (ptt) cc_final: 0.6623 (ptp) REVERT: 6 652 GLU cc_start: 0.6763 (tt0) cc_final: 0.6485 (tp30) REVERT: 7 48 ILE cc_start: 0.2380 (OUTLIER) cc_final: 0.1991 (pt) REVERT: 7 182 TYR cc_start: 0.6018 (m-80) cc_final: 0.5483 (m-80) REVERT: 7 221 TYR cc_start: 0.6840 (t80) cc_final: 0.6459 (t80) REVERT: 7 238 GLN cc_start: 0.6571 (OUTLIER) cc_final: 0.6106 (tm-30) REVERT: 7 299 GLN cc_start: 0.7547 (tp-100) cc_final: 0.7290 (tp-100) REVERT: 7 369 MET cc_start: 0.5007 (ttt) cc_final: 0.4389 (mmm) REVERT: 7 402 GLN cc_start: 0.6897 (mt0) cc_final: 0.6609 (mt0) REVERT: 7 427 MET cc_start: 0.2843 (mmm) cc_final: 0.1396 (mmm) REVERT: 7 439 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8119 (mt0) REVERT: 7 475 MET cc_start: 0.5140 (pmm) cc_final: 0.4314 (pmm) REVERT: 7 552 LYS cc_start: 0.5465 (mppt) cc_final: 0.5159 (tptt) REVERT: 7 627 LYS cc_start: 0.6777 (tptp) cc_final: 0.6201 (tttm) REVERT: A 6 LEU cc_start: 0.3301 (OUTLIER) cc_final: 0.2358 (pp) REVERT: A 101 HIS cc_start: 0.6265 (OUTLIER) cc_final: 0.5512 (p90) REVERT: A 166 ASP cc_start: 0.0543 (OUTLIER) cc_final: -0.1886 (t0) REVERT: A 230 MET cc_start: 0.6012 (mmm) cc_final: 0.4996 (mtt) REVERT: A 303 MET cc_start: 0.7806 (mtt) cc_final: 0.7348 (mtt) REVERT: A 304 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.5888 (ttp80) REVERT: A 312 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6434 (mp10) REVERT: A 440 PHE cc_start: 0.5689 (t80) cc_final: 0.5404 (t80) REVERT: A 533 LYS cc_start: 0.7421 (ttmt) cc_final: 0.6973 (mmmt) REVERT: A 535 PHE cc_start: 0.4888 (m-80) cc_final: 0.4616 (m-80) REVERT: A 541 LYS cc_start: 0.8346 (tptt) cc_final: 0.7711 (tmmt) REVERT: A 567 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6360 (mm) REVERT: H 19 LEU cc_start: 0.2168 (OUTLIER) cc_final: 0.1913 (tp) REVERT: H 39 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6536 (tm-30) REVERT: H 76 ARG cc_start: 0.5069 (tpt170) cc_final: 0.3453 (ptm-80) REVERT: H 131 CYS cc_start: 0.5182 (m) cc_final: 0.4797 (p) REVERT: H 198 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6781 (tt) REVERT: L 27 HIS cc_start: 0.4519 (OUTLIER) cc_final: 0.4205 (t70) REVERT: L 56 GLN cc_start: 0.7884 (mp10) cc_final: 0.7501 (mp10) REVERT: L 100 MET cc_start: 0.7550 (mmt) cc_final: 0.7297 (mmm) REVERT: L 114 ARG cc_start: 0.6987 (tmm160) cc_final: 0.5501 (mmm-85) REVERT: L 167 ILE cc_start: 0.7011 (mp) cc_final: 0.6781 (mp) REVERT: M 45 ASP cc_start: 0.3104 (OUTLIER) cc_final: 0.2299 (m-30) REVERT: M 125 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8443 (tp) REVERT: N 80 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7420 (pp) outliers start: 269 outliers final: 187 residues processed: 880 average time/residue: 0.4945 time to fit residues: 710.1082 Evaluate side-chains 858 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 643 time to evaluate : 4.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 216 VAL Chi-restraints excluded: chain 2 residue 253 LEU Chi-restraints excluded: chain 2 residue 277 GLU Chi-restraints excluded: chain 2 residue 282 PHE Chi-restraints excluded: chain 2 residue 294 LEU Chi-restraints excluded: chain 2 residue 296 VAL Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 375 ILE Chi-restraints excluded: chain 2 residue 379 LYS Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 398 GLU Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 402 ILE Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 520 TYR Chi-restraints excluded: chain 2 residue 524 VAL Chi-restraints excluded: chain 2 residue 532 THR Chi-restraints excluded: chain 2 residue 574 PHE Chi-restraints excluded: chain 2 residue 584 SER Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 604 SER Chi-restraints excluded: chain 2 residue 616 ASN Chi-restraints excluded: chain 2 residue 647 VAL Chi-restraints excluded: chain 2 residue 698 ARG Chi-restraints excluded: chain 2 residue 727 LEU Chi-restraints excluded: chain 2 residue 741 VAL Chi-restraints excluded: chain 2 residue 785 PHE Chi-restraints excluded: chain 2 residue 797 LYS Chi-restraints excluded: chain 3 residue 20 LEU Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 118 LEU Chi-restraints excluded: chain 3 residue 121 MET Chi-restraints excluded: chain 3 residue 122 VAL Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 234 ILE Chi-restraints excluded: chain 3 residue 238 TYR Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 256 VAL Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 277 ASP Chi-restraints excluded: chain 3 residue 290 ILE Chi-restraints excluded: chain 3 residue 293 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 315 LEU Chi-restraints excluded: chain 3 residue 326 ASN Chi-restraints excluded: chain 3 residue 333 ASP Chi-restraints excluded: chain 3 residue 371 VAL Chi-restraints excluded: chain 3 residue 394 VAL Chi-restraints excluded: chain 3 residue 397 ASP Chi-restraints excluded: chain 3 residue 420 VAL Chi-restraints excluded: chain 3 residue 448 ASN Chi-restraints excluded: chain 3 residue 479 VAL Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 557 LEU Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 221 PHE Chi-restraints excluded: chain 4 residue 248 PHE Chi-restraints excluded: chain 4 residue 277 LEU Chi-restraints excluded: chain 4 residue 296 SER Chi-restraints excluded: chain 4 residue 316 THR Chi-restraints excluded: chain 4 residue 338 HIS Chi-restraints excluded: chain 4 residue 347 SER Chi-restraints excluded: chain 4 residue 363 ASP Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 396 ILE Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 424 PHE Chi-restraints excluded: chain 4 residue 556 ARG Chi-restraints excluded: chain 4 residue 573 CYS Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 613 THR Chi-restraints excluded: chain 4 residue 626 TRP Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 671 LEU Chi-restraints excluded: chain 4 residue 686 MET Chi-restraints excluded: chain 4 residue 689 LEU Chi-restraints excluded: chain 4 residue 752 SER Chi-restraints excluded: chain 4 residue 764 TRP Chi-restraints excluded: chain 5 residue 52 ASP Chi-restraints excluded: chain 5 residue 123 LEU Chi-restraints excluded: chain 5 residue 130 THR Chi-restraints excluded: chain 5 residue 144 VAL Chi-restraints excluded: chain 5 residue 154 SER Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 308 TYR Chi-restraints excluded: chain 5 residue 311 ILE Chi-restraints excluded: chain 5 residue 314 ASP Chi-restraints excluded: chain 5 residue 339 SER Chi-restraints excluded: chain 5 residue 371 ASP Chi-restraints excluded: chain 5 residue 377 LEU Chi-restraints excluded: chain 5 residue 384 LYS Chi-restraints excluded: chain 5 residue 394 VAL Chi-restraints excluded: chain 5 residue 421 THR Chi-restraints excluded: chain 5 residue 444 PHE Chi-restraints excluded: chain 5 residue 529 LEU Chi-restraints excluded: chain 5 residue 556 SER Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 590 SER Chi-restraints excluded: chain 5 residue 608 THR Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 56 GLU Chi-restraints excluded: chain 6 residue 57 VAL Chi-restraints excluded: chain 6 residue 121 THR Chi-restraints excluded: chain 6 residue 132 SER Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 166 PHE Chi-restraints excluded: chain 6 residue 167 LYS Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 363 GLN Chi-restraints excluded: chain 6 residue 381 ASP Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 426 VAL Chi-restraints excluded: chain 6 residue 529 VAL Chi-restraints excluded: chain 6 residue 531 GLU Chi-restraints excluded: chain 6 residue 630 ASN Chi-restraints excluded: chain 6 residue 644 LEU Chi-restraints excluded: chain 7 residue 6 TYR Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 7 residue 72 ARG Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain 7 residue 149 ILE Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 195 VAL Chi-restraints excluded: chain 7 residue 198 LEU Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 238 GLN Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 262 THR Chi-restraints excluded: chain 7 residue 295 GLU Chi-restraints excluded: chain 7 residue 329 GLN Chi-restraints excluded: chain 7 residue 358 LEU Chi-restraints excluded: chain 7 residue 362 VAL Chi-restraints excluded: chain 7 residue 374 ASN Chi-restraints excluded: chain 7 residue 397 LEU Chi-restraints excluded: chain 7 residue 436 LEU Chi-restraints excluded: chain 7 residue 458 ILE Chi-restraints excluded: chain 7 residue 484 ILE Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 555 ASP Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 505 CYS Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 27 HIS Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 135 PHE Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 154 HIS Chi-restraints excluded: chain M residue 15 ASP Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 58 TYR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 115 PHE Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 211 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 290 optimal weight: 7.9990 chunk 187 optimal weight: 0.7980 chunk 280 optimal weight: 0.1980 chunk 141 optimal weight: 0.0000 chunk 92 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 chunk 319 optimal weight: 2.9990 chunk 232 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 368 optimal weight: 5.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 754 HIS ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 620 ASN ** 4 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 57 ASN ** 6 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 270 HIS H 71 HIS ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 HIS N 118 HIS N 162 ASN N 224 GLN N 226 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 moved from start: 0.9184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40466 Z= 0.205 Angle : 0.723 17.739 54822 Z= 0.360 Chirality : 0.045 0.219 6193 Planarity : 0.005 0.086 6950 Dihedral : 11.492 106.018 5893 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer: Outliers : 5.15 % Allowed : 27.10 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.11), residues: 4789 helix: -1.07 (0.13), residues: 1543 sheet: -2.41 (0.21), residues: 577 loop : -3.05 (0.11), residues: 2669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 170 HIS 0.010 0.001 HIS 7 536 PHE 0.067 0.002 PHE 6 641 TYR 0.039 0.002 TYR 3 588 ARG 0.008 0.000 ARG 6 478 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 686 time to evaluate : 4.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 250 ASP cc_start: 0.7707 (t0) cc_final: 0.7179 (t0) REVERT: 2 253 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6873 (mp) REVERT: 2 294 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7512 (tt) REVERT: 2 329 ASN cc_start: 0.3705 (m-40) cc_final: 0.3168 (t0) REVERT: 2 350 MET cc_start: 0.4445 (mmt) cc_final: 0.3658 (ptp) REVERT: 2 351 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.6145 (mt-10) REVERT: 2 379 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7463 (tptp) REVERT: 2 398 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6962 (mt-10) REVERT: 2 454 LYS cc_start: 0.7836 (mttp) cc_final: 0.7477 (mptt) REVERT: 2 645 LEU cc_start: 0.5788 (tt) cc_final: 0.4749 (mp) REVERT: 2 662 LYS cc_start: 0.7625 (mttt) cc_final: 0.7237 (mtmt) REVERT: 2 723 MET cc_start: 0.5573 (mmt) cc_final: 0.4239 (tmm) REVERT: 2 727 LEU cc_start: 0.5711 (OUTLIER) cc_final: 0.5471 (mp) REVERT: 2 792 ARG cc_start: 0.7517 (mpt180) cc_final: 0.6730 (mtt180) REVERT: 3 14 ARG cc_start: 0.8277 (tpp80) cc_final: 0.8053 (mmt180) REVERT: 3 62 LEU cc_start: 0.7071 (tp) cc_final: 0.6848 (tp) REVERT: 3 468 ASP cc_start: 0.8589 (t70) cc_final: 0.8273 (t0) REVERT: 3 499 MET cc_start: 0.5921 (tpp) cc_final: 0.5493 (mmp) REVERT: 3 590 ARG cc_start: 0.6239 (tpp-160) cc_final: 0.5691 (tpm170) REVERT: 3 617 ARG cc_start: 0.4699 (mpp80) cc_final: 0.4363 (mtt90) REVERT: 3 637 HIS cc_start: 0.7240 (m-70) cc_final: 0.6386 (t-170) REVERT: 4 189 ILE cc_start: 0.3691 (tt) cc_final: 0.3164 (mp) REVERT: 4 221 PHE cc_start: 0.5019 (OUTLIER) cc_final: 0.4252 (t80) REVERT: 4 242 MET cc_start: 0.2208 (tpp) cc_final: 0.0887 (ptt) REVERT: 4 248 PHE cc_start: 0.6662 (OUTLIER) cc_final: 0.6416 (m-10) REVERT: 4 463 ARG cc_start: 0.6253 (mtt180) cc_final: 0.5593 (ttt-90) REVERT: 4 487 PHE cc_start: 0.6622 (m-80) cc_final: 0.6168 (m-80) REVERT: 4 521 MET cc_start: 0.7798 (ttp) cc_final: 0.7421 (ptm) REVERT: 4 532 SER cc_start: 0.8697 (t) cc_final: 0.8415 (p) REVERT: 4 556 ARG cc_start: 0.5973 (OUTLIER) cc_final: 0.5166 (ttt-90) REVERT: 4 697 ARG cc_start: 0.8948 (mmm160) cc_final: 0.8635 (ttt180) REVERT: 4 772 LYS cc_start: 0.0902 (tptt) cc_final: 0.0360 (tppt) REVERT: 5 123 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6702 (mp) REVERT: 5 220 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6869 (tp40) REVERT: 5 259 LEU cc_start: 0.7715 (mt) cc_final: 0.7462 (mt) REVERT: 5 308 TYR cc_start: 0.4491 (OUTLIER) cc_final: 0.4081 (m-10) REVERT: 5 361 ARG cc_start: 0.8197 (ptm160) cc_final: 0.7727 (ttt90) REVERT: 6 90 ASN cc_start: 0.7434 (t0) cc_final: 0.6865 (t0) REVERT: 6 95 ARG cc_start: 0.3598 (mtm-85) cc_final: 0.2469 (mtm180) REVERT: 6 167 LYS cc_start: 0.6271 (OUTLIER) cc_final: 0.5441 (ttpt) REVERT: 6 170 ASN cc_start: 0.5504 (m-40) cc_final: 0.4840 (p0) REVERT: 6 299 THR cc_start: -0.1343 (OUTLIER) cc_final: -0.1558 (m) REVERT: 6 330 TYR cc_start: 0.8293 (t80) cc_final: 0.7992 (m-80) REVERT: 6 382 ILE cc_start: 0.8347 (pt) cc_final: 0.8113 (pt) REVERT: 6 519 MET cc_start: 0.7079 (ptt) cc_final: 0.6537 (ptp) REVERT: 6 621 GLU cc_start: 0.5076 (pp20) cc_final: 0.4120 (pt0) REVERT: 6 652 GLU cc_start: 0.6774 (tt0) cc_final: 0.6524 (tp30) REVERT: 7 3 ARG cc_start: 0.4576 (ttp80) cc_final: 0.3662 (mmt-90) REVERT: 7 48 ILE cc_start: 0.2265 (OUTLIER) cc_final: 0.1866 (pt) REVERT: 7 182 TYR cc_start: 0.6248 (m-80) cc_final: 0.5808 (m-80) REVERT: 7 238 GLN cc_start: 0.6739 (OUTLIER) cc_final: 0.6426 (tm-30) REVERT: 7 299 GLN cc_start: 0.7320 (tp-100) cc_final: 0.7013 (tp-100) REVERT: 7 397 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6778 (mm) REVERT: 7 427 MET cc_start: 0.2649 (mmm) cc_final: 0.1295 (mmm) REVERT: 7 439 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8027 (mt0) REVERT: 7 475 MET cc_start: 0.4763 (pmm) cc_final: 0.4063 (pmm) REVERT: 7 552 LYS cc_start: 0.5478 (mppt) cc_final: 0.5177 (tptt) REVERT: 7 556 MET cc_start: 0.4636 (pmm) cc_final: 0.4148 (ppp) REVERT: 7 627 LYS cc_start: 0.6775 (tptp) cc_final: 0.6219 (mttt) REVERT: A 6 LEU cc_start: 0.3259 (OUTLIER) cc_final: 0.2438 (pp) REVERT: A 17 LYS cc_start: 0.3663 (tmtt) cc_final: 0.2569 (tptt) REVERT: A 230 MET cc_start: 0.5947 (mmm) cc_final: 0.5431 (mtt) REVERT: A 303 MET cc_start: 0.7521 (mtt) cc_final: 0.7055 (mtt) REVERT: A 304 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.7038 (ttp80) REVERT: A 312 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6335 (mp10) REVERT: A 513 MET cc_start: 0.6515 (ppp) cc_final: 0.2460 (mmm) REVERT: A 533 LYS cc_start: 0.7419 (ttmt) cc_final: 0.7005 (mmmt) REVERT: A 535 PHE cc_start: 0.4869 (m-80) cc_final: 0.4573 (m-80) REVERT: A 541 LYS cc_start: 0.8277 (tptt) cc_final: 0.7681 (tmmt) REVERT: H 19 LEU cc_start: 0.2316 (OUTLIER) cc_final: 0.2084 (tp) REVERT: H 39 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6504 (tm-30) REVERT: H 76 ARG cc_start: 0.5114 (tpt170) cc_final: 0.3745 (ptm-80) REVERT: H 131 CYS cc_start: 0.5157 (m) cc_final: 0.4785 (p) REVERT: H 198 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7154 (tt) REVERT: L 56 GLN cc_start: 0.7839 (mp10) cc_final: 0.7119 (pp30) REVERT: L 100 MET cc_start: 0.7455 (mmt) cc_final: 0.7146 (mmm) REVERT: L 114 ARG cc_start: 0.6777 (tmm160) cc_final: 0.5428 (mmm-85) REVERT: L 170 TYR cc_start: 0.4489 (t80) cc_final: 0.4147 (t80) REVERT: M 34 MET cc_start: 0.6470 (mmp) cc_final: 0.5812 (mmp) REVERT: N 80 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7176 (pp) outliers start: 220 outliers final: 167 residues processed: 843 average time/residue: 0.4933 time to fit residues: 677.5627 Evaluate side-chains 844 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 654 time to evaluate : 4.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 184 PHE Chi-restraints excluded: chain 2 residue 216 VAL Chi-restraints excluded: chain 2 residue 253 LEU Chi-restraints excluded: chain 2 residue 277 GLU Chi-restraints excluded: chain 2 residue 294 LEU Chi-restraints excluded: chain 2 residue 351 GLU Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 375 ILE Chi-restraints excluded: chain 2 residue 379 LYS Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 398 GLU Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 402 ILE Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 509 ASP Chi-restraints excluded: chain 2 residue 520 TYR Chi-restraints excluded: chain 2 residue 524 VAL Chi-restraints excluded: chain 2 residue 532 THR Chi-restraints excluded: chain 2 residue 574 PHE Chi-restraints excluded: chain 2 residue 584 SER Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 616 ASN Chi-restraints excluded: chain 2 residue 647 VAL Chi-restraints excluded: chain 2 residue 698 ARG Chi-restraints excluded: chain 2 residue 727 LEU Chi-restraints excluded: chain 2 residue 785 PHE Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 121 MET Chi-restraints excluded: chain 3 residue 122 VAL Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 234 ILE Chi-restraints excluded: chain 3 residue 238 TYR Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 290 ILE Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 315 LEU Chi-restraints excluded: chain 3 residue 333 ASP Chi-restraints excluded: chain 3 residue 371 VAL Chi-restraints excluded: chain 3 residue 394 VAL Chi-restraints excluded: chain 3 residue 397 ASP Chi-restraints excluded: chain 3 residue 420 VAL Chi-restraints excluded: chain 3 residue 448 ASN Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 557 LEU Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 221 PHE Chi-restraints excluded: chain 4 residue 248 PHE Chi-restraints excluded: chain 4 residue 277 LEU Chi-restraints excluded: chain 4 residue 296 SER Chi-restraints excluded: chain 4 residue 316 THR Chi-restraints excluded: chain 4 residue 338 HIS Chi-restraints excluded: chain 4 residue 347 SER Chi-restraints excluded: chain 4 residue 363 ASP Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 396 ILE Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 486 LEU Chi-restraints excluded: chain 4 residue 535 THR Chi-restraints excluded: chain 4 residue 556 ARG Chi-restraints excluded: chain 4 residue 573 CYS Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 613 THR Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 671 LEU Chi-restraints excluded: chain 4 residue 686 MET Chi-restraints excluded: chain 4 residue 752 SER Chi-restraints excluded: chain 4 residue 764 TRP Chi-restraints excluded: chain 5 residue 52 ASP Chi-restraints excluded: chain 5 residue 123 LEU Chi-restraints excluded: chain 5 residue 130 THR Chi-restraints excluded: chain 5 residue 144 VAL Chi-restraints excluded: chain 5 residue 154 SER Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 226 GLU Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 308 TYR Chi-restraints excluded: chain 5 residue 314 ASP Chi-restraints excluded: chain 5 residue 371 ASP Chi-restraints excluded: chain 5 residue 377 LEU Chi-restraints excluded: chain 5 residue 394 VAL Chi-restraints excluded: chain 5 residue 421 THR Chi-restraints excluded: chain 5 residue 444 PHE Chi-restraints excluded: chain 5 residue 529 LEU Chi-restraints excluded: chain 5 residue 556 SER Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 590 SER Chi-restraints excluded: chain 5 residue 608 THR Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 56 GLU Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 104 CYS Chi-restraints excluded: chain 6 residue 132 SER Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 166 PHE Chi-restraints excluded: chain 6 residue 167 LYS Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 381 ASP Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 426 VAL Chi-restraints excluded: chain 6 residue 529 VAL Chi-restraints excluded: chain 6 residue 531 GLU Chi-restraints excluded: chain 6 residue 630 ASN Chi-restraints excluded: chain 6 residue 644 LEU Chi-restraints excluded: chain 7 residue 6 TYR Chi-restraints excluded: chain 7 residue 31 PHE Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 72 ARG Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain 7 residue 143 THR Chi-restraints excluded: chain 7 residue 149 ILE Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 195 VAL Chi-restraints excluded: chain 7 residue 198 LEU Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 238 GLN Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 262 THR Chi-restraints excluded: chain 7 residue 329 GLN Chi-restraints excluded: chain 7 residue 336 LEU Chi-restraints excluded: chain 7 residue 344 ILE Chi-restraints excluded: chain 7 residue 358 LEU Chi-restraints excluded: chain 7 residue 397 LEU Chi-restraints excluded: chain 7 residue 436 LEU Chi-restraints excluded: chain 7 residue 458 ILE Chi-restraints excluded: chain 7 residue 484 ILE Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 555 ASP Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 135 PHE Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain M residue 15 ASP Chi-restraints excluded: chain M residue 58 TYR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 115 HIS Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 115 PHE Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 426 optimal weight: 0.3980 chunk 449 optimal weight: 0.0870 chunk 410 optimal weight: 2.9990 chunk 437 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 190 optimal weight: 0.3980 chunk 343 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 chunk 395 optimal weight: 0.0770 chunk 413 optimal weight: 0.9990 chunk 435 optimal weight: 0.8980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 57 ASN ** 6 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 HIS N 118 HIS N 162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5933 moved from start: 0.9374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 40466 Z= 0.179 Angle : 0.699 16.895 54822 Z= 0.346 Chirality : 0.044 0.249 6193 Planarity : 0.005 0.097 6950 Dihedral : 11.220 96.854 5893 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 4.43 % Allowed : 28.18 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.11), residues: 4789 helix: -0.90 (0.13), residues: 1529 sheet: -2.23 (0.21), residues: 578 loop : -2.96 (0.11), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 170 HIS 0.009 0.001 HIS 7 536 PHE 0.049 0.001 PHE 6 641 TYR 0.031 0.001 TYR 3 588 ARG 0.013 0.000 ARG 5 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 683 time to evaluate : 4.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. REVERT: 2 250 ASP cc_start: 0.7628 (t0) cc_final: 0.7113 (t0) REVERT: 2 253 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7010 (mp) REVERT: 2 293 THR cc_start: 0.8292 (t) cc_final: 0.7433 (p) REVERT: 2 294 LEU cc_start: 0.8015 (pt) cc_final: 0.7377 (tt) REVERT: 2 329 ASN cc_start: 0.4125 (m-40) cc_final: 0.3614 (t0) REVERT: 2 350 MET cc_start: 0.4352 (mmt) cc_final: 0.3682 (ptp) REVERT: 2 351 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5960 (mt-10) REVERT: 2 379 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7398 (tptp) REVERT: 2 398 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6912 (mt-10) REVERT: 2 454 LYS cc_start: 0.7739 (mttp) cc_final: 0.7360 (mptt) REVERT: 2 645 LEU cc_start: 0.5599 (tt) cc_final: 0.4775 (mp) REVERT: 2 662 LYS cc_start: 0.7624 (mttt) cc_final: 0.7245 (mtmt) REVERT: 2 723 MET cc_start: 0.5732 (mmt) cc_final: 0.4653 (tmm) REVERT: 2 728 ARG cc_start: 0.5870 (tmm160) cc_final: 0.4831 (tpp-160) REVERT: 3 121 MET cc_start: 0.5849 (OUTLIER) cc_final: 0.5587 (ttt) REVERT: 3 462 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7723 (tm-30) REVERT: 3 468 ASP cc_start: 0.8535 (t70) cc_final: 0.8208 (t0) REVERT: 3 489 ASP cc_start: 0.4994 (p0) cc_final: 0.4736 (p0) REVERT: 3 637 HIS cc_start: 0.7176 (m-70) cc_final: 0.6407 (t-170) REVERT: 3 640 ILE cc_start: 0.7528 (tp) cc_final: 0.7176 (mt) REVERT: 3 641 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6615 (mt-10) REVERT: 4 189 ILE cc_start: 0.3648 (tt) cc_final: 0.3113 (mp) REVERT: 4 242 MET cc_start: 0.2180 (tpp) cc_final: 0.0886 (ptt) REVERT: 4 248 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.6415 (m-10) REVERT: 4 463 ARG cc_start: 0.6200 (mtt180) cc_final: 0.5487 (ttt-90) REVERT: 4 556 ARG cc_start: 0.5969 (OUTLIER) cc_final: 0.5219 (ttt-90) REVERT: 4 580 LYS cc_start: 0.8359 (tppt) cc_final: 0.7862 (tppt) REVERT: 4 697 ARG cc_start: 0.8925 (mmm160) cc_final: 0.8691 (ttt180) REVERT: 4 772 LYS cc_start: 0.1238 (tptt) cc_final: 0.0627 (tppt) REVERT: 5 123 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6822 (mp) REVERT: 5 220 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6742 (tp40) REVERT: 5 259 LEU cc_start: 0.7765 (mt) cc_final: 0.7512 (mt) REVERT: 5 308 TYR cc_start: 0.4346 (OUTLIER) cc_final: 0.3805 (m-10) REVERT: 5 321 ARG cc_start: 0.6990 (tpt170) cc_final: 0.6081 (tpm170) REVERT: 5 361 ARG cc_start: 0.8194 (ptm160) cc_final: 0.7811 (ttt90) REVERT: 5 444 PHE cc_start: 0.1267 (OUTLIER) cc_final: 0.0857 (p90) REVERT: 5 499 GLU cc_start: 0.6639 (mm-30) cc_final: 0.6350 (tp30) REVERT: 6 90 ASN cc_start: 0.7375 (t0) cc_final: 0.6802 (t0) REVERT: 6 95 ARG cc_start: 0.3598 (mtm-85) cc_final: 0.2708 (mtm180) REVERT: 6 167 LYS cc_start: 0.6240 (OUTLIER) cc_final: 0.5496 (ttpt) REVERT: 6 170 ASN cc_start: 0.5429 (m-40) cc_final: 0.4746 (p0) REVERT: 6 299 THR cc_start: -0.1346 (OUTLIER) cc_final: -0.1567 (m) REVERT: 6 330 TYR cc_start: 0.8405 (t80) cc_final: 0.8097 (m-80) REVERT: 6 382 ILE cc_start: 0.8393 (pt) cc_final: 0.8155 (pt) REVERT: 6 519 MET cc_start: 0.6773 (ptt) cc_final: 0.6219 (ptp) REVERT: 6 548 HIS cc_start: 0.5027 (m-70) cc_final: 0.4606 (m90) REVERT: 6 621 GLU cc_start: 0.5044 (pp20) cc_final: 0.4062 (pt0) REVERT: 6 652 GLU cc_start: 0.6707 (tt0) cc_final: 0.6426 (tp30) REVERT: 7 3 ARG cc_start: 0.4549 (ttp80) cc_final: 0.3641 (mmt-90) REVERT: 7 48 ILE cc_start: 0.2165 (OUTLIER) cc_final: 0.1760 (pt) REVERT: 7 182 TYR cc_start: 0.6300 (m-80) cc_final: 0.5935 (m-80) REVERT: 7 299 GLN cc_start: 0.7300 (tp-100) cc_final: 0.6993 (tp-100) REVERT: 7 369 MET cc_start: 0.4821 (ttt) cc_final: 0.4274 (mmm) REVERT: 7 397 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6662 (mm) REVERT: 7 427 MET cc_start: 0.2608 (mmm) cc_final: 0.1290 (mmm) REVERT: 7 439 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8006 (mt0) REVERT: 7 449 LYS cc_start: 0.6479 (mtpt) cc_final: 0.5931 (mptt) REVERT: 7 459 HIS cc_start: 0.7257 (m-70) cc_final: 0.6431 (t-90) REVERT: 7 475 MET cc_start: 0.4655 (pmm) cc_final: 0.3959 (pmm) REVERT: 7 552 LYS cc_start: 0.5440 (mppt) cc_final: 0.5154 (tptt) REVERT: 7 627 LYS cc_start: 0.6831 (tptp) cc_final: 0.6267 (mttt) REVERT: A 6 LEU cc_start: 0.3505 (OUTLIER) cc_final: 0.2670 (pp) REVERT: A 17 LYS cc_start: 0.3460 (tmtt) cc_final: 0.2456 (tptt) REVERT: A 101 HIS cc_start: 0.6041 (OUTLIER) cc_final: 0.5607 (p90) REVERT: A 230 MET cc_start: 0.6072 (mmm) cc_final: 0.5614 (mtt) REVERT: A 284 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8536 (p) REVERT: A 303 MET cc_start: 0.7464 (mtt) cc_final: 0.6845 (mtt) REVERT: A 312 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.6162 (mp10) REVERT: A 513 MET cc_start: 0.6722 (ppp) cc_final: 0.2823 (mmm) REVERT: A 533 LYS cc_start: 0.7145 (ttmt) cc_final: 0.6899 (mmmt) REVERT: A 535 PHE cc_start: 0.4906 (m-80) cc_final: 0.4636 (m-80) REVERT: A 541 LYS cc_start: 0.8241 (tptt) cc_final: 0.7703 (tmmt) REVERT: H 19 LEU cc_start: 0.2317 (OUTLIER) cc_final: 0.2094 (tp) REVERT: H 39 GLU cc_start: 0.6862 (mt-10) cc_final: 0.6522 (tm-30) REVERT: H 76 ARG cc_start: 0.5317 (tpt170) cc_final: 0.3669 (ptm-80) REVERT: H 131 CYS cc_start: 0.5252 (m) cc_final: 0.4821 (p) REVERT: H 198 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7152 (tt) REVERT: L 48 MET cc_start: 0.8520 (mtt) cc_final: 0.8139 (mtm) REVERT: L 100 MET cc_start: 0.7417 (mmt) cc_final: 0.7048 (mmm) REVERT: L 114 ARG cc_start: 0.6780 (tmm160) cc_final: 0.5213 (mmt90) REVERT: L 170 TYR cc_start: 0.4240 (t80) cc_final: 0.3910 (t80) REVERT: M 50 ARG cc_start: 0.6661 (mtm180) cc_final: 0.6304 (mtm-85) REVERT: N 80 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7092 (pp) outliers start: 189 outliers final: 143 residues processed: 815 average time/residue: 0.4990 time to fit residues: 663.3708 Evaluate side-chains 819 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 654 time to evaluate : 4.