Starting phenix.real_space_refine on Tue Apr 16 06:43:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raz_4788/04_2024/6raz_4788_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raz_4788/04_2024/6raz_4788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raz_4788/04_2024/6raz_4788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raz_4788/04_2024/6raz_4788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raz_4788/04_2024/6raz_4788_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raz_4788/04_2024/6raz_4788_updated.pdb" } resolution = 4.46 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= 0.001 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 39 5.49 5 S 209 5.16 5 C 24015 2.51 5 N 6711 2.21 5 O 7320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 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 PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A GLU 220": "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 GLU 412": "OE1" <-> "OE2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A GLU 465": "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 GLU 524": "OE1" <-> "OE2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 565": "NH1" <-> "NH2" Residue "H GLU 20": "OE1" <-> "OE2" Residue "H GLU 172": "OE1" <-> "OE2" Residue "L GLU 7": "OE1" <-> "OE2" Residue "L GLU 64": "OE1" <-> "OE2" Residue "L GLU 78": "OE1" <-> "OE2" Residue "M GLU 14": "OE1" <-> "OE2" Residue "N GLU 25": "OE1" <-> "OE2" Residue "N GLU 31": "OE1" <-> "OE2" Residue "N GLU 40": "OE1" <-> "OE2" Residue "N GLU 64": "OE1" <-> "OE2" Residue "N PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 167": "OE1" <-> "OE2" Residue "2 ARG 177": "NH1" <-> "NH2" Residue "2 ARG 183": "NH1" <-> "NH2" Residue "2 PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 278": "OE1" <-> "OE2" Residue "2 ARG 292": "NH1" <-> "NH2" Residue "2 ARG 356": "NH1" <-> "NH2" Residue "2 GLU 365": "OE1" <-> "OE2" 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 494": "OE1" <-> "OE2" Residue "2 ARG 499": "NH1" <-> "NH2" Residue "2 GLU 522": "OE1" <-> "OE2" Residue "2 ARG 552": "NH1" <-> "NH2" Residue "2 GLU 557": "OE1" <-> "OE2" Residue "2 ARG 621": "NH1" <-> "NH2" Residue "2 ARG 641": "NH1" <-> "NH2" Residue "2 ARG 698": "NH1" <-> "NH2" Residue "2 ARG 709": "NH1" <-> "NH2" Residue "2 ARG 728": "NH1" <-> "NH2" Residue "2 ARG 742": "NH1" <-> "NH2" Residue "2 ARG 756": "NH1" <-> "NH2" Residue "2 ARG 760": "NH1" <-> "NH2" Residue "2 ARG 773": "NH1" <-> "NH2" Residue "5 ARG 39": "NH1" <-> "NH2" Residue "5 ARG 62": "NH1" <-> "NH2" Residue "5 GLU 68": "OE1" <-> "OE2" Residue "5 GLU 70": "OE1" <-> "OE2" Residue "5 ARG 99": "NH1" <-> "NH2" Residue "5 GLU 111": "OE1" <-> "OE2" Residue "5 GLU 113": "OE1" <-> "OE2" Residue "5 GLU 114": "OE1" <-> "OE2" Residue "5 ARG 162": "NH1" <-> "NH2" Residue "5 ARG 199": "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 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 GLU 427": "OE1" <-> "OE2" Residue "5 GLU 449": "OE1" <-> "OE2" Residue "5 GLU 457": "OE1" <-> "OE2" Residue "5 GLU 499": "OE1" <-> "OE2" Residue "5 ARG 626": "NH1" <-> "NH2" Residue "6 ARG 20": "NH1" <-> "NH2" Residue "6 ARG 42": "NH1" <-> "NH2" Residue "6 GLU 48": "OE1" <-> "OE2" Residue "6 TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 95": "NH1" <-> "NH2" Residue "6 ARG 114": "NH1" <-> "NH2" Residue "6 ARG 118": "NH1" <-> "NH2" Residue "6 ARG 160": "NH1" <-> "NH2" Residue "6 ARG 182": "NH1" <-> "NH2" Residue "6 ARG 201": "NH1" <-> "NH2" Residue "6 ARG 211": "NH1" <-> "NH2" Residue "6 ARG 216": "NH1" <-> "NH2" Residue "6 GLU 228": "OE1" <-> "OE2" Residue "6 ARG 287": "NH1" <-> "NH2" Residue "6 ARG 336": "NH1" <-> "NH2" Residue "6 ARG 358": "NH1" <-> "NH2" Residue "6 GLU 374": "OE1" <-> "OE2" Residue "6 ARG 379": "NH1" <-> "NH2" Residue "6 ARG 407": "NH1" <-> "NH2" Residue "6 GLU 430": "OE1" <-> "OE2" Residue "6 ARG 460": "NH1" <-> "NH2" Residue "6 ARG 504": "NH1" <-> "NH2" Residue "6 ARG 521": "NH1" <-> "NH2" Residue "6 GLU 534": "OE1" <-> "OE2" Residue "6 ARG 542": "NH1" <-> "NH2" Residue "6 ARG 557": "NH1" <-> "NH2" Residue "6 ARG 561": "NH1" <-> "NH2" Residue "6 GLU 581": "OE1" <-> "OE2" Residue "6 ARG 594": "NH1" <-> "NH2" Residue "6 ARG 596": "NH1" <-> "NH2" Residue "6 ARG 611": "NH1" <-> "NH2" Residue "6 ARG 631": "NH1" <-> "NH2" Residue "6 ARG 635": "NH1" <-> "NH2" Residue "6 ARG 642": "NH1" <-> "NH2" 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 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 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 ARG 387": "NH1" <-> "NH2" Residue "3 GLU 389": "OE1" <-> "OE2" Residue "3 GLU 405": "OE1" <-> "OE2" Residue "3 ARG 414": "NH1" <-> "NH2" Residue "3 GLU 419": "OE1" <-> "OE2" Residue "3 ARG 425": "NH1" <-> "NH2" Residue "3 ARG 453": "NH1" <-> "NH2" Residue "3 ARG 501": "NH1" <-> "NH2" Residue "3 ARG 503": "NH1" <-> "NH2" Residue "3 ARG 550": "NH1" <-> "NH2" Residue "3 ARG 552": "NH1" <-> "NH2" Residue "3 ARG 563": "NH1" <-> "NH2" Residue "3 ARG 590": "NH1" <-> "NH2" Residue "3 ARG 603": "NH1" <-> "NH2" Residue "3 GLU 613": "OE1" <-> "OE2" Residue "3 ARG 624": "NH1" <-> "NH2" Residue "4 ARG 174": "NH1" <-> "NH2" Residue "4 GLU 187": "OE1" <-> "OE2" Residue "4 ARG 227": "NH1" <-> "NH2" Residue "4 GLU 246": "OE1" <-> "OE2" 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 GLU 446": "OE1" <-> "OE2" Residue "4 ARG 447": "NH1" <-> "NH2" Residue "4 ARG 463": "NH1" <-> "NH2" Residue "4 ARG 499": "NH1" <-> "NH2" Residue "4 PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 538": "NH1" <-> "NH2" Residue "4 LEU 545": "CD1" <-> "CD2" Residue "4 ARG 629": "NH1" <-> "NH2" Residue "4 ARG 663": "NH1" <-> "NH2" Residue "4 ARG 676": "NH1" <-> "NH2" Residue "4 ARG 690": "NH1" <-> "NH2" Residue "4 ARG 711": "NH1" <-> "NH2" Residue "4 ARG 726": "NH1" <-> "NH2" Residue "4 ARG 734": "NH1" <-> "NH2" Residue "4 GLU 737": "OE1" <-> "OE2" Residue "4 ARG 765": "NH1" <-> "NH2" Residue "7 ARG 3": "NH1" <-> "NH2" Residue "7 ARG 4": "NH1" <-> "NH2" Residue "7 ARG 10": "NH1" <-> "NH2" Residue "7 GLU 57": "OE1" <-> "OE2" Residue "7 ARG 71": "NH1" <-> "NH2" Residue "7 ARG 72": "NH1" <-> "NH2" Residue "7 GLU 129": "OE1" <-> "OE2" Residue "7 ARG 133": "NH1" <-> "NH2" Residue "7 ARG 258": "NH1" <-> "NH2" Residue "7 GLU 260": "OE1" <-> "OE2" Residue "7 ARG 302": "NH1" <-> "NH2" Residue "7 GLU 323": "OE1" <-> "OE2" Residue "7 GLU 325": "OE1" <-> "OE2" 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 GLU 463": "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 GLU 587": "OE1" <-> "OE2" Residue "7 ARG 590": "NH1" <-> "NH2" Residue "7 GLU 591": "OE1" <-> "OE2" 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 ARG 635": "NH1" <-> "NH2" Residue "7 GLU 638": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 38294 Number of models: 1 Model: "" Number of chains: 18 Chain: "X" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 425 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "Y" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Classifications: {'DNA': 2} Link IDs: {'rna3p': 1} Chain: "A" Number of atoms: 4190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4190 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 13, 'TRANS': 505} Chain breaks: 1 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: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1457 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 14, 'TRANS': 164} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1259 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1661 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} 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: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4442 Classifications: {'peptide': 559} Link IDs: {'PTRANS': 23, 'TRANS': 535} Chain breaks: 7 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "5" Number of atoms: 4459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4459 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 26, 'TRANS': 544} Chain breaks: 10 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "6" Number of atoms: 4609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4609 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 18, 'TRANS': 569} Chain breaks: 4 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 5, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "3" Number of atoms: 4585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4585 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 22, 'TRANS': 567} Chain breaks: 9 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "4" Number of atoms: 4811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4811 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 25, 'TRANS': 580} Chain breaks: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "7" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4594 Classifications: {'peptide': 601} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 38} Link IDs: {'PTRANS': 23, 'TRANS': 577} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 62 Chain: "5" 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: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.99, per 1000 atoms: 0.52 Number of scatterers: 38294 At special positions: 0 Unit cell: (187.92, 183.6, 153.36, 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 209 16.00 P 39 15.00 O 7320 8.00 N 6711 7.00 C 24015 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 5 192 " - pdb=" SG CYS 5 202 " distance=2.04 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 Atom "HETATM38259 O4' ATP 4 901 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.97 Conformation dependent library (CDL) restraints added in 6.9 seconds 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9072 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 157 helices and 23 sheets defined 31.0% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.66 Creating SS restraints... 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 42 removed outlier: 4.446A pdb=" N ILE A 35 " --> pdb=" O CYS A 31 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS A 41 " --> pdb=" O GLN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 65 removed outlier: 4.122A pdb=" N LYS A 59 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG A 60 " --> pdb=" O GLY A 57 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 61 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 62 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLY A 63 " --> pdb=" O ARG A 60 " (cutoff:3.500A) 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 129 through 132 No H-bonds generated for 'chain 'A' and resid 129 through 132' Processing helix chain 'A' and resid 186 through 197 Processing helix chain 'A' and resid 216 through 225 removed outlier: 4.730A pdb=" N LYS A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 removed outlier: 3.790A pdb=" N GLN A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 265 removed outlier: 4.018A pdb=" N LEU A 258 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE A 261 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 305 Processing helix chain 'A' and resid 307 through 310 No H-bonds generated for 'chain 'A' and resid 307 through 310' Processing helix chain 'A' and resid 319 through 331 removed outlier: 3.841A pdb=" N GLU A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 360 removed outlier: 5.162A pdb=" N PHE A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N SER A 355 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 395 removed outlier: 4.051A pdb=" N VAL A 390 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N TYR A 391 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU A 394 " --> pdb=" O TYR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 414 Processing helix chain 'A' and resid 423 through 447 removed outlier: 4.303A pdb=" N ALA A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE A 440 " --> pdb=" O HIS A 436 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N SER A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 483 removed outlier: 4.490A pdb=" N LEU A 479 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 480 " --> pdb=" O GLY A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 530 through 541 removed outlier: 3.670A pdb=" N ALA A 534 " --> pdb=" O PHE A 531 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N PHE A 535 " --> pdb=" O GLY A 532 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA A 538 " --> pdb=" O PHE A 535 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 541 " --> pdb=" O ALA A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 570 Processing helix chain 'H' and resid 12 through 19 removed outlier: 5.112A pdb=" N LYS H 17 " --> pdb=" O PHE H 13 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU H 18 " --> pdb=" O ASP H 14 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 39 Processing helix chain 'H' and resid 45 through 49 Processing helix chain 'H' and resid 61 through 98 Proline residue: H 65 - end of helix removed outlier: 3.635A pdb=" N PHE H 69 " --> pdb=" O PRO H 65 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG H 88 " --> pdb=" O TYR H 84 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 132 removed outlier: 4.146A pdb=" N VAL H 116 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN H 120 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU H 126 " --> pdb=" O SER H 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 12 No H-bonds generated for 'chain 'L' and resid 10 through 12' Processing helix chain 'L' and resid 49 through 53 removed outlier: 3.698A pdb=" N ARG L 53 " --> pdb=" O THR L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 80 removed outlier: 5.271A pdb=" N GLU L 76 " --> pdb=" O GLU L 72 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LYS L 79 " --> pdb=" O LYS L 75 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ARG L 80 " --> pdb=" O GLU L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 105 removed outlier: 3.814A pdb=" N THR L 102 " --> pdb=" O LEU L 98 " (cutoff:3.500A) Proline residue: L 104 - end of helix Processing helix chain 'L' and resid 112 through 130 removed outlier: 3.857A pdb=" N ASP L 122 " --> pdb=" O LYS L 118 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ILE L 123 " --> pdb=" O ASP L 119 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU L 128 " --> pdb=" O ARG L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 153 through 157 Processing helix chain 'L' and resid 160 through 168 removed outlier: 5.256A pdb=" N HIS L 166 " --> pdb=" O TYR L 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 60 Processing helix chain 'M' and resid 79 through 85 removed outlier: 4.930A pdb=" N VAL M 84 " --> pdb=" O VAL M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 108 Processing helix chain 'M' and resid 118 through 130 removed outlier: 4.408A pdb=" N PHE M 122 " --> pdb=" O GLY M 118 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG M 128 " --> pdb=" O THR M 124 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL M 129 " --> pdb=" O LEU M 125 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARG M 130 " --> pdb=" O ARG M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 171 removed outlier: 3.754A pdb=" N ASN M 164 " --> pdb=" O GLY M 160 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU M 169 " --> pdb=" O SER M 165 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 47 removed outlier: 3.893A pdb=" N GLU N 40 " --> pdb=" O GLN N 36 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE N 42 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU N 43 " --> pdb=" O LEU N 39 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR N 44 " --> pdb=" O GLU N 40 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ALA N 45 " --> pdb=" O ILE N 41 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TRP N 46 " --> pdb=" O ILE N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 79 removed outlier: 5.195A pdb=" N MET N 66 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL N 67 " --> pdb=" O GLU N 64 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL N 70 " --> pdb=" O VAL N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 114 removed outlier: 4.776A pdb=" N ILE N 100 " --> pdb=" O ARG N 96 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET N 101 " --> pdb=" O VAL N 97 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU N 105 " --> pdb=" O MET N 101 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLN N 110 " --> pdb=" O ARG N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 119 through 126 Processing helix chain 'N' and resid 135 through 154 removed outlier: 3.677A pdb=" N ALA N 141 " --> pdb=" O GLU N 137 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN N 142 " --> pdb=" O THR N 138 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS N 154 " --> pdb=" O GLU N 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 219 through 222 No H-bonds generated for 'chain 'N' and resid 219 through 222' Processing helix chain '2' and resid 175 through 188 removed outlier: 3.765A pdb=" N ILE 2 180 " --> pdb=" O ARG 2 177 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA 2 181 " --> pdb=" O THR 2 178 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER 2 186 " --> pdb=" O ARG 2 183 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU 2 188 " --> pdb=" O GLN 2 185 " (cutoff:3.500A) Processing helix chain '2' and resid 199 through 210 removed outlier: 4.155A pdb=" N ILE 2 204 " --> pdb=" O TYR 2 200 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ARG 2 205 " --> pdb=" O ARG 2 201 " (cutoff:3.500A) Processing helix chain '2' and resid 219 through 226 Processing helix chain '2' and resid 237 through 255 removed outlier: 4.251A pdb=" N VAL 2 247 " --> pdb=" O ILE 2 243 " (cutoff:3.500A) removed outlier: 3.829A 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 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: 5.787A pdb=" N VAL 2 462 " --> pdb=" O VAL 2 459 " (cutoff:3.500A) Processing helix chain '2' and resid 474 through 483 removed outlier: 3.686A pdb=" N ARG 2 478 " --> pdb=" O ASP 2 474 " (cutoff:3.500A) Processing helix chain '2' and resid 519 through 524 removed outlier: 3.854A pdb=" N LYS 2 523 " --> pdb=" O TYR 2 520 " (cutoff:3.500A) Processing helix chain '2' and resid 574 through 576 No H-bonds generated for 'chain '2' and resid 574 through 576' Processing helix chain '2' and resid 579 through 587 removed outlier: 4.178A pdb=" N SER 2 584 " --> pdb=" O GLN 2 580 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU 2 587 " --> pdb=" O THR 2 583 " (cutoff:3.500A) Processing helix chain '2' and resid 636 through 641 removed outlier: 4.751A pdb=" N ARG 2 641 " --> pdb=" O PRO 2 637 " (cutoff:3.500A) Processing helix chain '2' and resid 660 through 667 Processing helix chain '2' and resid 698 through 706 Processing helix chain '2' and resid 717 through 725 removed outlier: 3.970A pdb=" N TYR 2 724 " --> pdb=" O ALA 2 721 " (cutoff:3.500A) Processing helix chain '2' and resid 742 through 758 removed outlier: 4.225A pdb=" N VAL 2 747 " --> pdb=" O HIS 2 743 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET 2 750 " --> pdb=" O SER 2 746 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU 2 752 " --> pdb=" O ILE 2 748 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA 2 753 " --> pdb=" O ARG 2 749 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA 2 755 " --> pdb=" O SER 2 751 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG 2 756 " --> pdb=" O GLU 2 752 " (cutoff:3.500A) Processing helix chain '2' and resid 765 through 782 removed outlier: 4.040A pdb=" N ILE 2 780 " --> pdb=" O LEU 2 776 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU 2 781 " --> pdb=" O GLU 2 777 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA 2 782 " --> pdb=" O SER 2 778 " (cutoff:3.500A) Processing helix chain '2' and resid 788 through 797 removed outlier: 4.196A pdb=" N SER 2 793 " --> pdb=" O LYS 2 789 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLN 2 796 " --> pdb=" O ARG 2 792 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LYS 2 797 " --> pdb=" O SER 2 793 " (cutoff:3.500A) Processing helix chain '5' and resid 28 through 31 No H-bonds generated for 'chain '5' and resid 28 through 31' Processing helix chain '5' and resid 33 through 40 Processing helix chain '5' and resid 53 through 57 Processing helix chain '5' and resid 79 through 85 removed outlier: 3.704A pdb=" N LYS 5 85 " --> pdb=" O ASP 5 81 " (cutoff:3.500A) Processing helix chain '5' and resid 87 through 106 removed outlier: 4.995A pdb=" N GLU 5 92 " --> pdb=" O THR 5 88 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU 5 104 " --> pdb=" O GLU 5 100 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE 5 105 " --> pdb=" O VAL 5 101 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR 5 106 " --> pdb=" O ALA 5 102 " (cutoff:3.500A) Processing helix chain '5' and resid 211 through 213 No H-bonds generated for 'chain '5' and resid 211 through 213' Processing helix chain '5' and resid 313 through 324 removed outlier: 4.209A pdb=" N MET 5 322 " --> pdb=" O HIS 5 318 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA 5 323 " --> pdb=" O PHE 5 319 " (cutoff:3.500A) Processing helix chain '5' and resid 332 through 334 No H-bonds generated for 'chain '5' and resid 332 through 334' Processing helix chain '5' and resid 344 through 350 removed outlier: 4.511A pdb=" N LYS 5 348 " --> pdb=" O ASP 5 345 " (cutoff:3.500A) Processing helix chain '5' and resid 384 through 393 removed outlier: 4.067A pdb=" N LEU 5 388 " --> pdb=" O LYS 5 384 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS 5 393 " --> pdb=" O LYS 5 389 " (cutoff:3.500A) Processing helix chain '5' and resid 450 through 452 No H-bonds generated for 'chain '5' and resid 450 through 452' Processing helix chain '5' and resid 454 through 458 Processing helix chain '5' and resid 490 through 494 Processing helix chain '5' and resid 523 through 531 removed outlier: 3.703A pdb=" N ILE 5 527 " --> pdb=" O GLU 5 523 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR 5 528 " --> pdb=" O SER 5 524 " (cutoff:3.500A) Processing helix chain '5' and resid 534 through 537 No H-bonds generated for 'chain '5' and resid 534 through 537' Processing helix chain '5' and resid 555 through 565 Processing helix chain '5' and resid 609 through 619 removed outlier: 4.624A pdb=" N VAL 5 615 " --> pdb=" O ARG 5 610 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE 5 616 " --> pdb=" O GLN 5 611 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ARG 5 617 " --> pdb=" O LEU 5 612 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE 5 618 " --> pdb=" O GLU 5 613 " (cutoff:3.500A) Processing helix chain '5' and resid 621 through 625 Processing helix chain '5' and resid 636 through 647 removed outlier: 4.219A pdb=" N GLN 5 644 " --> pdb=" O ARG 5 641 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL 5 645 " --> pdb=" O LEU 5 642 " (cutoff:3.500A) Processing helix chain '6' and resid 14 through 29 removed outlier: 3.676A pdb=" N LEU 6 24 " --> pdb=" O ALA 6 21 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE 6 28 " --> pdb=" O PHE 6 25 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 48 removed outlier: 4.365A pdb=" N GLU 6 48 " --> pdb=" O ALA 6 44 " (cutoff:3.500A) Processing helix chain '6' and resid 60 through 64 Processing helix chain '6' and resid 70 through 72 No H-bonds generated for 'chain '6' and resid 70 through 72' Processing helix chain '6' and resid 77 through 94 Proline residue: 6 82 - end of helix removed outlier: 3.646A pdb=" N ASP 6 94 " --> pdb=" O ASN 6 90 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 124 No H-bonds generated for 'chain '6' and resid 122 through 124' Processing helix chain '6' and resid 324 through 334 removed outlier: 4.480A pdb=" N HIS 6 327 " --> pdb=" O ALA 6 324 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR 6 330 " --> pdb=" O HIS 6 327 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU 6 331 " --> pdb=" O LYS 6 328 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS 6 334 " --> pdb=" O GLU 6 331 " (cutoff:3.500A) Processing helix chain '6' and resid 336 through 344 Processing helix chain '6' and resid 356 through 358 No H-bonds generated for 'chain '6' and resid 356 through 358' Processing helix chain '6' and resid 360 through 364 Processing helix chain '6' and resid 396 through 404 removed outlier: 3.702A pdb=" N SER 6 402 " --> pdb=" O LEU 6 398 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP 6 403 " --> pdb=" O LYS 6 399 " (cutoff:3.500A) Processing helix chain '6' and resid 418 through 420 No H-bonds generated for 'chain '6' and resid 418 through 420' Processing helix chain '6' and resid 461 through 467 removed outlier: 4.407A pdb=" N HIS 6 466 " --> pdb=" O VAL 6 463 " (cutoff:3.500A) Processing helix chain '6' and resid 508 through 512 removed outlier: 3.789A pdb=" N ILE 6 512 " --> pdb=" O LEU 6 508 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 508 through 512' Processing helix chain '6' and resid 518 through 521 No H-bonds generated for 'chain '6' and resid 518 through 521' Processing helix chain '6' and resid 535 through 546 removed outlier: 3.745A pdb=" N ALA 6 539 " --> pdb=" O VAL 6 535 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE 6 540 " --> pdb=" O VAL 6 536 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA 6 541 " --> pdb=" O ASP 6 537 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG 6 542 " --> pdb=" O TYR 6 538 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASP 6 546 " --> pdb=" O ARG 6 542 " (cutoff:3.500A) Processing helix chain '6' and resid 561 through 573 removed outlier: 4.391A pdb=" N THR 6 569 " --> pdb=" O LEU 6 565 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE 6 570 " --> pdb=" O ARG 6 566 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA 6 571 " --> pdb=" O TYR 6 567 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG 6 572 " --> pdb=" O VAL 6 568 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN 6 573 " --> pdb=" O THR 6 569 " (cutoff:3.500A) Processing helix chain '6' and resid 581 through 598 removed outlier: 5.041A pdb=" N VAL 6 587 " --> pdb=" O GLY 6 583 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLU 6 588 " --> pdb=" O HIS 6 584 " (cutoff:3.500A) Processing helix chain '6' and resid 610 through 626 removed outlier: 4.022A pdb=" N SER 6 615 " --> pdb=" O ARG 6 611 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER 6 620 " --> pdb=" O MET 6 616 " (cutoff:3.500A) Processing helix chain '6' and resid 634 through 649 removed outlier: 3.846A pdb=" N GLU 6 639 " --> pdb=" O HIS 6 636 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU 6 643 " --> pdb=" O ALA 6 640 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE 6 648 " --> pdb=" O ASN 6 645 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 19 removed outlier: 3.689A pdb=" N LYS 3 10 " --> pdb=" O GLN 3 7 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP 3 18 " --> pdb=" O GLU 3 15 " (cutoff:3.500A) Processing helix chain '3' and resid 23 through 28 Processing helix chain '3' and resid 48 through 54 Processing helix chain '3' and resid 56 through 63 removed outlier: 3.827A pdb=" N LEU 3 62 " --> pdb=" O ARG 3 58 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU 3 63 " --> pdb=" O ALA 3 59 " (cutoff:3.500A) Processing helix chain '3' and resid 69 through 82 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 275 through 286 removed outlier: 3.637A pdb=" N MET 3 279 " --> pdb=" O ARG 3 275 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS 3 283 " --> pdb=" O MET 3 279 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU 3 284 " --> pdb=" O LEU 3 280 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA 3 285 " --> pdb=" O CYS 3 281 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LYS 3 286 " --> pdb=" O LYS 3 282 " (cutoff:3.500A) Processing helix chain '3' and resid 290 through 296 Processing helix chain '3' and resid 311 through 317 removed outlier: 4.244A pdb=" N CYS 3 314 " --> pdb=" O ALA 3 311 " (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 406 through 408 No H-bonds generated for 'chain '3' and resid 406 through 408' Processing helix chain '3' and resid 415 through 423 removed outlier: 3.510A pdb=" N GLU 3 419 " --> pdb=" O THR 3 415 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL 3 420 " --> pdb=" O ALA 3 416 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU 3 422 " --> pdb=" O HIS 3 418 " (cutoff:3.500A) Processing helix chain '3' and resid 487 through 502 removed outlier: 4.454A pdb=" N MET 3 491 " --> pdb=" O ASP 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 559 through 565 removed outlier: 4.278A pdb=" N TYR 3 565 " --> pdb=" O PHE 3 561 " (cutoff:3.500A) Processing helix chain '3' and resid 569 through 571 No H-bonds generated for 'chain '3' and resid 569 through 571' Processing helix chain '3' and resid 580 through 596 removed outlier: 4.442A pdb=" N ALA 3 585 " --> pdb=" O CYS 3 581 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN 3 586 " --> pdb=" O GLU 3 582 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER 3 593 " --> pdb=" O SER 3 589 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ALA 3 596 " --> pdb=" O ARG 3 592 " (cutoff:3.500A) Processing helix chain '3' and resid 610 through 625 removed outlier: 3.709A pdb=" N LEU 3 615 " --> pdb=" O LEU 3 612 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU 3 618 " --> pdb=" O LEU 3 615 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR 3 620 " --> pdb=" O ARG 3 617 " (cutoff:3.500A) Processing helix chain '3' and resid 633 through 639 removed outlier: 3.832A pdb=" N ALA 3 638 " --> pdb=" O ASP 3 634 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA 3 639 " --> pdb=" O ASP 3 635 " (cutoff:3.500A) Processing helix chain '4' and resid 161 through 173 Processing helix chain '4' and resid 195 through 202 Processing helix chain '4' and resid 216 through 219 removed outlier: 3.675A pdb=" N LYS 4 219 " --> pdb=" O ALA 4 216 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 216 through 219' Processing helix chain '4' and resid 223 through 231 Processing helix chain '4' and resid 237 through 251 removed outlier: 5.062A pdb=" N PHE 4 249 " --> pdb=" O ASN 4 245 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU 4 250 " --> pdb=" O GLU 4 246 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG 4 251 " --> pdb=" O MET 4 247 " (cutoff:3.500A) Processing helix chain '4' and resid 448 through 455 removed outlier: 3.672A pdb=" N GLN 4 452 " --> pdb=" O VAL 4 448 " (cutoff:3.500A) Processing helix chain '4' and resid 458 through 461 removed outlier: 3.740A pdb=" N TYR 4 461 " --> pdb=" O PRO 4 458 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 458 through 461' Processing helix chain '4' and resid 465 through 468 No H-bonds generated for 'chain '4' and resid 465 through 468' Processing helix chain '4' and resid 477 through 484 removed outlier: 4.177A pdb=" N LEU 4 484 " --> pdb=" O LYS 4 480 " (cutoff:3.500A) Processing helix chain '4' and resid 520 through 528 Processing helix chain '4' and resid 592 through 594 No H-bonds generated for 'chain '4' and resid 592 through 594' Processing helix chain '4' and resid 632 through 634 No H-bonds generated for 'chain '4' and resid 632 through 634' Processing helix chain '4' and resid 661 through 674 removed outlier: 4.175A pdb=" N ALA 4 665 " --> pdb=" O ASP 4 661 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER 4 670 " --> pdb=" O SER 4 666 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU 4 671 " --> pdb=" O HIS 4 667 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N TYR 4 672 " --> pdb=" O LEU 4 668 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N TYR 4 673 " --> pdb=" O VAL 4 669 " (cutoff:3.500A) Processing helix chain '4' and resid 693 through 695 No H-bonds generated for 'chain '4' and resid 693 through 695' Processing helix chain '4' and resid 710 through 723 removed outlier: 5.103A pdb=" N VAL 4 717 " --> pdb=" O ILE 4 713 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASP 4 718 " --> pdb=" O GLN 4 714 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL 4 722 " --> pdb=" O ASP 4 718 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLY 4 723 " --> pdb=" O MET 4 719 " (cutoff:3.500A) Processing helix chain '4' and resid 735 through 744 removed outlier: 3.998A pdb=" N GLU 4 744 " --> pdb=" O ILE 4 740 " (cutoff:3.500A) Processing helix chain '4' and resid 758 through 769 removed outlier: 3.867A pdb=" N HIS 4 767 " --> pdb=" O TRP 4 764 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ARG 4 768 " --> pdb=" O ARG 4 765 " (cutoff:3.500A) 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 56 Processing helix chain '7' and resid 72 through 82 Processing helix chain '7' and resid 98 through 107 removed outlier: 3.828A pdb=" N GLU 7 104 " --> pdb=" O ASP 7 100 " (cutoff:3.500A) 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 259 through 261 No H-bonds generated for 'chain '7' and resid 259 through 261' Processing helix chain '7' and resid 324 through 329 Processing helix chain '7' and resid 334 through 339 Processing helix chain '7' and resid 348 through 359 removed outlier: 3.679A pdb=" N LEU 7 357 " --> pdb=" O ALA 7 353 " (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 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 447 through 450 No H-bonds generated for 'chain '7' and resid 447 through 450' Processing helix chain '7' and resid 453 through 462 removed outlier: 3.880A pdb=" N ALA 7 457 " --> pdb=" O ASP 7 454 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE 7 458 " --> pdb=" O ARG 7 455 " (cutoff:3.500A) Processing helix chain '7' and resid 509 through 514 removed outlier: 3.549A pdb=" N ARG 7 514 " --> pdb=" O ALA 7 510 " (cutoff:3.500A) Processing helix chain '7' and resid 529 through 542 removed outlier: 3.830A pdb=" N LEU 7 533 " --> pdb=" O ASN 7 529 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL 7 540 " --> pdb=" O HIS 7 536 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS 7 541 " --> pdb=" O ILE 7 537 " (cutoff:3.500A) Processing helix chain '7' and resid 556 through 565 Processing helix chain '7' and resid 575 through 593 removed outlier: 3.679A pdb=" N ASP 7 579 " --> pdb=" O GLU 7 576 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE 7 581 " --> pdb=" O THR 7 578 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL 7 582 " --> pdb=" O ASP 7 579 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR 7 585 " --> pdb=" O VAL 7 582 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG 7 590 " --> pdb=" O GLU 7 587 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA 7 592 " --> pdb=" O ARG 7 589 " (cutoff:3.500A) Processing helix chain '7' and resid 603 through 620 removed outlier: 4.195A pdb=" N SER 7 613 " --> pdb=" O ILE 7 609 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR 7 614 " --> pdb=" O LEU 7 610 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA 7 615 " --> pdb=" O ARG 7 611 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU 7 616 " --> pdb=" O LEU 7 612 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA 7 617 " --> pdb=" O SER 7 613 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG 7 618 " --> pdb=" O THR 7 614 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU 7 619 " --> pdb=" O ALA 7 615 " (cutoff:3.500A) Processing helix chain '7' and resid 627 through 640 removed outlier: 4.007A pdb=" N ALA 7 633 " --> pdb=" O ASP 7 629 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 284 through 288 removed outlier: 4.694A pdb=" N THR A 284 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR A 375 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 459 through 461 Processing sheet with id= C, first strand: chain 'L' and resid 14 through 19 removed outlier: 4.351A pdb=" N PHE L 40 " --> pdb=" O PRO L 19 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 215 through 218 Processing sheet with id= E, first strand: chain '2' and resid 358 through 360 removed outlier: 4.160A pdb=" N GLN 2 359 " --> pdb=" O LEU 2 383 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU 2 383 " --> pdb=" O GLN 2 359 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain '2' and resid 397 through 399 Processing sheet with id= G, first strand: chain '5' and resid 146 through 149 removed outlier: 3.502A pdb=" N ILE 5 146 " --> pdb=" O ILE 5 260 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '5' and resid 375 through 378 removed outlier: 4.057A pdb=" N PHE 5 515 " --> pdb=" O LEU 5 375 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU 5 377 " --> pdb=" O PHE 5 515 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '5' and resid 439 through 441 Processing sheet with id= J, first strand: chain '6' and resid 217 through 220 removed outlier: 3.561A pdb=" N ILE 6 220 " --> pdb=" O ILE 6 200 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS 6 199 " --> pdb=" O HIS 6 139 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARG 6 137 " --> pdb=" O ARG 6 201 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '3' and resid 230 through 236 removed outlier: 4.192A pdb=" N ASP 3 230 " --> pdb=" O VAL 3 128 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN 3 199 " --> pdb=" O ILE 3 127 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR 3 129 " --> pdb=" O THR 3 197 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR 3 197 " --> pdb=" O THR 3 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU 3 196 " --> pdb=" O ILE 3 216 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '3' and resid 134 through 138 Processing sheet with id= M, first strand: chain '3' and resid 140 through 143 Processing sheet with id= N, first strand: chain '3' and resid 237 through 239 Processing sheet with id= O, first strand: chain '4' and resid 285 through 291 removed outlier: 4.179A pdb=" N THR 4 392 " --> pdb=" O ARG 4 425 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR 4 394 " --> pdb=" O HIS 4 423 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N HIS 4 423 " --> pdb=" O THR 4 394 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '4' and resid 304 through 306 Processing sheet with id= Q, first strand: chain '4' and resid 355 through 358 removed outlier: 3.809A pdb=" N VAL 4 355 " --> pdb=" O LEU 4 375 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU 4 375 " --> pdb=" O VAL 4 355 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '4' and resid 397 through 400 Processing sheet with id= S, first strand: chain '4' and resid 532 through 536 removed outlier: 6.844A pdb=" N VAL 4 572 " --> pdb=" O GLN 4 533 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N THR 4 535 " --> pdb=" O VAL 4 572 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N CYS 4 574 " --> pdb=" O THR 4 535 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N SER 4 614 " --> pdb=" O CYS 4 573 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE 4 575 " --> pdb=" O SER 4 614 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU 4 616 " --> pdb=" O ILE 4 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain '7' and resid 47 through 49 removed outlier: 6.755A pdb=" N GLU 7 135 " --> pdb=" O ILE 7 48 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain '7' and resid 253 through 258 Processing sheet with id= V, first strand: chain '7' and resid 440 through 445 removed outlier: 3.504A pdb=" N LEU 7 485 " --> pdb=" O CYS 7 442 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA 7 487 " --> pdb=" O ILE 7 444 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain '7' and resid 176 through 179 removed outlier: 7.308A pdb=" N LYS 7 228 " --> pdb=" O VAL 7 178 " (cutoff:3.500A) 769 hydrogen bonds defined for protein. 1770 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: 10.31 Time building geometry restraints manager: 17.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.72 - 0.94: 1 0.94 - 1.16: 1 1.16 - 1.39: 15411 1.39 - 1.61: 23214 1.61 - 1.83: 359 Bond restraints: 38986 Sorted by residual: bond pdb=" C LYS 4 491 " pdb=" N LYS 4 492 " ideal model delta sigma weight residual 1.332 0.718 0.614 1.40e-02 5.10e+03 1.92e+03 bond pdb=" C ILE 5 507 " pdb=" N LEU 5 508 " ideal model delta sigma weight residual 1.332 1.041 0.291 1.40e-02 5.10e+03 4.32e+02 bond pdb=" C4 ATP 4 901 " pdb=" C5 ATP 4 901 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.11e+01 bond pdb=" C LEU 7 220 " pdb=" N TYR 7 221 " ideal model delta sigma weight residual 1.332 1.450 -0.117 1.40e-02 5.10e+03 7.04e+01 bond pdb=" C4 ATP 6 902 " pdb=" C5 ATP 6 902 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.39e+01 ... (remaining 38981 not shown) Histogram of bond angle deviations from ideal: 77.85 - 91.35: 3 91.35 - 104.84: 829 104.84 - 118.34: 29785 118.34 - 131.83: 22090 131.83 - 145.33: 71 Bond angle restraints: 52778 Sorted by residual: angle pdb=" O LYS 4 491 " pdb=" C LYS 4 491 " pdb=" N LYS 4 492 " ideal model delta sigma weight residual 123.29 94.09 29.20 1.18e+00 7.18e-01 6.12e+02 angle pdb=" CA ILE 5 507 " pdb=" C ILE 5 507 " pdb=" N LEU 5 508 " ideal model delta sigma weight residual 116.60 82.15 34.45 1.45e+00 4.76e-01 5.64e+02 angle pdb=" PB ATP 6 902 " pdb=" O3B ATP 6 902 " pdb=" PG ATP 6 902 " ideal model delta sigma weight residual 139.87 116.67 23.20 1.00e+00 1.00e+00 5.38e+02 angle pdb=" CA LYS 4 491 " pdb=" C LYS 4 491 " pdb=" N LYS 4 492 " ideal model delta sigma weight residual 116.28 145.33 -29.05 1.26e+00 6.30e-01 5.32e+02 angle pdb=" C ILE 5 507 " pdb=" N LEU 5 508 " pdb=" CA LEU 5 508 " ideal model delta sigma weight residual 121.54 77.85 43.69 1.91e+00 2.74e-01 5.23e+02 ... (remaining 52773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.59: 22232 28.59 - 57.19: 1513 57.19 - 85.78: 138 85.78 - 114.37: 17 114.37 - 142.96: 8 Dihedral angle restraints: 23908 sinusoidal: 9970 harmonic: 13938 Sorted by residual: dihedral pdb=" CD ARG 2 641 " pdb=" NE ARG 2 641 " pdb=" CZ ARG 2 641 " pdb=" NH1 ARG 2 641 " ideal model delta sinusoidal sigma weight residual 0.00 118.09 -118.09 1 1.00e+01 1.00e-02 1.41e+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 180.00 120.94 59.06 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CD ARG 6 611 " pdb=" NE ARG 6 611 " pdb=" CZ ARG 6 611 " pdb=" NH1 ARG 6 611 " ideal model delta sinusoidal sigma weight residual 0.00 107.05 -107.05 1 1.00e+01 1.00e-02 1.24e+02 ... (remaining 23905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.583: 5960 0.583 - 1.166: 0 1.166 - 1.749: 24 1.749 - 2.332: 5 2.332 - 2.914: 1 Chirality restraints: 5990 Sorted by residual: chirality pdb=" CG LEU 4 545 " pdb=" CB LEU 4 545 " pdb=" CD1 LEU 4 545 " pdb=" CD2 LEU 4 545 " both_signs ideal model delta sigma weight residual False -2.59 0.32 -2.91 2.00e-01 2.50e+01 2.12e+02 chirality pdb=" CG LEU 4 766 " pdb=" CB LEU 4 766 " pdb=" CD1 LEU 4 766 " pdb=" CD2 LEU 4 766 " both_signs ideal model delta sigma weight residual False -2.59 -0.58 -2.01 2.00e-01 2.50e+01 1.01e+02 chirality pdb=" CG LEU 4 450 " pdb=" CB LEU 4 450 " pdb=" CD1 LEU 4 450 " pdb=" CD2 LEU 4 450 " both_signs ideal model delta sigma weight residual False -2.59 -0.67 -1.92 2.00e-01 2.50e+01 9.18e+01 ... (remaining 5987 not shown) Planarity restraints: 6735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE 5 507 " -0.080 2.00e-02 2.50e+03 2.08e-01 4.34e+02 pdb=" C ILE 5 507 " 0.358 2.00e-02 2.50e+03 pdb=" O ILE 5 507 " -0.148 2.00e-02 2.50e+03 pdb=" N LEU 5 508 " -0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 3 610 " -0.448 9.50e-02 1.11e+02 2.27e-01 1.63e+02 pdb=" NE ARG 3 610 " 0.101 2.00e-02 2.50e+03 pdb=" CZ ARG 3 610 " -0.198 2.00e-02 2.50e+03 pdb=" NH1 ARG 3 610 " 0.066 2.00e-02 2.50e+03 pdb=" NH2 ARG 3 610 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 6 611 " 0.936 9.50e-02 1.11e+02 4.24e-01 1.53e+02 pdb=" NE ARG 6 611 " -0.099 2.00e-02 2.50e+03 pdb=" CZ ARG 6 611 " 0.106 2.00e-02 2.50e+03 pdb=" NH1 ARG 6 611 " -0.022 2.00e-02 2.50e+03 pdb=" NH2 ARG 6 611 " -0.027 2.00e-02 2.50e+03 ... (remaining 6732 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 27 2.03 - 2.74: 5739 2.74 - 3.46: 59519 3.46 - 4.18: 91307 4.18 - 4.90: 147490 Nonbonded interactions: 304082 Sorted by model distance: nonbonded pdb=" O LYS 3 78 " pdb=" OG SER 3 82 " model vdw 1.308 2.440 nonbonded pdb=" NH1 ARG 2 374 " pdb=" OE1 GLN 6 231 " model vdw 1.431 2.520 nonbonded pdb=" OG1 THR 7 500 " pdb=" OE1 GLN 7 503 " model vdw 1.502 2.440 nonbonded pdb=" CZ ARG 2 374 " pdb=" OE1 GLN 6 231 " model vdw 1.610 3.270 nonbonded pdb=" CD ARG 6 521 " pdb=" NH1 ARG 6 611 " model vdw 1.642 3.520 ... (remaining 304077 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: 2.350 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: 0.040 Extract box with map and model: 13.630 Check model and map are aligned: 0.570 Set scattering table: 0.380 Process input model: 96.300 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.150 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.614 38986 Z= 0.671 Angle : 1.601 43.690 52778 Z= 0.910 Chirality : 0.144 2.914 5990 Planarity : 0.014 0.466 6735 Dihedral : 18.700 142.964 14833 Min Nonbonded Distance : 1.308 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.97 % Allowed : 17.65 % Favored : 81.38 % Rotamer: Outliers : 6.20 % Allowed : 15.07 % Favored : 78.73 % Cbeta Deviations : 0.64 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.30 % Twisted General : 1.13 % 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: -5.70 (0.09), residues: 4657 helix: -3.84 (0.09), residues: 1381 sheet: -3.70 (0.21), residues: 417 loop : -3.99 (0.10), residues: 2859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.005 TRP 2 554 HIS 0.035 0.004 HIS H 199 PHE 0.060 0.005 PHE 4 526 TYR 0.056 0.005 TYR 3 238 ARG 0.203 0.004 ARG 3 610 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1283 residues out of total 4193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1029 time to evaluate : 4.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (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 TARDY: cannot create tardy model for: "SER L 185 " (corrupted residue). Skipping it. 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 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: A 18 ARG cc_start: 0.7333 (ptp90) cc_final: 0.5060 (ptt-90) REVERT: A 45 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6389 (mmt) REVERT: A 66 GLN cc_start: 0.8270 (tp40) cc_final: 0.7823 (pm20) REVERT: A 188 ARG cc_start: 0.8676 (ttt90) cc_final: 0.7965 (ptp-170) REVERT: A 217 MET cc_start: 0.7795 (mmt) cc_final: 0.7584 (mpp) REVERT: A 261 ILE cc_start: 0.6118 (OUTLIER) cc_final: 0.5801 (mm) REVERT: A 300 THR cc_start: 0.6221 (OUTLIER) cc_final: 0.5933 (p) REVERT: A 326 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8059 (tp30) REVERT: A 442 GLN cc_start: 0.7692 (mp10) cc_final: 0.7170 (tp40) REVERT: A 459 PHE cc_start: 0.8285 (m-80) cc_final: 0.7836 (m-80) REVERT: A 519 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.6784 (mp) REVERT: H 10 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8042 (mp0) REVERT: H 69 PHE cc_start: 0.7760 (t80) cc_final: 0.7334 (t80) REVERT: H 86 TYR cc_start: 0.8399 (t80) cc_final: 0.8137 (t80) REVERT: H 129 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.7375 (t80) REVERT: L 47 TRP cc_start: 0.7963 (p-90) cc_final: 0.7683 (p-90) REVERT: L 51 HIS cc_start: 0.8049 (m90) cc_final: 0.7834 (m-70) REVERT: L 64 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8184 (mp0) REVERT: L 77 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8476 (mt-10) REVERT: L 89 CYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6198 (t) REVERT: L 112 GLU cc_start: 0.8753 (mp0) cc_final: 0.8499 (mp0) REVERT: L 136 ILE cc_start: 0.8030 (pt) cc_final: 0.7621 (pt) REVERT: L 141 THR cc_start: 0.6703 (p) cc_final: 0.6072 (p) REVERT: L 180 ASP cc_start: 0.5308 (m-30) cc_final: 0.4696 (t0) REVERT: M 17 PHE cc_start: 0.5922 (t80) cc_final: 0.5059 (t80) REVERT: M 53 ASN cc_start: 0.8156 (m110) cc_final: 0.7590 (p0) REVERT: M 112 ASP cc_start: 0.8703 (p0) cc_final: 0.8481 (p0) REVERT: M 167 TYR cc_start: 0.7847 (t80) cc_final: 0.7550 (t80) REVERT: N 105 LEU cc_start: 0.8931 (mt) cc_final: 0.8026 (mt) REVERT: N 109 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8312 (mt) REVERT: N 110 GLN cc_start: 0.8559 (mp10) cc_final: 0.8122 (mp10) REVERT: N 111 LYS cc_start: 0.8982 (mttm) cc_final: 0.8596 (mmmm) REVERT: N 144 PHE cc_start: 0.8078 (t80) cc_final: 0.7820 (t80) REVERT: N 182 PHE cc_start: 0.6274 (m-80) cc_final: 0.5311 (m-80) REVERT: 2 356 ARG cc_start: 0.8313 (ptt90) cc_final: 0.8032 (ptt-90) REVERT: 2 485 PHE cc_start: 0.6663 (m-80) cc_final: 0.4979 (m-80) REVERT: 2 499 ARG cc_start: 0.4033 (OUTLIER) cc_final: 0.3199 (mpt-90) REVERT: 2 534 GLN cc_start: 0.5756 (OUTLIER) cc_final: 0.5426 (tm-30) REVERT: 2 546 ARG cc_start: 0.2048 (OUTLIER) cc_final: 0.1498 (mtm180) REVERT: 2 703 TYR cc_start: 0.8000 (m-10) cc_final: 0.7585 (m-80) REVERT: 2 764 MET cc_start: 0.3780 (tpp) cc_final: 0.3477 (mmm) REVERT: 2 781 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7557 (pt0) REVERT: 2 788 MET cc_start: 0.7786 (ptm) cc_final: 0.7531 (ttt) REVERT: 2 795 PHE cc_start: 0.6394 (m-10) cc_final: 0.5937 (m-80) REVERT: 5 59 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.6826 (tt) REVERT: 5 93 ILE cc_start: 0.8436 (tp) cc_final: 0.8205 (tp) REVERT: 5 96 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8562 (mm-30) REVERT: 5 115 HIS cc_start: 0.7465 (t70) cc_final: 0.7250 (t70) REVERT: 5 226 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6881 (pp20) REVERT: 5 249 CYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6545 (p) REVERT: 5 285 VAL cc_start: 0.7550 (OUTLIER) cc_final: 0.7195 (t) REVERT: 5 426 MET cc_start: 0.1921 (mmt) cc_final: 0.1635 (mmp) REVERT: 5 441 ILE cc_start: 0.5452 (OUTLIER) cc_final: 0.5013 (tp) REVERT: 5 452 ARG cc_start: 0.3952 (OUTLIER) cc_final: 0.3647 (ttp-170) REVERT: 5 560 LYS cc_start: 0.5040 (mptt) cc_final: 0.3689 (ttmt) REVERT: 6 113 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.7766 (m) REVERT: 6 120 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.6898 (mt) REVERT: 6 199 LYS cc_start: 0.8347 (ttpp) cc_final: 0.8080 (ttpp) REVERT: 6 208 GLU cc_start: 0.8081 (tp30) cc_final: 0.7437 (tt0) REVERT: 6 236 TYR cc_start: 0.4164 (OUTLIER) cc_final: 0.3084 (p90) REVERT: 6 341 ASN cc_start: 0.6694 (OUTLIER) cc_final: 0.6462 (m-40) REVERT: 6 374 GLU cc_start: 0.8940 (pp20) cc_final: 0.8582 (pm20) REVERT: 6 398 LEU cc_start: 0.8477 (mp) cc_final: 0.8258 (mp) REVERT: 6 433 ASP cc_start: 0.6862 (t0) cc_final: 0.6208 (p0) REVERT: 6 454 PHE cc_start: 0.7590 (m-80) cc_final: 0.7136 (m-80) REVERT: 6 478 ARG cc_start: 0.7371 (mmt-90) cc_final: 0.7095 (mmt-90) REVERT: 6 492 LEU cc_start: 0.4017 (OUTLIER) cc_final: 0.3568 (mm) REVERT: 6 514 LEU cc_start: 0.1605 (OUTLIER) cc_final: 0.1115 (mt) REVERT: 6 613 LEU cc_start: 0.8197 (tp) cc_final: 0.7943 (mt) REVERT: 3 73 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.7795 (m-80) REVERT: 3 77 LEU cc_start: 0.9514 (mp) cc_final: 0.9290 (tt) REVERT: 3 111 ARG cc_start: 0.7581 (tpt90) cc_final: 0.7192 (ptm160) REVERT: 3 116 ILE cc_start: 0.8901 (tt) cc_final: 0.8637 (mm) REVERT: 3 219 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.7949 (m-30) REVERT: 3 466 LEU cc_start: 0.5520 (OUTLIER) cc_final: 0.4582 (pt) REVERT: 3 478 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7356 (m-10) REVERT: 3 480 MET cc_start: 0.7049 (ttm) cc_final: 0.6221 (tmm) REVERT: 3 572 MET cc_start: 0.7840 (mmp) cc_final: 0.7625 (mmm) REVERT: 4 221 PHE cc_start: 0.7033 (t80) cc_final: 0.6632 (t80) REVERT: 4 248 PHE cc_start: 0.9285 (m-80) cc_final: 0.8924 (m-80) REVERT: 4 291 MET cc_start: 0.7135 (mtt) cc_final: 0.6602 (ttm) REVERT: 4 302 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7804 (tpp) REVERT: 4 335 ASN cc_start: 0.9192 (m-40) cc_final: 0.8476 (t0) REVERT: 4 538 ARG cc_start: 0.5688 (tpp80) cc_final: 0.5401 (mmm-85) REVERT: 4 578 PHE cc_start: 0.7646 (t80) cc_final: 0.7394 (t80) REVERT: 4 649 ILE cc_start: 0.6608 (mp) cc_final: 0.6128 (pt) REVERT: 7 20 PHE cc_start: 0.7317 (t80) cc_final: 0.6537 (t80) REVERT: 7 173 VAL cc_start: 0.7639 (OUTLIER) cc_final: 0.7364 (p) REVERT: 7 176 MET cc_start: 0.6650 (ttp) cc_final: 0.5935 (tpp) REVERT: 7 196 ASN cc_start: 0.7769 (t0) cc_final: 0.6482 (m110) REVERT: 7 264 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7012 (mtp) REVERT: 7 327 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7788 (mt) REVERT: 7 329 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8458 (mt0) REVERT: 7 345 TYR cc_start: 0.8549 (t80) cc_final: 0.8188 (t80) REVERT: 7 365 ARG cc_start: 0.8502 (mmm-85) cc_final: 0.8095 (tpp-160) REVERT: 7 435 VAL cc_start: 0.7963 (t) cc_final: 0.7730 (t) REVERT: 7 484 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.8943 (mm) REVERT: 7 541 HIS cc_start: 0.7291 (m-70) cc_final: 0.6831 (m-70) REVERT: 7 550 ARG cc_start: 0.7082 (tpt170) cc_final: 0.6601 (tpp-160) REVERT: 7 556 MET cc_start: 0.8659 (ptt) cc_final: 0.8427 (ptt) REVERT: 7 590 ARG cc_start: 0.9187 (ppt170) cc_final: 0.8051 (tpt90) REVERT: 7 627 LYS cc_start: 0.8788 (mttt) cc_final: 0.8520 (tptp) outliers start: 254 outliers final: 88 residues processed: 1238 average time/residue: 0.5469 time to fit residues: 1060.7218 Evaluate side-chains 822 residues out of total 4193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 702 time to evaluate : 4.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 399 optimal weight: 0.3980 chunk 358 optimal weight: 4.9990 chunk 198 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 chunk 370 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 225 optimal weight: 0.9990 chunk 275 optimal weight: 2.9990 chunk 429 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 HIS ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN A 290 HIS ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 GLN ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 200 HIS L 20 ASN L 154 HIS L 171 GLN M 53 ASN M 127 GLN M 166 GLN N 36 GLN ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 ASN N 164 GLN N 170 GLN N 209 HIS N 214 GLN 2 210 GLN 2 286 HIS ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 591 GLN 2 659 GLN 2 666 HIS 2 672 HIS ** 5 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 176 ASN 5 196 GLN ** 5 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 239 HIS 5 241 GLN 5 261 GLN ** 5 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 373 ASN 5 423 ASN ** 5 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 198 GLN 6 496 ASN 6 550 ASN 6 584 HIS 6 645 ASN 3 26 GLN ** 3 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 199 GLN ** 3 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 467 GLN 3 490 GLN 3 605 GLN ** 3 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 182 GLN 4 204 HIS ** 4 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 333 ASN ** 4 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 378 HIS 4 379 ASN ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 485 GLN 4 523 GLN 4 596 GLN 4 746 HIS 7 45 GLN 7 59 ASN 7 196 ASN 7 266 GLN ** 7 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 503 GLN ** 7 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 557 ASN 7 564 ASN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 38986 Z= 0.256 Angle : 0.884 12.591 52778 Z= 0.457 Chirality : 0.051 0.324 5990 Planarity : 0.007 0.153 6735 Dihedral : 12.923 138.591 5584 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.53 % Favored : 86.41 % Rotamer: Outliers : 0.49 % Allowed : 7.72 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.24 % 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: -4.69 (0.11), residues: 4657 helix: -2.88 (0.11), residues: 1365 sheet: -3.03 (0.20), residues: 462 loop : -3.42 (0.11), residues: 2830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 2 554 HIS 0.010 0.002 HIS 4 423 PHE 0.041 0.002 PHE 6 570 TYR 0.045 0.003 TYR 6 559 ARG 0.013 0.001 ARG 5 286 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 4193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 942 time to evaluate : 4.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER L 185 " (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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 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 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 50 VAL cc_start: 0.7975 (t) cc_final: 0.7754 (t) REVERT: A 66 GLN cc_start: 0.8102 (tp40) cc_final: 0.7863 (pm20) REVERT: A 72 VAL cc_start: 0.7942 (t) cc_final: 0.7721 (t) REVERT: A 73 VAL cc_start: 0.8617 (t) cc_final: 0.8173 (t) REVERT: A 188 ARG cc_start: 0.8624 (ttt90) cc_final: 0.7914 (mpt180) REVERT: A 326 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7939 (tp30) REVERT: A 380 TYR cc_start: 0.7184 (m-80) cc_final: 0.6803 (m-10) REVERT: A 442 GLN cc_start: 0.7918 (mp10) cc_final: 0.7311 (tp40) REVERT: A 459 PHE cc_start: 0.8200 (m-80) cc_final: 0.7546 (m-10) REVERT: A 483 LEU cc_start: 0.8551 (mt) cc_final: 0.8188 (mt) REVERT: H 10 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7685 (tp30) REVERT: H 69 PHE cc_start: 0.7306 (t80) cc_final: 0.6738 (t80) REVERT: L 47 TRP cc_start: 0.7727 (p-90) cc_final: 0.7219 (p-90) REVERT: L 64 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8101 (mp0) REVERT: L 68 MET cc_start: 0.8479 (ppp) cc_final: 0.8271 (ppp) REVERT: L 77 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8336 (mt-10) REVERT: L 80 ARG cc_start: 0.8721 (ptt-90) cc_final: 0.8235 (ptt-90) REVERT: L 136 ILE cc_start: 0.8025 (pt) cc_final: 0.7268 (pt) REVERT: L 141 THR cc_start: 0.6745 (p) cc_final: 0.6061 (m) REVERT: M 17 PHE cc_start: 0.6054 (t80) cc_final: 0.5348 (t80) REVERT: M 53 ASN cc_start: 0.7998 (m-40) cc_final: 0.7683 (p0) REVERT: M 112 ASP cc_start: 0.8636 (p0) cc_final: 0.8402 (p0) REVERT: M 169 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7548 (tp30) REVERT: N 95 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8241 (mt-10) REVERT: N 99 TYR cc_start: 0.3267 (t80) cc_final: 0.2464 (t80) REVERT: N 105 LEU cc_start: 0.9126 (mt) cc_final: 0.8372 (mt) REVERT: N 182 PHE cc_start: 0.6501 (m-80) cc_final: 0.5470 (m-80) REVERT: 2 195 ARG cc_start: 0.8558 (mpp80) cc_final: 0.8055 (ptt-90) REVERT: 2 240 MET cc_start: 0.7639 (mmm) cc_final: 0.7305 (mmm) REVERT: 2 278 GLU cc_start: 0.7577 (tp30) cc_final: 0.7035 (tp30) REVERT: 2 466 MET cc_start: 0.4910 (tmm) cc_final: 0.4571 (tmm) REVERT: 2 589 MET cc_start: 0.2169 (mpp) cc_final: 0.1355 (mpp) REVERT: 2 764 MET cc_start: 0.3459 (tpp) cc_final: 0.3095 (mmm) REVERT: 2 774 MET cc_start: 0.4849 (mtp) cc_final: 0.4636 (mtp) REVERT: 2 781 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7508 (pt0) REVERT: 5 165 ILE cc_start: -0.0276 (mp) cc_final: -0.0548 (mp) REVERT: 5 245 ASP cc_start: 0.7026 (p0) cc_final: 0.6355 (m-30) REVERT: 5 291 ARG cc_start: 0.8117 (ptm-80) cc_final: 0.7793 (ptm160) REVERT: 5 292 VAL cc_start: 0.8308 (t) cc_final: 0.8076 (t) REVERT: 5 426 MET cc_start: 0.1607 (mmt) cc_final: 0.1336 (mmp) REVERT: 5 507 ILE cc_start: 0.6445 (OUTLIER) cc_final: 0.6154 (mm) REVERT: 6 186 MET cc_start: 0.6787 (mtp) cc_final: 0.6197 (mmt) REVERT: 6 208 GLU cc_start: 0.8372 (tp30) cc_final: 0.7613 (tt0) REVERT: 6 220 ILE cc_start: 0.8519 (tt) cc_final: 0.8096 (tt) REVERT: 6 286 TYR cc_start: 0.7266 (m-80) cc_final: 0.7023 (m-80) REVERT: 6 317 MET cc_start: 0.2215 (tmm) cc_final: 0.1948 (tmm) REVERT: 6 363 GLN cc_start: 0.7832 (tt0) cc_final: 0.7589 (tt0) REVERT: 6 381 ASP cc_start: 0.7053 (t0) cc_final: 0.6390 (t0) REVERT: 6 433 ASP cc_start: 0.6240 (t0) cc_final: 0.5928 (p0) REVERT: 6 451 ILE cc_start: 0.8434 (mm) cc_final: 0.8169 (mm) REVERT: 6 478 ARG cc_start: 0.7329 (mmt-90) cc_final: 0.7104 (mmt-90) REVERT: 6 542 ARG cc_start: 0.7746 (mtt90) cc_final: 0.7496 (ttp80) REVERT: 6 544 ILE cc_start: 0.0048 (OUTLIER) cc_final: -0.0267 (tt) REVERT: 6 560 THR cc_start: 0.8720 (p) cc_final: 0.8484 (t) REVERT: 6 623 MET cc_start: 0.9046 (mtm) cc_final: 0.8718 (mtm) REVERT: 3 35 ASP cc_start: 0.7241 (m-30) cc_final: 0.6551 (m-30) REVERT: 3 73 PHE cc_start: 0.8811 (m-10) cc_final: 0.8560 (m-80) REVERT: 3 77 LEU cc_start: 0.9417 (mp) cc_final: 0.9136 (tt) REVERT: 3 100 GLU cc_start: 0.6586 (tm-30) cc_final: 0.6255 (tm-30) REVERT: 3 111 ARG cc_start: 0.7950 (tpt90) cc_final: 0.7312 (ptm160) REVERT: 3 219 ASP cc_start: 0.8163 (t70) cc_final: 0.7881 (m-30) REVERT: 3 254 ARG cc_start: 0.8224 (tpm170) cc_final: 0.7926 (tpm170) REVERT: 3 572 MET cc_start: 0.8199 (mmp) cc_final: 0.7795 (mmm) REVERT: 3 573 LYS cc_start: 0.8550 (ttpp) cc_final: 0.8290 (mtpp) REVERT: 4 221 PHE cc_start: 0.6883 (t80) cc_final: 0.6451 (t80) REVERT: 4 248 PHE cc_start: 0.9095 (m-80) cc_final: 0.8626 (m-80) REVERT: 4 274 MET cc_start: 0.6610 (tmm) cc_final: 0.6328 (tmm) REVERT: 4 281 ASP cc_start: 0.8892 (m-30) cc_final: 0.8432 (t0) REVERT: 4 291 MET cc_start: 0.7501 (mtt) cc_final: 0.6953 (ttm) REVERT: 4 302 MET cc_start: 0.7820 (ttp) cc_final: 0.7397 (tpp) REVERT: 4 335 ASN cc_start: 0.9223 (m-40) cc_final: 0.8524 (t0) REVERT: 4 390 ARG cc_start: 0.6933 (mtm180) cc_final: 0.5520 (mmm160) REVERT: 4 570 ASN cc_start: 0.7670 (t0) cc_final: 0.7445 (t0) REVERT: 4 574 CYS cc_start: 0.7785 (m) cc_final: 0.7158 (m) REVERT: 4 578 PHE cc_start: 0.7983 (t80) cc_final: 0.7366 (t80) REVERT: 4 579 ASP cc_start: 0.8788 (t0) cc_final: 0.8554 (t0) REVERT: 4 596 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7582 (pm20) REVERT: 4 683 MET cc_start: 0.5406 (tpt) cc_final: 0.5067 (tpp) REVERT: 4 692 TYR cc_start: 0.7076 (p90) cc_final: 0.6869 (p90) REVERT: 7 20 PHE cc_start: 0.7453 (t80) cc_final: 0.6710 (t80) REVERT: 7 83 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7959 (mm-30) REVERT: 7 104 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8752 (mt-10) REVERT: 7 232 PHE cc_start: 0.7320 (t80) cc_final: 0.7004 (t80) REVERT: 7 253 MET cc_start: 0.2846 (ptt) cc_final: 0.2627 (ptt) REVERT: 7 541 HIS cc_start: 0.7417 (m-70) cc_final: 0.6936 (m-70) REVERT: 7 550 ARG cc_start: 0.6809 (tpt170) cc_final: 0.6374 (tpp-160) REVERT: 7 562 TYR cc_start: 0.8503 (t80) cc_final: 0.8147 (m-80) REVERT: 7 602 SER cc_start: 0.8819 (t) cc_final: 0.7826 (p) REVERT: 7 605 ASN cc_start: 0.8159 (t0) cc_final: 0.7914 (m110) REVERT: 7 625 VAL cc_start: 0.8672 (t) cc_final: 0.8266 (t) outliers start: 20 outliers final: 4 residues processed: 957 average time/residue: 0.5479 time to fit residues: 828.1890 Evaluate side-chains 718 residues out of total 4193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 711 time to evaluate : 4.