Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 19 05:57:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raw_4785/10_2023/6raw_4785_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raw_4785/10_2023/6raw_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_4785/10_2023/6raw_4785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raw_4785/10_2023/6raw_4785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raw_4785/10_2023/6raw_4785_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raw_4785/10_2023/6raw_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-1.21rc1-5097/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: 19.84, per 1000 atoms: 0.50 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: 15.90 Conformation dependent library (CDL) restraints added in 5.4 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: 6.92 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: 10.36 Time building geometry restraints manager: 17.22 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: 22743 26.68 - 53.35: 1667 53.35 - 80.03: 195 80.03 - 106.71: 43 106.71 - 133.38: 4 Dihedral angle restraints: 24652 sinusoidal: 10402 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 24649 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: 0.010 Normalize map: mean=0, sd=1: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 13.410 Check model and map are aligned: 0.580 Set scattering table: 0.380 Process input model: 95.500 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.140 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.790 ------------------------------------------------------------------------------- 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 : 18.208 133.383 15385 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 *********************** 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 : 4.623 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. outliers start: 272 outliers final: 73 residues processed: 1274 average time/residue: 0.5857 time to fit residues: 1174.9601 Evaluate side-chains 711 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 638 time to evaluate : 4.060 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET 5 652 " (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. outliers start: 73 outliers final: 4 residues processed: 73 average time/residue: 0.3698 time to fit residues: 57.3434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 204 optimal weight: 0.3980 chunk 126 optimal weight: 0.1980 chunk 248 optimal weight: 0.7980 chunk 197 optimal weight: 0.3980 chunk 381 optimal weight: 0.4980 chunk 147 optimal weight: 5.9990 chunk 232 optimal weight: 0.7980 chunk 284 optimal weight: 3.9990 chunk 442 optimal weight: 5.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 289 GLN 2 352 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 65 ASN 3 199 GLN ** 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** 3 418 HIS 3 448 ASN 3 495 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 4 735 GLN 4 746 HIS 5 57 ASN 5 90 HIS ** 5 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 69 ASN ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 479 ASN 7 496 ASN ** 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 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 HIS ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 171 GLN 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: 0.5140 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 40466 Z= 0.231 Angle : 0.838 15.652 54822 Z= 0.419 Chirality : 0.049 0.375 6193 Planarity : 0.006 0.074 6950 Dihedral : 12.189 119.743 5752 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 3.94 % Allowed : 19.04 % Favored : 77.02 % 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: -4.48 (0.10), residues: 4789 helix: -2.04 (0.11), residues: 1565 sheet: -3.61 (0.18), residues: 483 loop : -3.58 (0.10), residues: 2741 *********************** 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 922 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 754 time to evaluate : 4.337 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 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: "ILE H 201 " (corrupted residue). Skipping it. 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. outliers start: 168 outliers final: 79 residues processed: 872 average time/residue: 0.5316 time to fit residues: 746.0328 Evaluate side-chains 684 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 605 time to evaluate : 4.054 Switching outliers to nearest non-outliers revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. 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. outliers start: 79 outliers final: 5 residues processed: 79 average time/residue: 0.3565 time to fit residues: 59.0733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 245 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 368 optimal weight: 10.0000 chunk 301 optimal weight: 5.9990 chunk 121 optimal weight: 0.0030 chunk 443 optimal weight: 0.8980 chunk 478 optimal weight: 5.9990 chunk 394 optimal weight: 0.6980 chunk 439 optimal weight: 0.5980 chunk 151 optimal weight: 0.7980 chunk 355 optimal weight: 0.4980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 364 GLN 2 534 GLN ** 2 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 310 GLN 3 418 HIS 3 495 HIS 3 553 HIS 4 192 ASN 4 198 GLN ** 4 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 223 GLN 4 353 GLN ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 485 GLN 4 557 GLN 4 735 GLN 5 84 ASN ** 5 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 373 ASN ** 5 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 644 GLN 6 231 GLN 6 630 ASN 6 636 HIS 7 105 HIS 7 155 GLN 7 453 GLN ** 7 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN M 9 ASN N 48 ASN N 186 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5339 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 40466 Z= 0.203 Angle : 0.746 11.278 54822 Z= 0.373 Chirality : 0.046 0.368 6193 Planarity : 0.005 0.073 6950 Dihedral : 11.513 127.468 5752 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.67 % Favored : 87.33 % Rotamer: Outliers : 3.12 % Allowed : 21.48 % Favored : 75.40 % 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: -3.90 (0.11), residues: 