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 184 PHE Chi-restraints excluded: chain 2 residue 253 LEU Chi-restraints excluded: chain 2 residue 277 GLU Chi-restraints excluded: chain 2 residue 282 PHE Chi-restraints excluded: chain 2 residue 351 GLU Chi-restraints excluded: chain 2 residue 375 ILE Chi-restraints excluded: chain 2 residue 379 LYS Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 398 GLU Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 402 ILE Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 520 TYR Chi-restraints excluded: chain 2 residue 524 VAL Chi-restraints excluded: chain 2 residue 532 THR Chi-restraints excluded: chain 2 residue 574 PHE Chi-restraints excluded: chain 2 residue 584 SER Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 616 ASN Chi-restraints excluded: chain 2 residue 647 VAL Chi-restraints excluded: chain 2 residue 741 VAL Chi-restraints excluded: chain 2 residue 774 MET Chi-restraints excluded: chain 2 residue 785 PHE Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 121 MET Chi-restraints excluded: chain 3 residue 122 VAL Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 238 TYR Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 333 ASP Chi-restraints excluded: chain 3 residue 371 VAL Chi-restraints excluded: chain 3 residue 397 ASP Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 557 LEU Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 248 PHE Chi-restraints excluded: chain 4 residue 277 LEU Chi-restraints excluded: chain 4 residue 296 SER Chi-restraints excluded: chain 4 residue 316 THR Chi-restraints excluded: chain 4 residue 338 HIS Chi-restraints excluded: chain 4 residue 347 SER Chi-restraints excluded: chain 4 residue 363 ASP Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 396 ILE Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 556 ARG Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 613 THR Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 671 LEU Chi-restraints excluded: chain 4 residue 752 SER Chi-restraints excluded: chain 4 residue 764 TRP Chi-restraints excluded: chain 5 residue 52 ASP Chi-restraints excluded: chain 5 residue 123 LEU Chi-restraints excluded: chain 5 residue 130 THR Chi-restraints excluded: chain 5 residue 144 VAL Chi-restraints excluded: chain 5 residue 154 SER Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 253 VAL Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 308 TYR Chi-restraints excluded: chain 5 residue 311 ILE Chi-restraints excluded: chain 5 residue 314 ASP Chi-restraints excluded: chain 5 residue 339 SER Chi-restraints excluded: chain 5 residue 377 LEU Chi-restraints excluded: chain 5 residue 394 VAL Chi-restraints excluded: chain 5 residue 444 PHE Chi-restraints excluded: chain 5 residue 556 SER Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 608 THR Chi-restraints excluded: chain 5 residue 622 LEU Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 56 GLU Chi-restraints excluded: chain 6 residue 57 VAL Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 166 PHE Chi-restraints excluded: chain 6 residue 167 LYS Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 381 ASP Chi-restraints excluded: chain 6 residue 426 VAL Chi-restraints excluded: chain 6 residue 529 VAL Chi-restraints excluded: chain 6 residue 531 GLU Chi-restraints excluded: chain 6 residue 630 ASN Chi-restraints excluded: chain 6 residue 644 LEU Chi-restraints excluded: chain 7 residue 6 TYR Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain 7 residue 143 THR Chi-restraints excluded: chain 7 residue 149 ILE Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 195 VAL Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 329 GLN Chi-restraints excluded: chain 7 residue 344 ILE Chi-restraints excluded: chain 7 residue 358 LEU Chi-restraints excluded: chain 7 residue 397 LEU Chi-restraints excluded: chain 7 residue 436 LEU Chi-restraints excluded: chain 7 residue 458 ILE Chi-restraints excluded: chain 7 residue 484 ILE Chi-restraints excluded: chain 7 residue 555 ASP Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 135 PHE Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 154 HIS Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain M residue 15 ASP Chi-restraints excluded: chain M residue 58 TYR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 115 HIS Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 115 PHE Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 223 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 287 optimal weight: 1.9990 chunk 462 optimal weight: 1.9990 chunk 282 optimal weight: 0.0570 chunk 219 optimal weight: 6.9990 chunk 321 optimal weight: 3.9990 chunk 485 optimal weight: 6.9990 chunk 446 optimal weight: 0.7980 chunk 386 optimal weight: 0.7980 chunk 40 optimal weight: 0.0980 chunk 298 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 754 HIS 3 261 ASN ** 4 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 57 ASN 5 334 GLN ** 6 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 248 HIS 7 479 ASN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 ASN L 91 HIS M 131 HIS N 162 ASN N 226 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5982 moved from start: 0.9604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40466 Z= 0.204 Angle : 0.713 16.386 54822 Z= 0.354 Chirality : 0.045 0.330 6193 Planarity : 0.005 0.084 6950 Dihedral : 11.211 91.660 5893 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.80 % Favored : 88.20 % Rotamer: Outliers : 4.40 % Allowed : 28.16 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.11), residues: 4789 helix: -0.90 (0.13), residues: 1544 sheet: -2.12 (0.21), residues: 578 loop : -2.95 (0.11), residues: 2667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 170 HIS 0.009 0.001 HIS 6 584 PHE 0.047 0.002 PHE 6 641 TYR 0.027 0.002 TYR 3 16 ARG 0.018 0.000 ARG 5 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 652 time to evaluate : 4.