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 238 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 357 optimal weight: 0.1980 chunk 292 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 430 optimal weight: 3.9990 chunk 464 optimal weight: 2.9990 chunk 383 optimal weight: 6.9990 chunk 426 optimal weight: 7.9990 chunk 146 optimal weight: 0.5980 chunk 345 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN A 206 GLN ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 GLN M 28 ASN N 209 HIS 2 289 GLN ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 21 GLN ** 5 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 318 HIS 5 476 ASN 5 486 ASN 5 500 ASN 5 532 HIS 5 611 GLN ** 5 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 67 GLN ** 6 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 198 GLN ** 6 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 645 ASN 3 7 GLN 3 107 HIS 3 120 ASN 3 260 ASN ** 3 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 418 HIS ** 3 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 495 HIS 3 567 HIS 3 637 HIS ** 4 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 523 GLN ** 4 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 710 GLN ** 4 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 196 ASN 7 233 GLN 7 248 HIS ** 7 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 439 GLN 7 503 GLN ** 7 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 543 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 38986 Z= 0.273 Angle : 0.840 12.163 52778 Z= 0.436 Chirality : 0.049 0.361 5990 Planarity : 0.006 0.107 6735 Dihedral : 12.410 153.083 5584 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 14.84 % Favored : 85.12 % Rotamer: Outliers : 0.29 % Allowed : 7.01 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -4.37 (0.11), residues: 4657 helix: -2.62 (0.11), residues: 1421 sheet: -2.83 (0.21), residues: 463 loop : -3.21 (0.11), residues: 2773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 2 554 HIS 0.010 0.002 HIS H 71 PHE 0.053 0.003 PHE 4 487 TYR 0.033 0.002 TYR 2 700 ARG 0.028 0.001 ARG 2 641 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 4193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 886 time to evaluate : 4.999 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 TARDY: cannot create tardy model for: "SER L 185 " (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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 revert: symmetry clash 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 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 66 GLN cc_start: 0.8268 (tp40) cc_final: 0.8063 (pm20) REVERT: A 229 ASN cc_start: 0.8917 (m-40) cc_final: 0.8463 (p0) REVERT: A 232 LEU cc_start: 0.9205 (mp) cc_final: 0.8322 (mp) REVERT: A 278 MET cc_start: 0.5757 (mmm) cc_final: 0.5279 (mmm) REVERT: A 326 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8089 (tp30) REVERT: A 345 MET cc_start: 0.8437 (mtp) cc_final: 0.7913 (mtp) REVERT: A 383 ARG cc_start: 0.8112 (tmm-80) cc_final: 0.7426 (tmm-80) REVERT: A 442 GLN cc_start: 0.7820 (mp10) cc_final: 0.7536 (mt0) REVERT: A 483 LEU cc_start: 0.8662 (mt) cc_final: 0.8359 (mt) REVERT: L 2 ASP cc_start: 0.7646 (m-30) cc_final: 0.7436 (m-30) REVERT: L 68 MET cc_start: 0.8545 (ppp) cc_final: 0.8123 (ppp) REVERT: L 97 GLN cc_start: 0.8491 (mt0) cc_final: 0.8186 (mt0) REVERT: L 100 MET cc_start: 0.7387 (ttt) cc_final: 0.7031 (ttt) REVERT: L 123 ILE cc_start: 0.8750 (pt) cc_final: 0.8498 (pt) REVERT: L 136 ILE cc_start: 0.8136 (pt) cc_final: 0.7523 (pt) REVERT: L 152 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8016 (mp0) REVERT: M 17 PHE cc_start: 0.6105 (t80) cc_final: 0.5236 (t80) REVERT: M 53 ASN cc_start: 0.7941 (m-40) cc_final: 0.7639 (p0) REVERT: M 57 TRP cc_start: 0.8338 (p-90) cc_final: 0.8081 (p-90) REVERT: N 39 LEU cc_start: 0.8435 (tt) cc_final: 0.8215 (tt) REVERT: N 91 SER cc_start: 0.9118 (m) cc_final: 0.8691 (p) REVERT: N 92 MET cc_start: 0.8403 (ptm) cc_final: 0.7976 (ttp) REVERT: N 95 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8082 (mt-10) REVERT: N 105 LEU cc_start: 0.9425 (mt) cc_final: 0.8865 (mt) REVERT: N 109 LEU cc_start: 0.8919 (mt) cc_final: 0.7962 (mt) REVERT: N 159 TYR cc_start: 0.6571 (t80) cc_final: 0.6107 (t80) REVERT: N 202 ASP cc_start: 0.8483 (t70) cc_final: 0.8096 (t70) REVERT: 2 240 MET cc_start: 0.7934 (mmm) cc_final: 0.7687 (mmm) REVERT: 2 396 GLU cc_start: 0.7439 (pm20) cc_final: 0.6829 (pm20) REVERT: 2 466 MET cc_start: 0.5006 (tmm) cc_final: 0.4389 (tmm) REVERT: 2 577 MET cc_start: 0.8304 (mmp) cc_final: 0.8054 (mmp) REVERT: 2 756 ARG cc_start: 0.6910 (mtt180) cc_final: 0.6604 (mtt180) REVERT: 2 757 MET cc_start: 0.9014 (mmp) cc_final: 0.8787 (mmt) REVERT: 2 764 MET cc_start: 0.3368 (tpp) cc_final: 0.2877 (mmm) REVERT: 2 781 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7478 (pt0) REVERT: 2 791 MET cc_start: 0.8199 (tmm) cc_final: 0.7961 (tmm) REVERT: 5 59 LEU cc_start: 0.7029 (tt) cc_final: 0.6615 (tt) REVERT: 5 69 MET cc_start: 0.2811 (ptt) cc_final: 0.2399 (tpt) REVERT: 5 71 ASP cc_start: 0.8182 (m-30) cc_final: 0.7947 (m-30) REVERT: 5 245 ASP cc_start: 0.7422 (p0) cc_final: 0.6940 (m-30) REVERT: 6 208 GLU cc_start: 0.8199 (tp30) cc_final: 0.7393 (pt0) REVERT: 6 220 ILE cc_start: 0.8692 (tt) cc_final: 0.8118 (tt) REVERT: 6 317 MET cc_start: 0.2040 (tmm) cc_final: 0.1681 (tmm) REVERT: 6 363 GLN cc_start: 0.7881 (tt0) cc_final: 0.7627 (tt0) REVERT: 6 433 ASP cc_start: 0.5921 (t0) cc_final: 0.5655 (p0) REVERT: 6 451 ILE cc_start: 0.8496 (mm) cc_final: 0.8270 (mm) REVERT: 6 454 PHE cc_start: 0.7425 (m-80) cc_final: 0.7134 (m-80) REVERT: 6 469 MET cc_start: 0.5826 (tpp) cc_final: 0.5422 (tpp) REVERT: 6 478 ARG cc_start: 0.7560 (mmt-90) cc_final: 0.7293 (mmt-90) REVERT: 6 544 ILE cc_start: 0.1457 (OUTLIER) cc_final: 0.0693 (tt) REVERT: 6 623 MET cc_start: 0.8944 (mtm) cc_final: 0.8410 (ptp) REVERT: 3 35 ASP cc_start: 0.7162 (m-30) cc_final: 0.6421 (m-30) REVERT: 3 73 PHE cc_start: 0.8738 (m-10) cc_final: 0.8370 (m-80) REVERT: 3 77 LEU cc_start: 0.9393 (mp) cc_final: 0.9142 (tt) REVERT: 3 111 ARG cc_start: 0.8147 (tpt90) cc_final: 0.7351 (ptm160) REVERT: 3 201 MET cc_start: 0.7070 (tpt) cc_final: 0.6667 (mmm) REVERT: 3 219 ASP cc_start: 0.8450 (t70) cc_final: 0.8187 (m-30) REVERT: 3 265 LEU cc_start: 0.8115 (pt) cc_final: 0.7397 (pt) REVERT: 3 296 LYS cc_start: 0.8952 (mttt) cc_final: 0.8560 (mtmm) REVERT: 3 423 GLN cc_start: 0.8843 (tt0) cc_final: 0.8580 (tt0) REVERT: 3 572 MET cc_start: 0.8363 (mmp) cc_final: 0.7957 (mmm) REVERT: 4 227 ARG cc_start: 0.7872 (mtm110) cc_final: 0.7660 (mtm-85) REVERT: 4 248 PHE cc_start: 0.9098 (m-80) cc_final: 0.8545 (m-80) REVERT: 4 274 MET cc_start: 0.6493 (tmm) cc_final: 0.5968 (ppp) REVERT: 4 278 ASN cc_start: 0.6838 (t0) cc_final: 0.6535 (t0) REVERT: 4 281 ASP cc_start: 0.8936 (m-30) cc_final: 0.8497 (t0) REVERT: 4 390 ARG cc_start: 0.6607 (mtm180) cc_final: 0.5583 (mmm160) REVERT: 4 574 CYS cc_start: 0.7696 (m) cc_final: 0.6836 (m) REVERT: 4 576 ASP cc_start: 0.5707 (m-30) cc_final: 0.5288 (m-30) REVERT: 4 579 ASP cc_start: 0.8863 (t0) cc_final: 0.8640 (t0) REVERT: 4 580 LYS cc_start: 0.8885 (tppt) cc_final: 0.8331 (tptp) REVERT: 4 683 MET cc_start: 0.5715 (tpt) cc_final: 0.5100 (tpp) REVERT: 7 33 TYR cc_start: 0.8752 (m-80) cc_final: 0.8157 (m-80) REVERT: 7 79 ASP cc_start: 0.8439 (p0) cc_final: 0.7874 (m-30) REVERT: 7 138 PHE cc_start: 0.6506 (m-80) cc_final: 0.6108 (m-80) REVERT: 7 166 ILE cc_start: 0.7018 (mp) cc_final: 0.6400 (mm) REVERT: 7 176 MET cc_start: 0.6989 (ttp) cc_final: 0.6392 (tmm) REVERT: 7 400 ARG cc_start: 0.7295 (tpp-160) cc_final: 0.6604 (tpp-160) REVERT: 7 541 HIS cc_start: 0.7384 (m-70) cc_final: 0.6823 (m90) REVERT: 7 562 TYR cc_start: 0.8746 (t80) cc_final: 0.8141 (m-80) outliers start: 12 outliers final: 3 residues processed: 894 average time/residue: 0.5471 time to fit residues: 774.6981 Evaluate side-chains 679 residues out of total 4193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 675 time to evaluate : 4.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 425 optimal weight: 0.5980 chunk 323 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 288 optimal weight: 6.9990 chunk 431 optimal weight: 8.9990 chunk 457 optimal weight: 8.9990 chunk 225 optimal weight: 0.4980 chunk 409 optimal weight: 0.0570 chunk 123 optimal weight: 1.9990 overall best weight: 1.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 ASN H 146 ASN L 23 ASN L 154 HIS ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 659 GLN ** 2 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 318 HIS 6 198 GLN ** 6 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 107 HIS ** 3 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 467 GLN 4 259 HIS ** 4 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 156 HIS 7 238 GLN 7 248 HIS ** 7 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 605 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 38986 Z= 0.231 Angle : 0.787 12.835 52778 Z= 0.404 Chirality : 0.048 0.363 5990 Planarity : 0.006 0.091 6735 Dihedral : 12.088 146.670 5584 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.98 % Favored : 85.98 % Rotamer: Outliers : 0.20 % Allowed : 5.03 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -4.09 (0.11), residues: 4657 helix: -2.38 (0.12), residues: 1396 sheet: -2.66 (0.22), residues: 456 loop : -3.04 (0.11), residues: 2805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 47 HIS 0.011 0.001 HIS 2 754 PHE 0.034 0.002 PHE 4 487 TYR 0.033 0.002 TYR 7 102 ARG 0.011 0.001 ARG 7 604 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 4193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 838 time to evaluate : 4.607 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 TARDY: cannot create tardy model for: "SER L 185 " (corrupted residue). Skipping it. 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 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 7 108 " (corrupted residue). Skipping it. REVERT: A 26 ASP cc_start: 0.9187 (t0) cc_final: 0.8891 (t0) REVERT: A 217 MET cc_start: 0.7937 (mpp) cc_final: 0.7731 (mpp) REVERT: A 383 ARG cc_start: 0.8067 (tmm-80) cc_final: 0.7264 (tmm-80) REVERT: A 430 ASP cc_start: 0.7405 (m-30) cc_final: 0.7204 (m-30) REVERT: A 442 GLN cc_start: 0.7788 (mp10) cc_final: 0.7489 (tt0) REVERT: A 466 GLU cc_start: 0.8025 (tt0) cc_final: 0.7045 (tm-30) REVERT: A 483 LEU cc_start: 0.8714 (mt) cc_final: 0.8381 (mt) REVERT: L 68 MET cc_start: 0.8339 (ppp) cc_final: 0.8030 (ppp) REVERT: L 133 ASP cc_start: 0.8573 (m-30) cc_final: 0.8327 (m-30) REVERT: L 136 ILE cc_start: 0.8087 (pt) cc_final: 0.7509 (pt) REVERT: M 53 ASN cc_start: 0.8026 (m-40) cc_final: 0.7561 (p0) REVERT: N 43 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7869 (mm-30) REVERT: N 91 SER cc_start: 0.9045 (m) cc_final: 0.8575 (p) REVERT: N 95 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8025 (mt-10) REVERT: N 105 LEU cc_start: 0.9389 (mt) cc_final: 0.9069 (mm) REVERT: N 109 LEU cc_start: 0.8824 (mt) cc_final: 0.8430 (mt) REVERT: N 159 TYR cc_start: 0.6474 (t80) cc_final: 0.6053 (t80) REVERT: N 202 ASP cc_start: 0.8264 (t70) cc_final: 0.7933 (t70) REVERT: 2 273 LEU cc_start: 0.7891 (mt) cc_final: 0.7509 (mt) REVERT: 2 358 TYR cc_start: 0.7593 (t80) cc_final: 0.7337 (t80) REVERT: 2 396 GLU cc_start: 0.7506 (pm20) cc_final: 0.6885 (pm20) REVERT: 2 466 MET cc_start: 0.5609 (tmm) cc_final: 0.4775 (tmm) REVERT: 2 589 MET cc_start: 0.2454 (mpp) cc_final: 0.2088 (mpp) REVERT: 2 764 MET cc_start: 0.5683 (tpp) cc_final: 0.5065 (mmm) REVERT: 2 774 MET cc_start: 0.5073 (mmm) cc_final: 0.4829 (mmt) REVERT: 2 781 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7636 (mt-10) REVERT: 2 788 MET cc_start: 0.7494 (ppp) cc_final: 0.7149 (ppp) REVERT: 5 59 LEU cc_start: 0.7076 (tt) cc_final: 0.6553 (tt) REVERT: 5 66 GLU cc_start: 0.7963 (mp0) cc_final: 0.7577 (mp0) REVERT: 5 69 MET cc_start: 0.2782 (ptt) cc_final: 0.2272 (tpt) REVERT: 5 71 ASP cc_start: 0.8261 (m-30) cc_final: 0.7964 (m-30) REVERT: 5 96 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8271 (mm-30) REVERT: 5 245 ASP cc_start: 0.7467 (p0) cc_final: 0.6975 (m-30) REVERT: 6 208 GLU cc_start: 0.7923 (tp30) cc_final: 0.7672 (pt0) REVERT: 6 220 ILE cc_start: 0.8706 (tt) cc_final: 0.8212 (tt) REVERT: 6 222 LEU cc_start: 0.8188 (pt) cc_final: 0.7878 (pp) REVERT: 6 286 TYR cc_start: 0.7091 (m-80) cc_final: 0.6518 (m-80) REVERT: 6 317 MET cc_start: 0.1635 (tmm) cc_final: -0.0592 (ppp) REVERT: 6 332 MET cc_start: 0.7816 (mpp) cc_final: 0.7540 (mpp) REVERT: 6 363 GLN cc_start: 0.7980 (tt0) cc_final: 0.7667 (tt0) REVERT: 6 451 ILE cc_start: 0.8643 (mm) cc_final: 0.8309 (mm) REVERT: 6 454 PHE cc_start: 0.7463 (m-80) cc_final: 0.7025 (m-80) REVERT: 6 478 ARG cc_start: 0.7730 (mmt-90) cc_final: 0.7421 (mmt-90) REVERT: 6 519 MET cc_start: 0.8865 (mpp) cc_final: 0.8653 (mpp) REVERT: 6 544 ILE cc_start: 0.1725 (OUTLIER) cc_final: 0.1024 (tt) REVERT: 6 623 MET cc_start: 0.8942 (mtm) cc_final: 0.8335 (mtm) REVERT: 3 35 ASP cc_start: 0.7298 (m-30) cc_final: 0.6588 (m-30) REVERT: 3 73 PHE cc_start: 0.8808 (m-10) cc_final: 0.8422 (m-80) REVERT: 3 77 LEU cc_start: 0.9453 (mp) cc_final: 0.9190 (tt) REVERT: 3 111 ARG cc_start: 0.8150 (tpt90) cc_final: 0.7422 (ptm160) REVERT: 3 423 GLN cc_start: 0.8839 (tt0) cc_final: 0.8490 (tt0) REVERT: 3 455 ASP cc_start: 0.7381 (m-30) cc_final: 0.7170 (m-30) REVERT: 3 491 MET cc_start: 0.5436 (ttm) cc_final: 0.5214 (mmp) REVERT: 3 572 MET cc_start: 0.8326 (mmp) cc_final: 0.7626 (mmm) REVERT: 3 610 ARG cc_start: 0.6698 (mtm180) cc_final: 0.6476 (mtp85) REVERT: 4 281 ASP cc_start: 0.9008 (m-30) cc_final: 0.8718 (t0) REVERT: 4 302 MET cc_start: 0.6934 (ttp) cc_final: 0.6499 (tpp) REVERT: 4 371 HIS cc_start: 0.4101 (p90) cc_final: 0.3772 (p90) REVERT: 4 390 ARG cc_start: 0.6339 (mtm180) cc_final: 0.5539 (mmm160) REVERT: 4 574 CYS cc_start: 0.7454 (m) cc_final: 0.6779 (m) REVERT: 4 580 LYS cc_start: 0.8826 (tppt) cc_final: 0.8531 (mmtp) REVERT: 4 683 MET cc_start: 0.5626 (tpt) cc_final: 0.5048 (tpp) REVERT: 4 695 TYR cc_start: 0.8681 (t80) cc_final: 0.8462 (t80) REVERT: 4 714 GLN cc_start: 0.8684 (tp40) cc_final: 0.8452 (mm-40) REVERT: 4 737 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8703 (mt-10) REVERT: 7 20 PHE cc_start: 0.8133 (t80) cc_final: 0.7153 (t80) REVERT: 7 33 TYR cc_start: 0.8821 (m-80) cc_final: 0.8426 (m-80) REVERT: 7 166 ILE cc_start: 0.7051 (mp) cc_final: 0.6624 (mm) REVERT: 7 176 MET cc_start: 0.6775 (ttp) cc_final: 0.6397 (tmm) REVERT: 7 340 LEU cc_start: 0.8984 (tp) cc_final: 0.8697 (tp) REVERT: 7 400 ARG cc_start: 0.7358 (tpp-160) cc_final: 0.6684 (tpp-160) REVERT: 7 456 THR cc_start: 0.8906 (p) cc_final: 0.8702 (p) REVERT: 7 541 HIS cc_start: 0.7347 (m-70) cc_final: 0.6715 (m90) REVERT: 7 562 TYR cc_start: 0.8762 (t80) cc_final: 0.8097 (m-80) REVERT: 7 605 ASN cc_start: 0.7923 (m110) cc_final: 0.7619 (m110) outliers start: 8 outliers final: 2 residues processed: 845 average time/residue: 0.5407 time to fit residues: 727.0069 Evaluate side-chains 661 residues out of total 4193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 658 time to evaluate : 4.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 380 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 340 optimal weight: 2.9990 chunk 188 optimal weight: 0.4980 chunk 390 optimal weight: 0.0770 chunk 316 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 233 optimal weight: 4.9990 chunk 410 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 overall best weight: 1.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 HIS M 114 ASN M 166 GLN ** N 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 659 GLN ** 2 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 60 ASN ** 5 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 318 HIS 5 537 HIS 6 198 GLN ** 6 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 107 HIS ** 3 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 467 GLN 3 594 GLN ** 4 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 527 ASN ** 4 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 196 ASN ** 7 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 38986 Z= 0.235 Angle : 0.774 13.266 52778 Z= 0.397 Chirality : 0.047 0.374 5990 Planarity : 0.006 0.116 6735 Dihedral : 11.992 172.596 5584 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 14.45 % Favored : 85.51 % Rotamer: Outliers : 0.17 % Allowed : 4.18 % Favored : 95.65 % 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: -4.02 (0.11), residues: 4657 helix: -2.28 (0.12), residues: 1427 sheet: -2.67 (0.21), residues: 507 loop : -3.00 (0.11), residues: 2723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP M 57 HIS 0.008 0.001 HIS 2 754 PHE 0.038 0.002 PHE 4 487 TYR 0.023 0.002 TYR 2 312 ARG 0.014 0.001 ARG 2 641 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 4193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 807 time to evaluate : 4.460 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 TARDY: cannot create tardy model for: "SER L 185 " (corrupted residue). Skipping it. 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 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 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.9251 (t0) cc_final: 0.8934 (t0) REVERT: A 217 MET cc_start: 0.8020 (mpp) cc_final: 0.7660 (mpp) REVERT: A 229 ASN cc_start: 0.8557 (p0) cc_final: 0.8147 (p0) REVERT: A 232 LEU cc_start: 0.9063 (mp) cc_final: 0.8640 (mp) REVERT: A 326 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8142 (tp30) REVERT: A 351 LYS cc_start: 0.8902 (mtmm) cc_final: 0.8471 (mttm) REVERT: A 383 ARG cc_start: 0.8090 (tmm-80) cc_final: 0.7279 (tmm-80) REVERT: A 442 GLN cc_start: 0.7910 (mp10) cc_final: 0.7509 (tt0) REVERT: A 466 GLU cc_start: 0.7983 (tt0) cc_final: 0.7228 (tm-30) REVERT: A 483 LEU cc_start: 0.8728 (mt) cc_final: 0.8402 (mt) REVERT: L 2 ASP cc_start: 0.7872 (m-30) cc_final: 0.7620 (m-30) REVERT: L 133 ASP cc_start: 0.8538 (m-30) cc_final: 0.8313 (m-30) REVERT: L 136 ILE cc_start: 0.8077 (pt) cc_final: 0.7520 (pt) REVERT: M 53 ASN cc_start: 0.7901 (m-40) cc_final: 0.7557 (p0) REVERT: N 30 MET cc_start: 0.2335 (mmt) cc_final: 0.2132 (mmt) REVERT: N 91 SER cc_start: 0.9020 (m) cc_final: 0.8635 (p) REVERT: N 95 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8091 (mt-10) REVERT: N 105 LEU cc_start: 0.9353 (mt) cc_final: 0.9054 (mm) REVERT: N 159 TYR cc_start: 0.6367 (t80) cc_final: 0.6151 (t80) REVERT: N 202 ASP cc_start: 0.8200 (t70) cc_final: 0.7825 (t70) REVERT: 2 240 MET cc_start: 0.7938 (mmm) cc_final: 0.7728 (mmm) REVERT: 2 273 LEU cc_start: 0.7881 (mt) cc_final: 0.7548 (mt) REVERT: 2 466 MET cc_start: 0.5667 (tmm) cc_final: 0.4998 (tmm) REVERT: 2 623 ASP cc_start: 0.8720 (m-30) cc_final: 0.8479 (m-30) REVERT: 2 764 MET cc_start: 0.5508 (tpp) cc_final: 0.4974 (mmm) REVERT: 2 781 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7589 (pt0) REVERT: 5 59 LEU cc_start: 0.7222 (tt) cc_final: 0.6735 (tt) REVERT: 5 69 MET cc_start: 0.2630 (ptt) cc_final: 0.2054 (tpt) REVERT: 5 71 ASP cc_start: 0.8180 (m-30) cc_final: 0.7863 (m-30) REVERT: 5 92 GLU cc_start: 0.8592 (tm-30) cc_final: 0.7977 (tm-30) REVERT: 5 96 GLU cc_start: 0.8570 (mm-30) cc_final: 0.7875 (mm-30) REVERT: 5 245 ASP cc_start: 0.7501 (p0) cc_final: 0.6929 (m-30) REVERT: 6 186 MET cc_start: 0.6710 (mmt) cc_final: 0.6408 (mmt) REVERT: 6 199 LYS cc_start: 0.8543 (ptmm) cc_final: 0.7883 (ptmm) REVERT: 6 204 GLU cc_start: 0.6327 (pp20) cc_final: 0.6049 (pp20) REVERT: 6 220 ILE cc_start: 0.8699 (tt) cc_final: 0.8431 (mp) REVERT: 6 222 LEU cc_start: 0.8175 (pt) cc_final: 0.7770 (pp) REVERT: 6 363 GLN cc_start: 0.8020 (tt0) cc_final: 0.7742 (tt0) REVERT: 6 544 ILE cc_start: 0.2184 (OUTLIER) cc_final: 0.1359 (tt) REVERT: 6 623 MET cc_start: 0.8958 (mtm) cc_final: 0.8329 (mtm) REVERT: 3 35 ASP cc_start: 0.7297 (m-30) cc_final: 0.6687 (m-30) REVERT: 3 73 PHE cc_start: 0.8840 (m-10) cc_final: 0.8465 (m-80) REVERT: 3 77 LEU cc_start: 0.9427 (mp) cc_final: 0.9181 (tt) REVERT: 3 85 ASP cc_start: 0.8116 (t0) cc_final: 0.7898 (t0) REVERT: 3 111 ARG cc_start: 0.8110 (tpt90) cc_final: 0.7394 (ptm160) REVERT: 3 393 MET cc_start: 0.6640 (ppp) cc_final: 0.6239 (ppp) REVERT: 3 423 GLN cc_start: 0.8902 (tt0) cc_final: 0.8514 (tt0) REVERT: 4 371 HIS cc_start: 0.4199 (p90) cc_final: 0.3919 (p90) REVERT: 4 374 LEU cc_start: 0.8649 (pt) cc_final: 0.8364 (pt) REVERT: 4 526 PHE cc_start: 0.8728 (p90) cc_final: 0.8516 (p90) REVERT: 4 574 CYS cc_start: 0.7401 (m) cc_final: 0.6439 (m) REVERT: 4 580 LYS cc_start: 0.8851 (tppt) cc_final: 0.8596 (mmtp) REVERT: 4 683 MET cc_start: 0.5696 (tpt) cc_final: 0.5267 (tpp) REVERT: 7 166 ILE cc_start: 0.7144 (mp) cc_final: 0.6917 (mm) REVERT: 7 174 LYS cc_start: 0.8154 (tptm) cc_final: 0.7863 (mmmm) REVERT: 7 176 MET cc_start: 0.6774 (ttp) cc_final: 0.6461 (tmm) REVERT: 7 400 ARG cc_start: 0.7266 (tpp-160) cc_final: 0.6716 (tpp-160) REVERT: 7 541 HIS cc_start: 0.7321 (m-70) cc_final: 0.6691 (m90) REVERT: 7 558 LEU cc_start: 0.9083 (tt) cc_final: 0.8749 (tt) REVERT: 7 562 TYR cc_start: 0.8830 (t80) cc_final: 0.8229 (m-80) outliers start: 7 outliers final: 2 residues processed: 813 average time/residue: 0.5275 time to fit residues: 686.5618 Evaluate side-chains 638 residues out of total 4193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 635 time to evaluate : 4.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 153 optimal weight: 0.0370 chunk 411 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 268 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 457 optimal weight: 2.9990 chunk 379 optimal weight: 7.9990 chunk 211 optimal weight: 0.0670 chunk 38 optimal weight: 0.0030 chunk 151 optimal weight: 0.9980 chunk 240 optimal weight: 10.0000 overall best weight: 0.4206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN ** A 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 364 GLN 2 491 ASN ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 659 GLN ** 2 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 120 GLN ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 261 GLN 5 318 HIS ** 5 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 139 HIS 6 170 ASN 6 198 GLN ** 6 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 467 GLN 4 259 HIS 4 338 HIS ** 4 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 596 GLN ** 4 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 238 GLN ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 402 GLN 7 605 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.6271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 38986 Z= 0.190 Angle : 0.733 11.174 52778 Z= 0.371 Chirality : 0.046 0.339 5990 Planarity : 0.005 0.087 6735 Dihedral : 11.682 174.169 5584 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.73 % Favored : 87.22 % Rotamer: Outliers : 0.12 % Allowed : 2.47 % Favored : 97.41 % 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: -3.70 (0.11), residues: 4657 helix: -1.92 (0.13), residues: 1386 sheet: -2.38 (0.21), residues: 507 loop : -2.88 (0.11), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 47 HIS 0.010 0.001 HIS 2 754 PHE 0.025 0.002 PHE 4 487 TYR 0.030 0.002 TYR 7 102 ARG 0.011 0.001 ARG 2 641 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 4193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 825 time to evaluate : 4.575 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: "SER L 185 " (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 revert: symmetry clash revert: symmetry clash 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 revert: symmetry clash 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: A 26 ASP cc_start: 0.9284 (t0) cc_final: 0.9042 (t0) REVERT: A 50 VAL cc_start: 0.8784 (m) cc_final: 0.8565 (m) REVERT: A 196 GLU cc_start: 0.9563 (mm-30) cc_final: 0.9276 (pt0) REVERT: A 217 MET cc_start: 0.8110 (mpp) cc_final: 0.7763 (mpp) REVERT: A 351 LYS cc_start: 0.8895 (mtmm) cc_final: 0.8622 (mttm) REVERT: A 383 ARG cc_start: 0.7882 (tmm-80) cc_final: 0.6825 (tmm-80) REVERT: A 430 ASP cc_start: 0.7819 (m-30) cc_final: 0.7456 (m-30) REVERT: A 442 GLN cc_start: 0.7984 (mp10) cc_final: 0.7416 (tt0) REVERT: A 466 GLU cc_start: 0.7857 (tt0) cc_final: 0.7074 (tm-30) REVERT: H 97 TRP cc_start: 0.3991 (m100) cc_final: 0.3765 (m100) REVERT: H 177 LYS cc_start: 0.6748 (tptp) cc_final: 0.6534 (mmmt) REVERT: L 47 TRP cc_start: 0.7637 (p-90) cc_final: 0.7403 (p-90) REVERT: L 68 MET cc_start: 0.8207 (ppp) cc_final: 0.7984 (ppp) REVERT: L 133 ASP cc_start: 0.8453 (m-30) cc_final: 0.8243 (m-30) REVERT: M 17 PHE cc_start: 0.5865 (t80) cc_final: 0.5199 (t80) REVERT: M 21 GLU cc_start: 0.6232 (mt-10) cc_final: 0.5556 (pp20) REVERT: M 53 ASN cc_start: 0.7936 (m-40) cc_final: 0.7524 (p0) REVERT: M 112 ASP cc_start: 0.8498 (p0) cc_final: 0.8228 (p0) REVERT: N 91 SER cc_start: 0.8958 (m) cc_final: 0.8491 (p) REVERT: N 92 MET cc_start: 0.8288 (ttp) cc_final: 0.7543 (ttm) REVERT: N 95 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8012 (mt-10) REVERT: N 105 LEU cc_start: 0.9240 (mt) cc_final: 0.8457 (tt) REVERT: N 140 PHE cc_start: 0.6995 (m-80) cc_final: 0.6748 (m-80) REVERT: N 159 TYR cc_start: 0.6398 (t80) cc_final: 0.6121 (t80) REVERT: N 202 ASP cc_start: 0.7931 (t70) cc_final: 0.7551 (t70) REVERT: 2 240 MET cc_start: 0.7851 (mmm) cc_final: 0.7548 (mmm) REVERT: 2 273 LEU cc_start: 0.7595 (mt) cc_final: 0.7231 (mt) REVERT: 2 466 MET cc_start: 0.5591 (tmm) cc_final: 0.4821 (tmm) REVERT: 2 623 ASP cc_start: 0.8917 (m-30) cc_final: 0.8690 (m-30) REVERT: 2 757 MET cc_start: 0.8937 (mpp) cc_final: 0.8419 (mpp) REVERT: 2 764 MET cc_start: 0.5656 (tpp) cc_final: 0.5085 (mmm) REVERT: 5 32 LYS cc_start: 0.8202 (mptt) cc_final: 0.7803 (mppt) REVERT: 5 62 ARG cc_start: 0.8098 (mpt-90) cc_final: 0.7584 (mpt-90) REVERT: 5 69 MET cc_start: 0.3581 (ptt) cc_final: 0.3110 (tpt) REVERT: 5 92 GLU cc_start: 0.8454 (tm-30) cc_final: 0.7672 (tm-30) REVERT: 5 96 GLU cc_start: 0.8544 (mm-30) cc_final: 0.7722 (mm-30) REVERT: 5 245 ASP cc_start: 0.7460 (p0) cc_final: 0.6647 (t0) REVERT: 5 261 GLN cc_start: 0.8118 (mm110) cc_final: 0.7880 (mm-40) REVERT: 5 291 ARG cc_start: 0.8160 (ptm-80) cc_final: 0.7880 (ptm160) REVERT: 5 431 MET cc_start: -0.0481 (mtt) cc_final: -0.0784 (mtm) REVERT: 6 16 GLU cc_start: 0.9561 (mm-30) cc_final: 0.9012 (mm-30) REVERT: 6 186 MET cc_start: 0.6717 (mmt) cc_final: 0.6393 (mmt) REVERT: 6 199 LYS cc_start: 0.8566 (ptmm) cc_final: 0.8081 (ptmm) REVERT: 6 204 GLU cc_start: 0.6063 (pp20) cc_final: 0.5520 (pp20) REVERT: 6 211 ARG cc_start: 0.8199 (tmt170) cc_final: 0.7980 (tmt170) REVERT: 6 222 LEU cc_start: 0.8167 (pt) cc_final: 0.7866 (pp) REVERT: 6 363 GLN cc_start: 0.7908 (tt0) cc_final: 0.7579 (tt0) REVERT: 6 519 MET cc_start: 0.8798 (mpp) cc_final: 0.8550 (mpp) REVERT: 6 596 ARG cc_start: 0.7690 (mmp-170) cc_final: 0.7310 (mmm160) REVERT: 6 623 MET cc_start: 0.8998 (mtm) cc_final: 0.8605 (ptm) REVERT: 3 18 ASP cc_start: 0.9338 (m-30) cc_final: 0.8338 (p0) REVERT: 3 35 ASP cc_start: 0.7228 (m-30) cc_final: 0.6439 (m-30) REVERT: 3 73 PHE cc_start: 0.8773 (m-10) cc_final: 0.8447 (m-80) REVERT: 3 77 LEU cc_start: 0.9418 (mp) cc_final: 0.9130 (tt) REVERT: 3 85 ASP cc_start: 0.7919 (t0) cc_final: 0.7631 (p0) REVERT: 3 111 ARG cc_start: 0.8150 (tpt90) cc_final: 0.7344 (ptm160) REVERT: 3 417 ILE cc_start: 0.9354 (mt) cc_final: 0.9146 (mt) REVERT: 3 421 MET cc_start: 0.8001 (mmm) cc_final: 0.7634 (mmm) REVERT: 3 423 GLN cc_start: 0.8793 (tt0) cc_final: 0.8386 (tt0) REVERT: 3 561 PHE cc_start: 0.8035 (t80) cc_final: 0.7758 (t80) REVERT: 4 374 LEU cc_start: 0.8584 (pt) cc_final: 0.8255 (pt) REVERT: 4 390 ARG cc_start: 0.6005 (mtm180) cc_final: 0.5339 (mpt180) REVERT: 4 447 ARG cc_start: 0.9088 (ttm110) cc_final: 0.8246 (mmp80) REVERT: 4 574 CYS cc_start: 0.7564 (m) cc_final: 0.6364 (m) REVERT: 4 683 MET cc_start: 0.5689 (tpt) cc_final: 0.5285 (tpp) REVERT: 7 20 PHE cc_start: 0.7947 (t80) cc_final: 0.6714 (t80) REVERT: 7 33 TYR cc_start: 0.8753 (m-80) cc_final: 0.8330 (m-80) REVERT: 7 64 GLU cc_start: 0.8313 (mp0) cc_final: 0.8103 (mp0) REVERT: 7 134 PHE cc_start: 0.8514 (p90) cc_final: 0.8178 (p90) REVERT: 7 176 MET cc_start: 0.6619 (ttp) cc_final: 0.6183 (tmm) REVERT: 7 238 GLN cc_start: 0.7807 (tp40) cc_final: 0.7574 (tp40) REVERT: 7 252 SER cc_start: 0.8282 (p) cc_final: 0.8073 (m) REVERT: 7 253 MET cc_start: 0.5618 (ppp) cc_final: 0.5052 (ppp) REVERT: 7 340 LEU cc_start: 0.8943 (tp) cc_final: 0.8625 (tp) REVERT: 7 380 MET cc_start: 0.8112 (tmm) cc_final: 0.7763 (tmm) REVERT: 7 400 ARG cc_start: 0.7169 (tpp-160) cc_final: 0.6578 (tpp-160) REVERT: 7 419 MET cc_start: 0.6163 (ttm) cc_final: 0.5946 (tpt) REVERT: 7 541 HIS cc_start: 0.7361 (m-70) cc_final: 0.6664 (m90) REVERT: 7 562 TYR cc_start: 0.8832 (t80) cc_final: 0.8226 (m-80) outliers start: 5 outliers final: 2 residues processed: 830 average time/residue: 0.5304 time to fit residues: 705.9804 Evaluate side-chains 659 residues out of total 4193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 657 time to evaluate : 4.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 441 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 334 optimal weight: 7.9990 chunk 258 optimal weight: 2.9990 chunk 385 optimal weight: 4.9990 chunk 255 optimal weight: 0.0070 chunk 455 optimal weight: 4.9990 chunk 285 optimal weight: 0.0170 chunk 277 optimal weight: 10.0000 chunk 210 optimal weight: 6.9990 overall best weight: 1.