4789 helix: -1.45 (0.12), residues: 1565 sheet: -3.14 (0.20), residues: 503 loop : -3.33 (0.10), residues: 2721 *********************** 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 845 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 712 time to evaluate : 4.405 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 TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash 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 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. outliers start: 133 outliers final: 57 residues processed: 811 average time/residue: 0.5407 time to fit residues: 708.1671 Evaluate side-chains 649 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 592 time to evaluate : 4.283 Switching outliers to nearest non-outliers 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: "THR M 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 57 outliers final: 5 residues processed: 57 average time/residue: 0.3921 time to fit residues: 47.7441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 437 optimal weight: 0.0870 chunk 333 optimal weight: 0.9980 chunk 229 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 chunk 297 optimal weight: 5.9990 chunk 444 optimal weight: 6.9990 chunk 470 optimal weight: 0.3980 chunk 232 optimal weight: 1.9990 chunk 421 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 694 GLN ** 3 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 335 ASN 3 355 ASN ** 4 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 527 ASN 4 767 HIS 5 57 ASN 5 239 HIS 5 256 ASN 5 541 ASN 6 337 ASN ** 6 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 459 HIS ** 7 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 HIS ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 HIS ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 153 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5508 moved from start: 0.5876 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= 0.206 Angle : 0.718 12.834 54822 Z= 0.357 Chirality : 0.045 0.261 6193 Planarity : 0.005 0.074 6950 Dihedral : 10.994 130.681 5752 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.09 % Favored : 88.91 % Rotamer: Outliers : 3.02 % Allowed : 22.93 % Favored : 74.05 % 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: -3.58 (0.11), residues: 4789 helix: -1.19 (0.13), residues: 1537 sheet: -2.57 (0.21), residues: 510 loop : -3.19 (0.10), residues: 2742 *********************** 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 844 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 715 time to evaluate : 4.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "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. 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: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 129 outliers final: 63 residues processed: 802 average time/residue: 0.5286 time to fit residues: 685.5143 Evaluate side-chains 684 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 621 time to evaluate : 4.546 Switching outliers to nearest non-outliers revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (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. outliers start: 63 outliers final: 4 residues processed: 63 average time/residue: 0.3586 time to fit residues: 49.0713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 392 optimal weight: 3.9990 chunk 267 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 350 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 401 optimal weight: 2.9990 chunk 325 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 240 optimal weight: 0.6980 chunk 422 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 267 HIS 2 329 ASN 2 415 GLN ** 2 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 754 HIS 3 233 GLN ** 4 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 378 HIS ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 494 HIS 4 595 GLN 5 57 ASN 5 233 GLN ** 5 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 644 GLN 6 134 GLN 6 198 GLN ** 6 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 337 ASN 6 341 ASN 6 466 HIS 6 486 ASN 6 645 ASN 7 45 GLN ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 301 HIS 7 347 HIS ** 7 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 543 HIS A 13 GLN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN A 487 HIS ** H 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 HIS N 186 ASN N 224 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5859 moved from start: 0.7497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 40466 Z= 0.287 Angle : 0.819 11.563 54822 Z= 0.414 Chirality : 0.048 0.226 6193 Planarity : 0.006 0.125 6950 Dihedral : 11.033 127.249 5752 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.68 % Favored : 86.32 % Rotamer: Outliers : 4.01 % Allowed : 23.87 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.11), residues: 4789 helix: -1.35 (0.12), residues: 1552 sheet: -2.78 (0.20), residues: 557 loop : -3.21 (0.10), residues: 2680 *********************** 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 861 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 690 time to evaluate : 4.707 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 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. 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: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 171 outliers final: 79 residues processed: 806 average time/residue: 0.5335 time to fit residues: 695.0487 Evaluate side-chains 685 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 606 time to evaluate : 4.315 Switching outliers to nearest non-outliers revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. 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. outliers start: 79 outliers final: 5 residues processed: 79 average time/residue: 0.3636 time to fit residues: 59.8780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 158 optimal weight: 1.9990 chunk 423 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 276 optimal weight: 0.2980 chunk 116 optimal weight: 0.9980 chunk 471 optimal weight: 3.9990 chunk 391 optimal weight: 0.8980 chunk 218 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 155 optimal weight: 0.0470 chunk 247 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: