Starting phenix.real_space_refine (version: dev) on Fri Feb 24 17:03:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmh_10521/02_2023/6tmh_10521_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmh_10521/02_2023/6tmh_10521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmh_10521/02_2023/6tmh_10521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmh_10521/02_2023/6tmh_10521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmh_10521/02_2023/6tmh_10521_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmh_10521/02_2023/6tmh_10521_trim_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.005 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 Process input model Symmetric amino acids flipped Residue "i ASP 62": "OD1" <-> "OD2" Residue "i TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i ASP 77": "OD1" <-> "OD2" Residue "i TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 129": "OD1" <-> "OD2" Residue "A ASP 130": "OD1" <-> "OD2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 366": "OD1" <-> "OD2" Residue "A TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 461": "OD1" <-> "OD2" Residue "A ASP 463": "OD1" <-> "OD2" Residue "A TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 129": "OD1" <-> "OD2" Residue "E ASP 245": "OD1" <-> "OD2" Residue "E TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 380": "OE1" <-> "OE2" Residue "C ASP 385": "OD1" <-> "OD2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 463": "OD1" <-> "OD2" Residue "C TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 310": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 431": "OD1" <-> "OD2" Residue "B ARG 435": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 473": "OD1" <-> "OD2" Residue "B GLU 477": "OE1" <-> "OE2" Residue "B ASP 479": "OD1" <-> "OD2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 196": "OD1" <-> "OD2" Residue "F PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 367": "OD1" <-> "OD2" Residue "F TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 473": "OD1" <-> "OD2" Residue "F ASP 479": "OD1" <-> "OD2" Residue "F PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 536": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 473": "OD1" <-> "OD2" Residue "D GLU 474": "OE1" <-> "OE2" Residue "D PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g GLU 169": "OE1" <-> "OE2" Residue "g PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g GLU 237": "OE1" <-> "OE2" Residue "d TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d ASP 101": "OD1" <-> "OD2" Residue "d PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d ASP 120": "OD1" <-> "OD2" Residue "d ASP 121": "OD1" <-> "OD2" Residue "d GLU 162": "OE1" <-> "OE2" Residue "e GLU 26": "OE1" <-> "OE2" Residue "e GLU 42": "OE1" <-> "OE2" Residue "e GLU 54": "OE1" <-> "OE2" Residue "e PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 109": "OD1" <-> "OD2" Residue "G ASP 168": "OD1" <-> "OD2" Residue "G TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 137": "OD1" <-> "OD2" Residue "M PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 136": "OE1" <-> "OE2" Residue "O TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 65358 Number of models: 1 Model: "" Number of chains: 26 Chain: "i" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 660 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 2, 'TRANS': 37} Chain: "A" Number of atoms: 7924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 7924 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 490} Chain: "E" Number of atoms: 7848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7848 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 486} Chain: "C" Number of atoms: 7521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 7521 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 466} Chain: "B" Number of atoms: 7314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 7314 Classifications: {'peptide': 479} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 454} Chain: "F" Number of atoms: 7265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7265 Classifications: {'peptide': 475} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 450} Chain: "D" Number of atoms: 7265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7265 Classifications: {'peptide': 475} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 450} Chain: "g" Number of atoms: 4289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4289 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 8, 'TRANS': 263} Chain: "d" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2145 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "e" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1077 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "G" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1618 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain breaks: 1 Chain: "H" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "I" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "J" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "K" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "L" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "M" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "N" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "O" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "P" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "Q" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 22.71, per 1000 atoms: 0.35 Number of scatterers: 65358 At special positions: 0 Unit cell: (135.29, 126.99, 229.