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 153 HIS ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 659 GLN ** 2 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 318 HIS ** 5 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 79 HIS 6 198 GLN ** 6 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 467 GLN ** 3 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 374 ASN 7 459 HIS 7 605 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.6584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 38986 Z= 0.223 Angle : 0.747 10.575 52778 Z= 0.382 Chirality : 0.047 0.370 5990 Planarity : 0.005 0.088 6735 Dihedral : 11.570 169.020 5584 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 22.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.85 % Favored : 86.11 % Rotamer: Outliers : 0.10 % Allowed : 2.61 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.68 (0.11), residues: 4657 helix: -1.97 (0.12), residues: 1426 sheet: -2.24 (0.22), residues: 490 loop : -2.87 (0.11), residues: 2741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP 4 626 HIS 0.009 0.001 HIS 4 667 PHE 0.029 0.002 PHE 4 487 TYR 0.033 0.002 TYR L 170 ARG 0.008 0.001 ARG 6 542 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 4193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 798 time to evaluate : 4.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER L 185 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 174 " (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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.9339 (t0) cc_final: 0.9061 (t0) REVERT: A 231 ASP cc_start: 0.8961 (p0) cc_final: 0.8757 (p0) REVERT: A 261 ILE cc_start: 0.6180 (mm) cc_final: 0.5976 (mm) REVERT: A 288 ASP cc_start: 0.8431 (t0) cc_final: 0.8134 (t0) REVERT: A 351 LYS cc_start: 0.8945 (mtmm) cc_final: 0.8701 (mttm) REVERT: A 383 ARG cc_start: 0.7873 (tmm-80) cc_final: 0.6951 (tmm-80) REVERT: A 430 ASP cc_start: 0.7778 (m-30) cc_final: 0.7550 (m-30) REVERT: A 442 GLN cc_start: 0.8090 (mp10) cc_final: 0.7384 (tt0) REVERT: A 466 GLU cc_start: 0.7891 (tt0) cc_final: 0.7172 (tm-30) REVERT: A 483 LEU cc_start: 0.8778 (mt) cc_final: 0.8553 (mt) REVERT: H 97 TRP cc_start: 0.4298 (m100) cc_final: 0.3932 (m100) REVERT: L 47 TRP cc_start: 0.7949 (p-90) cc_final: 0.7683 (p-90) REVERT: L 54 LYS cc_start: 0.8761 (mttt) cc_final: 0.8558 (mttt) REVERT: M 17 PHE cc_start: 0.5964 (t80) cc_final: 0.5255 (t80) REVERT: M 53 ASN cc_start: 0.7862 (m-40) cc_final: 0.7469 (p0) REVERT: M 78 ARG cc_start: 0.6360 (mmm160) cc_final: 0.5792 (mmm160) REVERT: M 112 ASP cc_start: 0.8580 (p0) cc_final: 0.8273 (p0) REVERT: N 91 SER cc_start: 0.8878 (m) cc_final: 0.8352 (p) REVERT: N 95 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8016 (mt-10) REVERT: N 105 LEU cc_start: 0.9180 (mt) cc_final: 0.8623 (tt) REVERT: N 110 GLN cc_start: 0.8428 (mp10) cc_final: 0.8110 (mp10) REVERT: N 159 TYR cc_start: 0.6440 (t80) cc_final: 0.6196 (t80) REVERT: N 202 ASP cc_start: 0.7695 (t70) cc_final: 0.7298 (t70) REVERT: 2 273 LEU cc_start: 0.7528 (mt) cc_final: 0.7306 (mt) REVERT: 2 350 MET cc_start: 0.5383 (ttt) cc_final: 0.4925 (tpt) REVERT: 2 466 MET cc_start: 0.5533 (tmm) cc_final: 0.4948 (tmm) REVERT: 2 757 MET cc_start: 0.8909 (mpp) cc_final: 0.8599 (mpp) REVERT: 2 764 MET cc_start: 0.5457 (tpp) cc_final: 0.4947 (mmm) REVERT: 5 59 LEU cc_start: 0.7366 (tt) cc_final: 0.6827 (tt) REVERT: 5 69 MET cc_start: 0.3048 (ptt) cc_final: 0.2482 (tpt) REVERT: 5 92 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7799 (tm-30) REVERT: 5 96 GLU cc_start: 0.8630 (mm-30) cc_final: 0.7994 (mm-30) REVERT: 5 245 ASP cc_start: 0.7420 (p0) cc_final: 0.6772 (t0) REVERT: 5 265 SER cc_start: 0.9121 (m) cc_final: 0.8805 (t) REVERT: 5 289 TYR cc_start: 0.7933 (p90) cc_final: 0.7320 (p90) REVERT: 5 431 MET cc_start: -0.0303 (mtt) cc_final: -0.0596 (mtm) REVERT: 5 447 MET cc_start: 0.5663 (mmm) cc_final: 0.4766 (mmm) REVERT: 6 16 GLU cc_start: 0.9568 (mm-30) cc_final: 0.9034 (mm-30) REVERT: 6 186 MET cc_start: 0.6526 (mmt) cc_final: 0.6260 (mmt) REVERT: 6 204 GLU cc_start: 0.6240 (pp20) cc_final: 0.5765 (pp20) REVERT: 6 222 LEU cc_start: 0.8437 (pt) cc_final: 0.8049 (pp) REVERT: 6 236 TYR cc_start: 0.6091 (p90) cc_final: 0.5431 (p90) REVERT: 6 317 MET cc_start: 0.3476 (ppp) cc_final: 0.2710 (ppp) REVERT: 6 339 TYR cc_start: 0.8267 (t80) cc_final: 0.7913 (t80) REVERT: 6 363 GLN cc_start: 0.8014 (tt0) cc_final: 0.7709 (tt0) REVERT: 6 519 MET cc_start: 0.8788 (mpp) cc_final: 0.8545 (mpp) REVERT: 6 590 TYR cc_start: 0.8808 (t80) cc_final: 0.8544 (t80) REVERT: 6 596 ARG cc_start: 0.7649 (mmp-170) cc_final: 0.7271 (mmm160) REVERT: 6 623 MET cc_start: 0.9047 (mtm) cc_final: 0.8596 (ptm) REVERT: 3 73 PHE cc_start: 0.8895 (m-10) cc_final: 0.8485 (m-80) REVERT: 3 107 HIS cc_start: 0.7945 (p90) cc_final: 0.7745 (p90) REVERT: 3 111 ARG cc_start: 0.7969 (tpt90) cc_final: 0.7230 (ptm160) REVERT: 3 423 GLN cc_start: 0.8839 (tt0) cc_final: 0.8347 (tt0) REVERT: 3 464 ILE cc_start: 0.8487 (mp) cc_final: 0.8062 (mm) REVERT: 3 561 PHE cc_start: 0.8001 (t80) cc_final: 0.7673 (t80) REVERT: 3 572 MET cc_start: 0.8308 (mmm) cc_final: 0.7561 (mtm) REVERT: 4 221 PHE cc_start: 0.6438 (t80) cc_final: 0.5826 (t80) REVERT: 4 227 ARG cc_start: 0.7873 (mtm110) cc_final: 0.7662 (mtm-85) REVERT: 4 272 ARG cc_start: 0.6995 (mmp80) cc_final: 0.6681 (mmm160) REVERT: 4 274 MET cc_start: 0.6613 (tmm) cc_final: 0.6037 (tmm) REVERT: 4 371 HIS cc_start: 0.4050 (p90) cc_final: 0.3709 (p90) REVERT: 4 574 CYS cc_start: 0.7714 (m) cc_final: 0.6477 (m) REVERT: 4 683 MET cc_start: 0.5823 (tpt) cc_final: 0.5423 (tpp) REVERT: 7 20 PHE cc_start: 0.7877 (t80) cc_final: 0.7053 (t80) REVERT: 7 33 TYR cc_start: 0.8754 (m-80) cc_final: 0.8381 (m-80) REVERT: 7 64 GLU cc_start: 0.8431 (mp0) cc_final: 0.8216 (mp0) REVERT: 7 134 PHE cc_start: 0.8475 (p90) cc_final: 0.8179 (p90) REVERT: 7 166 ILE cc_start: 0.6955 (mp) cc_final: 0.6606 (mm) REVERT: 7 176 MET cc_start: 0.6542 (ttp) cc_final: 0.6126 (tmm) REVERT: 7 253 MET cc_start: 0.6164 (ppp) cc_final: 0.5145 (ppp) REVERT: 7 340 LEU cc_start: 0.8869 (tp) cc_final: 0.8647 (tp) REVERT: 7 400 ARG cc_start: 0.7207 (tpp-160) cc_final: 0.6782 (tpp-160) REVERT: 7 541 HIS cc_start: 0.7305 (m-70) cc_final: 0.6599 (m90) REVERT: 7 562 TYR cc_start: 0.8868 (t80) cc_final: 0.8278 (m-80) REVERT: 7 590 ARG cc_start: 0.8882 (ptt90) cc_final: 0.7706 (mmm160) outliers start: 4 outliers final: 2 residues processed: 802 average time/residue: 0.5387 time to fit residues: 692.1745 Evaluate side-chains 644 residues out of total 4193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 642 time to evaluate : 4.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 282 optimal weight: 8.9990 chunk 182 optimal weight: 0.5980 chunk 272 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 289 optimal weight: 5.9990 chunk 310 optimal weight: 0.0040 chunk 225 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 358 optimal weight: 6.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 HIS L 154 HIS ** M 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 ASN ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 659 GLN ** 2 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 134 GLN ** 5 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 261 GLN 5 318 HIS 5 628 GLN 6 198 GLN ** 6 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 467 GLN 3 622 HIS ** 4 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 494 HIS ** 4 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 605 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.6885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 38986 Z= 0.180 Angle : 0.723 13.594 52778 Z= 0.366 Chirality : 0.046 0.348 5990 Planarity : 0.005 0.086 6735 Dihedral : 11.377 170.756 5584 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.01 % Favored : 86.94 % Rotamer: Outliers : 0.12 % Allowed : 1.61 % Favored : 98.27 % 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: -3.53 (0.11), residues: 4657 helix: -1.75 (0.13), residues: 1428 sheet: -2.09 (0.22), residues: 522 loop : -2.84 (0.11), residues: 2707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 193 HIS 0.009 0.001 HIS 2 754 PHE 0.021 0.002 PHE 5 41 TYR 0.023 0.002 TYR 6 559 ARG 0.012 0.001 ARG 6 211 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 4193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 808 time to evaluate : 4.414 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: "SER L 185 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 174 " (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: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 26 ASP cc_start: 0.9367 (t0) cc_final: 0.9098 (t0) REVERT: A 31 CYS cc_start: 0.8853 (m) cc_final: 0.8232 (p) REVERT: A 231 ASP cc_start: 0.8898 (p0) cc_final: 0.8683 (p0) REVERT: A 238 VAL cc_start: 0.8062 (t) cc_final: 0.7741 (t) REVERT: A 261 ILE cc_start: 0.6150 (mm) cc_final: 0.5925 (mm) REVERT: A 351 LYS cc_start: 0.8926 (mtmm) cc_final: 0.8696 (mttm) REVERT: A 383 ARG cc_start: 0.8052 (tmm-80) cc_final: 0.6982 (tmm-80) REVERT: A 442 GLN cc_start: 0.8038 (mp10) cc_final: 0.7315 (tt0) REVERT: A 466 GLU cc_start: 0.7589 (tt0) cc_final: 0.6970 (tm-30) REVERT: H 97 TRP cc_start: 0.4137 (m100) cc_final: 0.3773 (m100) REVERT: L 47 TRP cc_start: 0.7713 (p-90) cc_final: 0.7499 (p-90) REVERT: L 100 MET cc_start: 0.6347 (ttt) cc_final: 0.6113 (ttt) REVERT: L 106 ASP cc_start: 0.8319 (m-30) cc_final: 0.8038 (p0) REVERT: M 17 PHE cc_start: 0.6022 (t80) cc_final: 0.5337 (t80) REVERT: M 53 ASN cc_start: 0.7937 (m-40) cc_final: 0.7370 (p0) REVERT: M 78 ARG cc_start: 0.6283 (mmm160) cc_final: 0.6073 (mmm160) REVERT: M 112 ASP cc_start: 0.8476 (p0) cc_final: 0.8269 (p0) REVERT: M 119 ARG cc_start: 0.8608 (tpp80) cc_final: 0.8144 (tpp80) REVERT: M 158 GLU cc_start: 0.7232 (tp30) cc_final: 0.6862 (tp30) REVERT: N 91 SER cc_start: 0.8810 (m) cc_final: 0.8304 (p) REVERT: N 92 MET cc_start: 0.8423 (ttp) cc_final: 0.7635 (ttm) REVERT: N 95 GLU cc_start: 0.8247 (mt-10) cc_final: 0.8017 (mt-10) REVERT: N 105 LEU cc_start: 0.9202 (mt) cc_final: 0.8767 (mm) REVERT: N 202 ASP cc_start: 0.7505 (t70) cc_final: 0.7163 (t70) REVERT: 2 219 TYR cc_start: 0.8022 (t80) cc_final: 0.7585 (t80) REVERT: 2 350 MET cc_start: 0.5270 (ttt) cc_final: 0.4954 (tpt) REVERT: 2 358 TYR cc_start: 0.7562 (t80) cc_final: 0.7342 (t80) REVERT: 2 466 MET cc_start: 0.5381 (tmm) cc_final: 0.4904 (tmm) REVERT: 2 494 GLU cc_start: 0.5577 (tt0) cc_final: 0.5243 (tt0) REVERT: 2 623 ASP cc_start: 0.8592 (m-30) cc_final: 0.8355 (m-30) REVERT: 2 764 MET cc_start: 0.5421 (tpp) cc_final: 0.4892 (mmm) REVERT: 5 62 ARG cc_start: 0.8081 (mpt-90) cc_final: 0.7501 (mpt-90) REVERT: 5 66 GLU cc_start: 0.8005 (mp0) cc_final: 0.7535 (mp0) REVERT: 5 69 MET cc_start: 0.3526 (ptt) cc_final: 0.2884 (tpt) REVERT: 5 92 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7782 (tm-30) REVERT: 5 96 GLU cc_start: 0.8666 (mm-30) cc_final: 0.7855 (mm-30) REVERT: 5 210 MET cc_start: 0.8634 (mtt) cc_final: 0.8047 (mpp) REVERT: 5 245 ASP cc_start: 0.7528 (p0) cc_final: 0.6863 (t0) REVERT: 5 265 SER cc_start: 0.9083 (m) cc_final: 0.8823 (t) REVERT: 5 447 MET cc_start: 0.5758 (mmm) cc_final: 0.4911 (mmm) REVERT: 6 16 GLU cc_start: 0.9561 (mm-30) cc_final: 0.9055 (mm-30) REVERT: 6 204 GLU cc_start: 0.5988 (pp20) cc_final: 0.5582 (pp20) REVERT: 6 220 ILE cc_start: 0.7466 (mp) cc_final: 0.7247 (mm) REVERT: 6 222 LEU cc_start: 0.8268 (pt) cc_final: 0.7888 (pp) REVERT: 6 317 MET cc_start: 0.3099 (ppp) cc_final: 0.2395 (ppp) REVERT: 6 363 GLN cc_start: 0.7990 (tt0) cc_final: 0.7665 (tt0) REVERT: 6 472 GLN cc_start: 0.8327 (mm-40) cc_final: 0.8095 (mm-40) REVERT: 6 519 MET cc_start: 0.8781 (mpp) cc_final: 0.8558 (mpp) REVERT: 6 590 TYR cc_start: 0.8673 (t80) cc_final: 0.8388 (t80) REVERT: 6 623 MET cc_start: 0.9068 (mtm) cc_final: 0.8699 (ptm) REVERT: 3 73 PHE cc_start: 0.8683 (m-10) cc_final: 0.8446 (m-80) REVERT: 3 111 ARG cc_start: 0.7997 (tpt90) cc_final: 0.7233 (ptm160) REVERT: 3 423 GLN cc_start: 0.8819 (tt0) cc_final: 0.8438 (tt0) REVERT: 3 561 PHE cc_start: 0.7982 (t80) cc_final: 0.7618 (t80) REVERT: 3 572 MET cc_start: 0.8265 (mmm) cc_final: 0.7439 (mtm) REVERT: 4 272 ARG cc_start: 0.6984 (mmp80) cc_final: 0.6631 (mmm160) REVERT: 4 274 MET cc_start: 0.6589 (tmm) cc_final: 0.6189 (ppp) REVERT: 4 371 HIS cc_start: 0.3492 (p90) cc_final: 0.3244 (p90) REVERT: 4 574 CYS cc_start: 0.7933 (m) cc_final: 0.6746 (m) REVERT: 4 579 ASP cc_start: 0.8695 (t0) cc_final: 0.8425 (t0) REVERT: 4 683 MET cc_start: 0.5817 (tpt) cc_final: 0.5416 (tpp) REVERT: 7 20 PHE cc_start: 0.7787 (t80) cc_final: 0.6590 (t80) REVERT: 7 33 TYR cc_start: 0.8705 (m-80) cc_final: 0.8352 (m-80) REVERT: 7 64 GLU cc_start: 0.8363 (mp0) cc_final: 0.8081 (mp0) REVERT: 7 134 PHE cc_start: 0.8470 (p90) cc_final: 0.8158 (p90) REVERT: 7 166 ILE cc_start: 0.6791 (mp) cc_final: 0.6547 (mm) REVERT: 7 176 MET cc_start: 0.6451 (ttp) cc_final: 0.6065 (tmm) REVERT: 7 253 MET cc_start: 0.6106 (ppp) cc_final: 0.5096 (ppp) REVERT: 7 302 ARG cc_start: 0.8601 (ptp-170) cc_final: 0.8277 (mtt180) REVERT: 7 380 MET cc_start: 0.8024 (tmm) cc_final: 0.7610 (tmm) REVERT: 7 391 LEU cc_start: 0.9368 (mm) cc_final: 0.9110 (mm) REVERT: 7 400 ARG cc_start: 0.7048 (tpp-160) cc_final: 0.6784 (tpp-160) REVERT: 7 443 CYS cc_start: 0.8542 (m) cc_final: 0.8025 (t) REVERT: 7 541 HIS cc_start: 0.7361 (m-70) cc_final: 0.6744 (m-70) REVERT: 7 562 TYR cc_start: 0.8861 (t80) cc_final: 0.8234 (m-80) REVERT: 7 590 ARG cc_start: 0.8849 (ptt90) cc_final: 0.7788 (mmm160) REVERT: 7 625 VAL cc_start: 0.8247 (t) cc_final: 0.7856 (t) outliers start: 5 outliers final: 2 residues processed: 812 average time/residue: 0.5369 time to fit residues: 698.4952 Evaluate side-chains 656 residues out of total 4193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 654 time to evaluate : 4.