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 250 ASP cc_start: 0.7707 (t0) cc_final: 0.7192 (t0) REVERT: 2 253 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7043 (mp) REVERT: 2 293 THR cc_start: 0.8334 (t) cc_final: 0.7535 (p) REVERT: 2 294 LEU cc_start: 0.8099 (pt) cc_final: 0.7403 (tt) REVERT: 2 329 ASN cc_start: 0.4044 (m-40) cc_final: 0.3606 (t0) REVERT: 2 350 MET cc_start: 0.4255 (mmt) cc_final: 0.3867 (ptp) REVERT: 2 351 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.6104 (mt-10) REVERT: 2 379 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7443 (tptp) REVERT: 2 398 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6951 (mt-10) REVERT: 2 454 LYS cc_start: 0.7700 (mttp) cc_final: 0.7191 (mptt) REVERT: 2 645 LEU cc_start: 0.5730 (tt) cc_final: 0.4866 (mp) REVERT: 2 662 LYS cc_start: 0.7734 (mttt) cc_final: 0.7499 (mttt) REVERT: 2 723 MET cc_start: 0.5694 (mmt) cc_final: 0.4431 (tmm) REVERT: 2 727 LEU cc_start: 0.5747 (OUTLIER) cc_final: 0.5335 (mp) REVERT: 2 728 ARG cc_start: 0.5592 (tmm160) cc_final: 0.4892 (tpp-160) REVERT: 3 254 ARG cc_start: 0.8680 (mtp85) cc_final: 0.8355 (ptp-170) REVERT: 3 322 LYS cc_start: 0.7504 (mtmm) cc_final: 0.7235 (mttp) REVERT: 3 421 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7406 (mtt) REVERT: 3 468 ASP cc_start: 0.8548 (t70) cc_final: 0.8225 (t0) REVERT: 3 637 HIS cc_start: 0.7172 (m-70) cc_final: 0.6403 (t-170) REVERT: 4 189 ILE cc_start: 0.3658 (tt) cc_final: 0.3098 (mp) REVERT: 4 242 MET cc_start: 0.2187 (tpp) cc_final: 0.0894 (ptt) REVERT: 4 248 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.6419 (m-10) REVERT: 4 463 ARG cc_start: 0.6302 (mtt180) cc_final: 0.5613 (ttt-90) REVERT: 4 556 ARG cc_start: 0.6020 (OUTLIER) cc_final: 0.5156 (ttt-90) REVERT: 4 697 ARG cc_start: 0.8958 (mmm160) cc_final: 0.8726 (ttt180) REVERT: 4 772 LYS cc_start: 0.1254 (tptt) cc_final: 0.0674 (tppt) REVERT: 5 116 MET cc_start: 0.7987 (mmm) cc_final: 0.7716 (mmm) REVERT: 5 220 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.6960 (tp40) REVERT: 5 259 LEU cc_start: 0.7897 (mt) cc_final: 0.7665 (mt) REVERT: 5 308 TYR cc_start: 0.4588 (OUTLIER) cc_final: 0.4300 (m-10) REVERT: 5 361 ARG cc_start: 0.8232 (ptm160) cc_final: 0.7790 (ttt90) REVERT: 5 447 MET cc_start: 0.7094 (ttp) cc_final: 0.6695 (ttp) REVERT: 5 499 GLU cc_start: 0.6764 (mm-30) cc_final: 0.6496 (tp30) REVERT: 6 86 GLN cc_start: 0.8208 (mp10) cc_final: 0.7888 (mp10) REVERT: 6 90 ASN cc_start: 0.7445 (t0) cc_final: 0.6923 (t0) REVERT: 6 95 ARG cc_start: 0.3711 (mtm-85) cc_final: 0.2810 (mtm180) REVERT: 6 167 LYS cc_start: 0.6267 (OUTLIER) cc_final: 0.5430 (ttpt) REVERT: 6 170 ASN cc_start: 0.5382 (m-40) cc_final: 0.4683 (p0) REVERT: 6 299 THR cc_start: -0.1506 (OUTLIER) cc_final: -0.1781 (m) REVERT: 6 330 TYR cc_start: 0.8420 (t80) cc_final: 0.8128 (m-80) REVERT: 6 382 ILE cc_start: 0.8380 (pt) cc_final: 0.8143 (pt) REVERT: 6 519 MET cc_start: 0.6845 (ptt) cc_final: 0.6279 (ptp) REVERT: 6 548 HIS cc_start: 0.5229 (m-70) cc_final: 0.4813 (m90) REVERT: 6 621 GLU cc_start: 0.5019 (pp20) cc_final: 0.4020 (pt0) REVERT: 6 652 GLU cc_start: 0.6740 (tt0) cc_final: 0.6390 (tp30) REVERT: 7 3 ARG cc_start: 0.4587 (ttp80) cc_final: 0.3681 (mpt180) REVERT: 7 48 ILE cc_start: 0.2167 (OUTLIER) cc_final: 0.1775 (pt) REVERT: 7 182 TYR cc_start: 0.6609 (m-80) cc_final: 0.6060 (m-80) REVERT: 7 299 GLN cc_start: 0.7386 (tp-100) cc_final: 0.7068 (tp-100) REVERT: 7 369 MET cc_start: 0.4906 (ttt) cc_final: 0.4331 (mmm) REVERT: 7 397 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6449 (mm) REVERT: 7 402 GLN cc_start: 0.6903 (mt0) cc_final: 0.6652 (mt0) REVERT: 7 427 MET cc_start: 0.2631 (mmm) cc_final: 0.1256 (mmm) REVERT: 7 439 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8134 (mt0) REVERT: 7 449 LYS cc_start: 0.6443 (mtpt) cc_final: 0.5912 (mptt) REVERT: 7 475 MET cc_start: 0.4864 (pmm) cc_final: 0.4132 (pmm) REVERT: 7 552 LYS cc_start: 0.5399 (mppt) cc_final: 0.5134 (tptt) REVERT: 7 627 LYS cc_start: 0.6874 (tptp) cc_final: 0.6292 (mttt) REVERT: A 6 LEU cc_start: 0.3496 (OUTLIER) cc_final: 0.2630 (pp) REVERT: A 17 LYS cc_start: 0.3676 (tmtt) cc_final: 0.2641 (tptt) REVERT: A 101 HIS cc_start: 0.6032 (OUTLIER) cc_final: 0.5200 (p90) REVERT: A 230 MET cc_start: 0.6107 (mmm) cc_final: 0.5694 (mtt) REVERT: A 284 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8547 (p) REVERT: A 303 MET cc_start: 0.7469 (mtt) cc_final: 0.7045 (mtt) REVERT: A 312 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6337 (mp10) REVERT: A 535 PHE cc_start: 0.5001 (m-80) cc_final: 0.4690 (m-80) REVERT: A 541 LYS cc_start: 0.8242 (tptt) cc_final: 0.7674 (tmmt) REVERT: H 39 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6491 (tm-30) REVERT: H 76 ARG cc_start: 0.5266 (tpt170) cc_final: 0.3612 (ptm-80) REVERT: H 198 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7271 (tt) REVERT: L 48 MET cc_start: 0.8544 (mtt) cc_final: 0.8158 (mtm) REVERT: L 56 GLN cc_start: 0.7779 (mp10) cc_final: 0.7072 (pp30) REVERT: L 100 MET cc_start: 0.7422 (mmt) cc_final: 0.7028 (mmm) REVERT: L 114 ARG cc_start: 0.6849 (tmm160) cc_final: 0.5540 (mmm-85) REVERT: L 170 TYR cc_start: 0.4310 (t80) cc_final: 0.3926 (t80) REVERT: M 34 MET cc_start: 0.6488 (mmp) cc_final: 0.5779 (mmp) REVERT: M 131 HIS cc_start: 0.7081 (OUTLIER) cc_final: 0.6259 (t70) REVERT: N 80 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7126 (pp) outliers start: 188 outliers final: 144 residues processed: 782 average time/residue: 0.4996 time to fit residues: 636.9368 Evaluate side-chains 802 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 637 time to evaluate : 4.