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 414 optimal weight: 2.9990 chunk 436 optimal weight: 6.9990 chunk 398 optimal weight: 8.9990 chunk 424 optimal weight: 8.9990 chunk 255 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 333 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 383 optimal weight: 0.9980 chunk 401 optimal weight: 0.3980 chunk 423 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 HIS L 51 HIS L 171 GLN ** M 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 185 GLN 2 659 GLN ** 2 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 318 HIS 6 198 GLN ** 6 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 466 HIS 3 55 ASN ** 3 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 467 GLN 3 622 HIS 4 228 GLN ** 4 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.7144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 38986 Z= 0.189 Angle : 0.726 12.155 52778 Z= 0.368 Chirality : 0.046 0.340 5990 Planarity : 0.005 0.086 6735 Dihedral : 11.275 168.878 5584 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.71 % Favored : 87.25 % Rotamer: Outliers : 0.10 % Allowed : 0.95 % Favored : 98.95 % 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: -3.37 (0.11), residues: 4657 helix: -1.63 (0.13), residues: 1414 sheet: -1.77 (0.24), residues: 447 loop : -2.78 (0.11), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 193 HIS 0.008 0.001 HIS A 65 PHE 0.026 0.002 PHE 4 248 TYR 0.024 0.002 TYR 5 34 ARG 0.009 0.001 ARG 3 617 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 4193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 778 time to evaluate : 3.994 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: "SER L 185 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 174 " (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: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.9374 (t0) cc_final: 0.9105 (t0) REVERT: A 31 CYS cc_start: 0.8873 (m) cc_final: 0.8264 (p) REVERT: A 231 ASP cc_start: 0.8979 (p0) cc_final: 0.8747 (p0) REVERT: A 238 VAL cc_start: 0.8140 (t) cc_final: 0.7662 (t) REVERT: A 261 ILE cc_start: 0.6031 (mm) cc_final: 0.5816 (mm) REVERT: A 288 ASP cc_start: 0.8248 (t0) cc_final: 0.7917 (t0) REVERT: A 351 LYS cc_start: 0.8948 (mtmm) cc_final: 0.8711 (mttm) REVERT: A 383 ARG cc_start: 0.8044 (tmm-80) cc_final: 0.7085 (tmm-80) REVERT: A 430 ASP cc_start: 0.7601 (m-30) cc_final: 0.7236 (m-30) REVERT: A 442 GLN cc_start: 0.8116 (mp10) cc_final: 0.7247 (tt0) REVERT: A 466 GLU cc_start: 0.7554 (tt0) cc_final: 0.6956 (tm-30) REVERT: H 75 GLN cc_start: 0.8442 (mp10) cc_final: 0.8017 (mp10) REVERT: H 76 ARG cc_start: 0.8042 (mtt180) cc_final: 0.7763 (mtt180) REVERT: H 97 TRP cc_start: 0.3902 (m100) cc_final: 0.3623 (m100) REVERT: L 14 MET cc_start: 0.7751 (tmm) cc_final: 0.7338 (tpp) REVERT: L 53 ARG cc_start: 0.8073 (mmm-85) cc_final: 0.7604 (mmm-85) REVERT: L 54 LYS cc_start: 0.8730 (mttt) cc_final: 0.8515 (mttt) REVERT: L 76 GLU cc_start: 0.9247 (mp0) cc_final: 0.8693 (mp0) REVERT: L 100 MET cc_start: 0.6294 (ttt) cc_final: 0.6066 (ttt) REVERT: L 106 ASP cc_start: 0.8357 (m-30) cc_final: 0.8088 (p0) REVERT: L 129 ARG cc_start: 0.7866 (ttp-110) cc_final: 0.7609 (ttm110) REVERT: M 17 PHE cc_start: 0.5963 (t80) cc_final: 0.5303 (t80) REVERT: M 53 ASN cc_start: 0.7967 (m-40) cc_final: 0.7413 (p0) REVERT: M 112 ASP cc_start: 0.8522 (p0) cc_final: 0.8296 (p0) REVERT: M 119 ARG cc_start: 0.8449 (tpp80) cc_final: 0.8144 (tpp80) REVERT: M 158 GLU cc_start: 0.7181 (tp30) cc_final: 0.6859 (tp30) REVERT: N 91 SER cc_start: 0.8829 (m) cc_final: 0.8310 (p) REVERT: N 105 LEU cc_start: 0.9191 (mt) cc_final: 0.8796 (mm) REVERT: N 110 GLN cc_start: 0.8302 (mp10) cc_final: 0.8063 (mp10) REVERT: N 202 ASP cc_start: 0.7497 (t70) cc_final: 0.7184 (t70) REVERT: 2 358 TYR cc_start: 0.7567 (t80) cc_final: 0.7345 (t80) REVERT: 2 466 MET cc_start: 0.5440 (tmm) cc_final: 0.4976 (tmm) REVERT: 2 494 GLU cc_start: 0.5654 (tt0) cc_final: 0.5034 (tt0) REVERT: 2 757 MET cc_start: 0.8944 (mpp) cc_final: 0.8322 (mpp) REVERT: 2 764 MET cc_start: 0.5365 (tpp) cc_final: 0.4798 (mmm) REVERT: 5 62 ARG cc_start: 0.8086 (mpt-90) cc_final: 0.7461 (mpt-90) REVERT: 5 68 GLU cc_start: 0.7348 (tt0) cc_final: 0.6749 (tt0) REVERT: 5 69 MET cc_start: 0.3842 (ptt) cc_final: 0.2885 (tpt) REVERT: 5 71 ASP cc_start: 0.8064 (m-30) cc_final: 0.6811 (m-30) REVERT: 5 82 LYS cc_start: 0.8688 (mtmt) cc_final: 0.8456 (mtmt) REVERT: 5 92 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7790 (tm-30) REVERT: 5 96 GLU cc_start: 0.8626 (mm-30) cc_final: 0.7821 (mm-30) REVERT: 5 245 ASP cc_start: 0.7632 (p0) cc_final: 0.6693 (t0) REVERT: 5 265 SER cc_start: 0.9106 (m) cc_final: 0.8862 (t) REVERT: 5 447 MET cc_start: 0.5670 (mmm) cc_final: 0.4789 (mmm) REVERT: 6 16 GLU cc_start: 0.9549 (mm-30) cc_final: 0.9042 (mm-30) REVERT: 6 186 MET cc_start: 0.7172 (mmt) cc_final: 0.6376 (mmt) REVERT: 6 204 GLU cc_start: 0.5821 (pp20) cc_final: 0.5603 (pp20) REVERT: 6 222 LEU cc_start: 0.8269 (pt) cc_final: 0.7901 (pp) REVERT: 6 317 MET cc_start: 0.3081 (ppp) cc_final: 0.2373 (ppp) REVERT: 6 339 TYR cc_start: 0.8192 (t80) cc_final: 0.7944 (t80) REVERT: 6 363 GLN cc_start: 0.8032 (tt0) cc_final: 0.7720 (tt0) REVERT: 6 519 MET cc_start: 0.8762 (mpp) cc_final: 0.8549 (mpp) REVERT: 6 521 ARG cc_start: 0.6754 (ttm170) cc_final: 0.6198 (ttt180) REVERT: 6 623 MET cc_start: 0.9073 (mtm) cc_final: 0.8654 (ptm) REVERT: 3 73 PHE cc_start: 0.8696 (m-10) cc_final: 0.8454 (m-80) REVERT: 3 107 HIS cc_start: 0.8150 (p-80) cc_final: 0.7841 (p90) REVERT: 3 111 ARG cc_start: 0.7978 (tpt90) cc_final: 0.7314 (ptm160) REVERT: 3 409 MET cc_start: 0.3668 (ptt) cc_final: 0.3268 (tpp) REVERT: 3 423 GLN cc_start: 0.8961 (tt0) cc_final: 0.8506 (tt0) REVERT: 3 464 ILE cc_start: 0.8455 (mp) cc_final: 0.8007 (mm) REVERT: 3 561 PHE cc_start: 0.7897 (t80) cc_final: 0.7453 (t80) REVERT: 3 572 MET cc_start: 0.8257 (mmm) cc_final: 0.7475 (mtm) REVERT: 4 221 PHE cc_start: 0.6407 (t80) cc_final: 0.5766 (t80) REVERT: 4 272 ARG cc_start: 0.7027 (mmp80) cc_final: 0.6572 (mmm160) REVERT: 4 574 CYS cc_start: 0.7910 (m) cc_final: 0.6694 (m) REVERT: 4 683 MET cc_start: 0.6090 (tpt) cc_final: 0.5707 (tpp) REVERT: 7 20 PHE cc_start: 0.7755 (t80) cc_final: 0.6463 (t80) REVERT: 7 33 TYR cc_start: 0.8710 (m-80) cc_final: 0.8240 (m-80) REVERT: 7 64 GLU cc_start: 0.8415 (mp0) cc_final: 0.8150 (mp0) REVERT: 7 166 ILE cc_start: 0.6943 (mp) cc_final: 0.6685 (mm) REVERT: 7 176 MET cc_start: 0.6505 (ttp) cc_final: 0.6162 (tmm) REVERT: 7 253 MET cc_start: 0.6110 (ppp) cc_final: 0.5107 (ppp) REVERT: 7 302 ARG cc_start: 0.8519 (ptp-170) cc_final: 0.7990 (mtt180) REVERT: 7 340 LEU cc_start: 0.8806 (tp) cc_final: 0.8578 (tp) REVERT: 7 380 MET cc_start: 0.8069 (tmm) cc_final: 0.7702 (tmm) REVERT: 7 454 ASP cc_start: 0.8621 (m-30) cc_final: 0.8412 (p0) REVERT: 7 541 HIS cc_start: 0.7399 (m-70) cc_final: 0.6798 (m-70) REVERT: 7 562 TYR cc_start: 0.8895 (t80) cc_final: 0.8275 (m-80) REVERT: 7 590 ARG cc_start: 0.8817 (ptt90) cc_final: 0.7697 (mmm160) outliers start: 4 outliers final: 2 residues processed: 782 average time/residue: 0.5319 time to fit residues: 665.6503 Evaluate side-chains 646 residues out of total 4193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 644 time to evaluate : 4.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 278 optimal weight: 2.9990 chunk 449 optimal weight: 0.9990 chunk 274 optimal weight: 9.9990 chunk 213 optimal weight: 5.9990 chunk 312 optimal weight: 4.9990 chunk 471 optimal weight: 0.9990 chunk 433 optimal weight: 0.8980 chunk 375 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 289 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 HIS ** M 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 659 GLN 2 714 ASN ** 2 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 318 HIS 6 198 GLN 3 107 HIS ** 3 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 228 GLN 4 358 GLN 4 620 ASN ** 4 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 147 HIS 7 156 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.7363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 38986 Z= 0.223 Angle : 0.748 12.234 52778 Z= 0.381 Chirality : 0.047 0.333 5990 Planarity : 0.006 0.096 6735 Dihedral : 11.329 167.403 5584 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 14.06 % Favored : 85.89 % Rotamer: Outliers : 0.17 % Allowed : 0.54 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.41 (0.11), residues: 4657 helix: -1.77 (0.13), residues: 1453 sheet: -1.68 (0.24), residues: 460 loop : -2.76 (0.11), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 193 HIS 0.008 0.001 HIS 5 318 PHE 0.021 0.002 PHE 7 447 TYR 0.029 0.002 TYR 5 34 ARG 0.010 0.001 ARG 3 617 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 4193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 789 time to evaluate : 4.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER L 185 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 174 " (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: "MET 5 652 " (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 TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. REVERT: A 26 ASP cc_start: 0.9413 (t0) cc_final: 0.9131 (t0) REVERT: A 31 CYS cc_start: 0.8884 (m) cc_final: 0.8313 (p) REVERT: A 231 ASP cc_start: 0.9130 (p0) cc_final: 0.8897 (p0) REVERT: A 238 VAL cc_start: 0.7830 (t) cc_final: 0.7369 (t) REVERT: A 261 ILE cc_start: 0.6083 (mm) cc_final: 0.5857 (mm) REVERT: A 288 ASP cc_start: 0.8326 (t0) cc_final: 0.8094 (t0) REVERT: A 351 LYS cc_start: 0.8979 (mtmm) cc_final: 0.8660 (mttm) REVERT: A 365 ASP cc_start: 0.8266 (t70) cc_final: 0.7996 (t70) REVERT: A 383 ARG cc_start: 0.8078 (tmm-80) cc_final: 0.7063 (tmm-80) REVERT: A 430 ASP cc_start: 0.7528 (m-30) cc_final: 0.7215 (m-30) REVERT: A 442 GLN cc_start: 0.8196 (mp10) cc_final: 0.7263 (tt0) REVERT: A 466 GLU cc_start: 0.7532 (tt0) cc_final: 0.7074 (tm-30) REVERT: A 513 MET cc_start: 0.6680 (mmp) cc_final: 0.6132 (mmp) REVERT: H 76 ARG cc_start: 0.8162 (mtt180) cc_final: 0.7824 (mtt180) REVERT: H 97 TRP cc_start: 0.3901 (m100) cc_final: 0.3563 (m100) REVERT: H 159 CYS cc_start: 0.6901 (t) cc_final: 0.6672 (t) REVERT: L 53 ARG cc_start: 0.8293 (mmm-85) cc_final: 0.8080 (mmm-85) REVERT: L 100 MET cc_start: 0.6432 (ttt) cc_final: 0.6201 (ttt) REVERT: L 106 ASP cc_start: 0.8406 (m-30) cc_final: 0.8174 (p0) REVERT: L 129 ARG cc_start: 0.8019 (ttp-110) cc_final: 0.7607 (ttm110) REVERT: L 133 ASP cc_start: 0.8683 (m-30) cc_final: 0.8482 (m-30) REVERT: L 135 PHE cc_start: 0.8352 (t80) cc_final: 0.8004 (t80) REVERT: L 139 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7888 (pm20) REVERT: M 17 PHE cc_start: 0.5977 (t80) cc_final: 0.5605 (t80) REVERT: M 29 THR cc_start: 0.6345 (p) cc_final: 0.6007 (p) REVERT: M 89 THR cc_start: 0.7621 (t) cc_final: 0.7356 (t) REVERT: M 112 ASP cc_start: 0.8582 (p0) cc_final: 0.8297 (p0) REVERT: M 119 ARG cc_start: 0.8363 (tpp80) cc_final: 0.8035 (tpp80) REVERT: M 173 MET cc_start: 0.5634 (tpt) cc_final: 0.5023 (tpt) REVERT: N 91 SER cc_start: 0.8839 (m) cc_final: 0.8347 (p) REVERT: N 105 LEU cc_start: 0.9217 (mt) cc_final: 0.8837 (mm) REVERT: N 110 GLN cc_start: 0.8289 (mp10) cc_final: 0.7938 (mp10) REVERT: N 115 PHE cc_start: 0.7225 (t80) cc_final: 0.6973 (t80) REVERT: N 202 ASP cc_start: 0.7703 (t70) cc_final: 0.7404 (t70) REVERT: 2 358 TYR cc_start: 0.7617 (t80) cc_final: 0.7362 (t80) REVERT: 2 466 MET cc_start: 0.5535 (tmm) cc_final: 0.4934 (tmm) REVERT: 2 623 ASP cc_start: 0.9051 (m-30) cc_final: 0.8512 (t70) REVERT: 2 757 MET cc_start: 0.9168 (mpp) cc_final: 0.8816 (mpp) REVERT: 2 764 MET cc_start: 0.5091 (tpp) cc_final: 0.4633 (mmm) REVERT: 5 32 LYS cc_start: 0.8563 (mmtt) cc_final: 0.7978 (mptt) REVERT: 5 62 ARG cc_start: 0.8097 (mpt-90) cc_final: 0.7476 (mpt-90) REVERT: 5 68 GLU cc_start: 0.7359 (tt0) cc_final: 0.6699 (tt0) REVERT: 5 69 MET cc_start: 0.4034 (ptt) cc_final: 0.2986 (tpt) REVERT: 5 71 ASP cc_start: 0.8038 (m-30) cc_final: 0.6588 (m-30) REVERT: 5 82 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8552 (mtmt) REVERT: 5 92 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7869 (tm-30) REVERT: 5 96 GLU cc_start: 0.8658 (mm-30) cc_final: 0.7932 (mm-30) REVERT: 5 245 ASP cc_start: 0.7596 (p0) cc_final: 0.6800 (t0) REVERT: 5 265 SER cc_start: 0.9128 (m) cc_final: 0.8843 (t) REVERT: 5 447 MET cc_start: 0.5906 (mmm) cc_final: 0.5046 (mmm) REVERT: 6 16 GLU cc_start: 0.9553 (mm-30) cc_final: 0.9056 (mm-30) REVERT: 6 204 GLU cc_start: 0.5881 (pp20) cc_final: 0.5566 (pp20) REVERT: 6 222 LEU cc_start: 0.8163 (pt) cc_final: 0.7900 (pp) REVERT: 6 317 MET cc_start: 0.3160 (ppp) cc_final: 0.2514 (ppp) REVERT: 6 363 GLN cc_start: 0.8148 (tt0) cc_final: 0.7804 (tt0) REVERT: 6 519 MET cc_start: 0.8784 (mpp) cc_final: 0.8541 (mpp) REVERT: 6 542 ARG cc_start: 0.8781 (ttp80) cc_final: 0.8570 (ttm-80) REVERT: 6 623 MET cc_start: 0.9063 (mtm) cc_final: 0.8703 (ptm) REVERT: 3 36 MET cc_start: 0.6374 (pmm) cc_final: 0.6113 (pmm) REVERT: 3 73 PHE cc_start: 0.8698 (m-10) cc_final: 0.8490 (m-80) REVERT: 3 107 HIS cc_start: 0.8277 (p90) cc_final: 0.7988 (p90) REVERT: 3 111 ARG cc_start: 0.7974 (tpt90) cc_final: 0.7255 (ptm160) REVERT: 3 409 MET cc_start: 0.3229 (ptt) cc_final: 0.2770 (tpp) REVERT: 3 423 GLN cc_start: 0.8987 (tt0) cc_final: 0.8508 (tt0) REVERT: 3 464 ILE cc_start: 0.8469 (mp) cc_final: 0.8041 (mm) REVERT: 3 473 ARG cc_start: 0.8398 (mmm160) cc_final: 0.8022 (mmm160) REVERT: 3 561 PHE cc_start: 0.7953 (t80) cc_final: 0.7475 (t80) REVERT: 3 572 MET cc_start: 0.8250 (mmm) cc_final: 0.7477 (mtm) REVERT: 4 274 MET cc_start: 0.6771 (ppp) cc_final: 0.6116 (ppp) REVERT: 4 574 CYS cc_start: 0.7916 (m) cc_final: 0.6635 (m) REVERT: 4 683 MET cc_start: 0.6149 (tpt) cc_final: 0.5545 (tpp) REVERT: 4 686 MET cc_start: 0.7281 (ptp) cc_final: 0.6673 (pmm) REVERT: 4 692 TYR cc_start: 0.7072 (p90) cc_final: 0.6749 (p90) REVERT: 7 20 PHE cc_start: 0.7878 (t80) cc_final: 0.6461 (t80) REVERT: 7 33 TYR cc_start: 0.8745 (m-80) cc_final: 0.8268 (m-80) REVERT: 7 64 GLU cc_start: 0.8417 (mp0) cc_final: 0.8190 (mp0) REVERT: 7 150 ARG cc_start: 0.8481 (ttt-90) cc_final: 0.7481 (tmt-80) REVERT: 7 166 ILE cc_start: 0.7017 (mp) cc_final: 0.6745 (mm) REVERT: 7 176 MET cc_start: 0.6407 (ttp) cc_final: 0.5942 (tmm) REVERT: 7 253 MET cc_start: 0.6230 (ppp) cc_final: 0.5161 (ppp) REVERT: 7 302 ARG cc_start: 0.8681 (ptp-170) cc_final: 0.8119 (mtt180) REVERT: 7 340 LEU cc_start: 0.8830 (tp) cc_final: 0.8597 (tp) REVERT: 7 380 MET cc_start: 0.8115 (tmm) cc_final: 0.7782 (tmm) REVERT: 7 541 HIS cc_start: 0.6996 (m-70) cc_final: 0.6330 (m-70) REVERT: 7 556 MET cc_start: 0.8582 (ptp) cc_final: 0.8124 (ptt) REVERT: 7 562 TYR cc_start: 0.8919 (t80) cc_final: 0.8325 (m-80) REVERT: 7 586 VAL cc_start: 0.9012 (t) cc_final: 0.8804 (t) REVERT: 7 590 ARG cc_start: 0.8833 (ptt90) cc_final: 0.7712 (mmm160) outliers start: 7 outliers final: 3 residues processed: 793 average time/residue: 0.5401 time to fit residues: 685.7659 Evaluate side-chains 641 residues out of total 4193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 638 time to evaluate : 4.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 298 optimal weight: 2.9990 chunk 399 optimal weight: 0.3980 chunk 114 optimal weight: 0.0010 chunk 345 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 375 optimal weight: 8.9990 chunk 157 optimal weight: 0.0070 chunk 385 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 69 optimal weight: 0.0010 overall best weight: 0.2410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 HIS 2 659 GLN ** 2 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 198 GLN ** 6 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 472 GLN ** 3 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 467 GLN ** 4 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 459 HIS 7 543 HIS 7 605 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.190903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.169116 restraints weight = 128257.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.170486 restraints weight = 102392.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.172003 restraints weight = 82763.977| |-----------------------------------------------------------------------------| r_work (final): 0.4403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.7644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 38986 Z= 0.180 Angle : 0.723 13.335 52778 Z= 0.363 Chirality : 0.045 0.329 5990 Planarity : 0.005 0.086 6735 Dihedral : 11.115 167.678 5584 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.05 % Favored : 87.91 % Rotamer: Outliers : 0.07 % Allowed : 0.68 % Favored : 99.24 % 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: -3.22 (0.11), residues: 4657 helix: -1.56 (0.13), residues: 1414 sheet: -1.49 (0.24), residues: 462 loop : -2.69 (0.11), residues: 2781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 193 HIS 0.008 0.001 HIS 2 754 PHE 0.021 0.002 PHE 3 406 TYR 0.022 0.001 TYR 4 473 ARG 0.022 0.001 ARG 4 531 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11613.94 seconds wall clock time: 210 minutes 7.89 seconds (12607.89 seconds total)