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 184 PHE Chi-restraints excluded: chain 2 residue 253 LEU Chi-restraints excluded: chain 2 residue 277 GLU Chi-restraints excluded: chain 2 residue 351 GLU Chi-restraints excluded: chain 2 residue 375 ILE Chi-restraints excluded: chain 2 residue 379 LYS Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 398 GLU Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 402 ILE Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 520 TYR Chi-restraints excluded: chain 2 residue 524 VAL Chi-restraints excluded: chain 2 residue 532 THR Chi-restraints excluded: chain 2 residue 574 PHE Chi-restraints excluded: chain 2 residue 584 SER Chi-restraints excluded: chain 2 residue 616 ASN Chi-restraints excluded: chain 2 residue 647 VAL Chi-restraints excluded: chain 2 residue 698 ARG Chi-restraints excluded: chain 2 residue 727 LEU Chi-restraints excluded: chain 2 residue 741 VAL Chi-restraints excluded: chain 2 residue 785 PHE Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 122 VAL Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 238 TYR Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 261 ASN Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 333 ASP Chi-restraints excluded: chain 3 residue 371 VAL Chi-restraints excluded: chain 3 residue 397 ASP Chi-restraints excluded: chain 3 residue 420 VAL Chi-restraints excluded: chain 3 residue 421 MET Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 557 LEU Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 248 PHE Chi-restraints excluded: chain 4 residue 277 LEU Chi-restraints excluded: chain 4 residue 296 SER Chi-restraints excluded: chain 4 residue 338 HIS Chi-restraints excluded: chain 4 residue 347 SER Chi-restraints excluded: chain 4 residue 363 ASP Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 396 ILE Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 556 ARG Chi-restraints excluded: chain 4 residue 573 CYS Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 613 THR Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 671 LEU Chi-restraints excluded: chain 4 residue 752 SER Chi-restraints excluded: chain 4 residue 764 TRP Chi-restraints excluded: chain 5 residue 52 ASP Chi-restraints excluded: chain 5 residue 130 THR Chi-restraints excluded: chain 5 residue 144 VAL Chi-restraints excluded: chain 5 residue 154 SER Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 308 TYR Chi-restraints excluded: chain 5 residue 311 ILE Chi-restraints excluded: chain 5 residue 314 ASP Chi-restraints excluded: chain 5 residue 339 SER Chi-restraints excluded: chain 5 residue 371 ASP Chi-restraints excluded: chain 5 residue 377 LEU Chi-restraints excluded: chain 5 residue 394 VAL Chi-restraints excluded: chain 5 residue 444 PHE Chi-restraints excluded: chain 5 residue 556 SER Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 608 THR Chi-restraints excluded: chain 5 residue 622 LEU Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 56 GLU Chi-restraints excluded: chain 6 residue 57 VAL Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 166 PHE Chi-restraints excluded: chain 6 residue 167 LYS Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 381 ASP Chi-restraints excluded: chain 6 residue 426 VAL Chi-restraints excluded: chain 6 residue 531 GLU Chi-restraints excluded: chain 6 residue 630 ASN Chi-restraints excluded: chain 6 residue 644 LEU Chi-restraints excluded: chain 7 residue 6 TYR Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 7 residue 72 ARG Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain 7 residue 143 THR Chi-restraints excluded: chain 7 residue 149 ILE Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 195 VAL Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 262 THR Chi-restraints excluded: chain 7 residue 329 GLN Chi-restraints excluded: chain 7 residue 336 LEU Chi-restraints excluded: chain 7 residue 344 ILE Chi-restraints excluded: chain 7 residue 358 LEU Chi-restraints excluded: chain 7 residue 397 LEU Chi-restraints excluded: chain 7 residue 436 LEU Chi-restraints excluded: chain 7 residue 458 ILE Chi-restraints excluded: chain 7 residue 555 ASP Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 135 PHE Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 154 HIS Chi-restraints excluded: chain M residue 15 ASP Chi-restraints excluded: chain M residue 58 TYR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 115 HIS Chi-restraints excluded: chain M residue 131 HIS Chi-restraints excluded: chain M residue 167 TYR Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 115 PHE Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 223 ASN Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 306 optimal weight: 0.9990 chunk 411 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 356 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 386 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 397 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 754 HIS 3 261 ASN 3 288 ASN ** 4 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 610 ASN ** 4 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 57 ASN 5 261 GLN ** 6 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 589 ASN ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 248 HIS ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 HIS ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 ASN L 91 HIS ** N 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.268289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.237919 restraints weight = 58569.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.240528 restraints weight = 47706.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.242196 restraints weight = 33587.081| |-----------------------------------------------------------------------------| r_work (final): 0.4746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6197 moved from start: 0.9821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40466 Z= 0.213 Angle : 0.725 15.460 54822 Z= 0.359 Chirality : 0.045 0.294 6193 Planarity : 0.005 0.083 6950 Dihedral : 11.223 89.333 5892 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 4.43 % Allowed : 28.44 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.11), residues: 4789 helix: -0.92 (0.13), residues: 1560 sheet: -2.13 (0.21), residues: 583 loop : -2.90 (0.11), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 170 HIS 0.025 0.001 HIS N 153 PHE 0.046 0.002 PHE 6 641 TYR 0.029 0.002 TYR A 254 ARG 0.017 0.001 ARG M 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11971.63 seconds wall clock time: 219 minutes 2.21 seconds (13142.21 seconds total)