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 166 16.00 P 13 15.00 Mg 5 11.99 O 6200 8.00 N 5547 7.00 C 20479 6.00 H 32948 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 44.71 Conformation dependent library (CDL) restraints added in 4.2 seconds 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7754 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 149 helices and 25 sheets defined 49.0% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'i' and resid 58 through 87 removed outlier: 4.883A pdb=" N LEU i 85 " --> pdb=" O LEU i 81 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ALA i 86 " --> pdb=" O ARG i 82 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN i 87 " --> pdb=" O ASN i 83 " (cutoff:3.500A) Processing helix chain 'i' and resid 93 through 95 No H-bonds generated for 'chain 'i' and resid 93 through 95' Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 63 through 66 No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 202 through 207 Processing helix chain 'A' and resid 226 through 242 removed outlier: 4.131A pdb=" N GLN A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLU A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 240 " --> pdb=" O ASN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 removed outlier: 4.357A pdb=" N GLN A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 292 through 312 Proline residue: A 299 - end of helix removed outlier: 3.821A pdb=" N TRP A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE A 309 " --> pdb=" O MET A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 350 through 360 removed outlier: 4.258A pdb=" N ARG A 360 " --> pdb=" O ARG A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 407 through 410 No H-bonds generated for 'chain 'A' and resid 407 through 410' Processing helix chain 'A' and resid 427 through 430 Processing helix chain 'A' and resid 433 through 451 removed outlier: 4.277A pdb=" N VAL A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 457 removed outlier: 3.749A pdb=" N GLN A 457 " --> pdb=" O ALA A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 454 through 457' Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 467 through 480 Processing helix chain 'A' and resid 490 through 501 Processing helix chain 'A' and resid 510 through 527 removed outlier: 4.251A pdb=" N SER A 514 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU A 517 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 538 Processing helix chain 'A' and resid 543 through 559 Processing helix chain 'E' and resid 60 through 67 Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 202 through 207 Processing helix chain 'E' and resid 226 through 242 removed outlier: 4.163A pdb=" N GLN E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LYS E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU E 239 " --> pdb=" O ILE E 235 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE E 240 " --> pdb=" O ASN E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 274 Processing helix chain 'E' and resid 292 through 312 Proline residue: E 299 - end of helix removed outlier: 3.822A pdb=" N TRP E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE E 309 " --> pdb=" O MET E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 336 Processing helix chain 'E' and resid 343 through 345 No H-bonds generated for 'chain 'E' and resid 343 through 345' Processing helix chain 'E' and resid 350 through 358 Processing helix chain 'E' and resid 389 through 395 Processing helix chain 'E' and resid 406 through 411 Processing helix chain 'E' and resid 427 through 430 Processing helix chain 'E' and resid 433 through 455 removed outlier: 3.902A pdb=" N VAL E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR E 441 " --> pdb=" O GLN E 437 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ALA E 454 " --> pdb=" O ARG E 450 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N PHE E 455 " --> pdb=" O GLU E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 479 Processing helix chain 'E' and resid 490 through 502 Processing helix chain 'E' and resid 511 through 524 removed outlier: 3.678A pdb=" N SER E 514 " --> pdb=" O LYS E 511 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE E 516 " --> pdb=" O ILE E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 538 Processing helix chain 'E' and resid 543 through 559 Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 203 through 207 Processing helix chain 'C' and resid 226 through 242 removed outlier: 4.180A pdb=" N GLN C 237 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLU C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE C 240 " --> pdb=" O ASN C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 275 removed outlier: 3.760A pdb=" N ARG C 275 " --> pdb=" O ALA C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 312 Proline residue: C 299 - end of helix removed outlier: 3.750A pdb=" N TRP C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE C 309 " --> pdb=" O MET C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 336 Processing helix chain 'C' and resid 343 through 345 No H-bonds generated for 'chain 'C' and resid 343 through 345' Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 389 through 396 Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 427 through 430 Processing helix chain 'C' and resid 433 through 458 removed outlier: 3.998A pdb=" N VAL C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ALA C 454 " --> pdb=" O ARG C 450 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N PHE C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE C 458 " --> pdb=" O ALA C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 479 Processing helix chain 'C' and resid 490 through 501 Processing helix chain 'C' and resid 510 through 526 removed outlier: 4.055A pdb=" N SER C 514 " --> pdb=" O LYS C 511 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU C 517 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU C 519 " --> pdb=" O PHE C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 538 Processing helix chain 'C' and resid 543 through 559 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 261 through 273 Processing helix chain 'B' and resid 307 through 324 removed outlier: 4.510A pdb=" N ALA B 312 " --> pdb=" O ARG B 308 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU B 313 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 348 removed outlier: 3.618A pdb=" N GLY B 344 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 374 removed outlier: 3.761A pdb=" N LEU B 371 " --> pdb=" O ASP B 367 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG B 374 " --> pdb=" O GLN B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 399 through 407 removed outlier: 4.291A pdb=" N ALA B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N HIS B 407 " --> pdb=" O THR B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 removed outlier: 4.021A pdb=" N LEU B 421 " --> pdb=" O GLN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 462 removed outlier: 3.672A pdb=" N THR B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 469 Processing helix chain 'B' and resid 472 through 474 No H-bonds generated for 'chain 'B' and resid 472 through 474' Processing helix chain 'B' and resid 477 through 493 Processing helix chain 'B' and resid 499 through 504 removed outlier: 4.136A pdb=" N VAL B 502 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 504 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 525 Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 542 through 555 Processing helix chain 'F' and resid 159 through 161 No H-bonds generated for 'chain 'F' and resid 159 through 161' Processing helix chain 'F' and resid 209 through 214 Processing helix chain 'F' and resid 233 through 246 Processing helix chain 'F' and resid 261 through 274 Processing helix chain 'F' and resid 312 through 324 removed outlier: 3.795A pdb=" N PHE F 322 " --> pdb=" O VAL F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 350 Processing helix chain 'F' and resid 364 through 372 Processing helix chain 'F' and resid 392 through 394 No H-bonds generated for 'chain 'F' and resid 392 through 394' Processing helix chain 'F' and resid 399 through 404 Processing helix chain 'F' and resid 416 through 419 No H-bonds generated for 'chain 'F' and resid 416 through 419' Processing helix chain 'F' and resid 443 through 470 removed outlier: 3.768A pdb=" N TYR F 447 " --> pdb=" O GLY F 443 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ASP F 448 " --> pdb=" O GLN F 444 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE F 469 " --> pdb=" O ASP F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 492 Processing helix chain 'F' and resid 500 through 504 Processing helix chain 'F' and resid 513 through 525 Processing helix chain 'F' and resid 542 through 552 Processing helix chain 'D' and resid 209 through 214 Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 261 through 274 Processing helix chain 'D' and resid 311 through 324 removed outlier: 3.771A pdb=" N PHE D 322 " --> pdb=" O VAL D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 351 removed outlier: 3.583A pdb=" N GLY D 344 " --> pdb=" O PHE D 340 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU D 350 " --> pdb=" O GLU D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 372 removed outlier: 3.918A pdb=" N LEU D 371 " --> pdb=" O ASP D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' Processing helix chain 'D' and resid 399 through 407 removed outlier: 4.154A pdb=" N ALA D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N HIS D 407 " --> pdb=" O THR D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 444 through 469 removed outlier: 3.768A pdb=" N LEU D 463 " --> pdb=" O ASP D 459 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN D 464 " --> pdb=" O TYR D 460 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASP D 465 " --> pdb=" O LYS D 461 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 474 No H-bonds generated for 'chain 'D' and resid 472 through 474' Processing helix chain 'D' and resid 477 through 492 Processing helix chain 'D' and resid 499 through 504 removed outlier: 4.059A pdb=" N VAL D 502 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR D 504 " --> pdb=" O GLU D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 525 Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'g' and resid 44 through 81 Processing helix chain 'g' and resid 83 through 93 Proline residue: g 87 - end of helix Processing helix chain 'g' and resid 120 through 135 Processing helix chain 'g' and resid 149 through 159 removed outlier: 5.376A pdb=" N ARG g 157 " --> pdb=" O SER g 153 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N THR g 158 " --> pdb=" O ALA g 154 " (cutoff:3.500A) Processing helix chain 'g' and resid 177 through 189 removed outlier: 3.543A pdb=" N ILE g 182 " --> pdb=" O GLY g 178 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE g 183 " --> pdb=" O GLN g 179 " (cutoff:3.500A) Processing helix chain 'g' and resid 218 through 222 Processing helix chain 'g' and resid 227 through 229 No H-bonds generated for 'chain 'g' and resid 227 through 229' Processing helix chain 'g' and resid 238 through 311 removed outlier: 4.959A pdb=" N LYS g 243 " --> pdb=" O THR g 239 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASP g 244 " --> pdb=" O ASP g 240 " (cutoff:3.500A) Processing helix chain 'd' and resid 137 through 139 No H-bonds generated for 'chain 'd' and resid 137 through 139' Processing helix chain 'd' and resid 143 through 156 Processing helix chain 'd' and resid 162 through 181 Processing helix chain 'e' and resid 9 through 23 removed outlier: 3.691A pdb=" N LEU e 19 " --> pdb=" O GLU e 15 " (cutoff:3.500A) Processing helix chain 'e' and resid 26 through 34 removed outlier: 3.944A pdb=" N GLN e 31 " --> pdb=" O PRO e 27 " (cutoff:3.500A) Processing helix chain 'e' and resid 59 through 64 Processing helix chain 'G' and resid 75 through 89 Processing helix chain 'G' and resid 94 through 110 Processing helix chain 'G' and resid 113 through 118 Processing helix chain 'G' and resid 124 through 136 Processing helix chain 'G' and resid 142 through 153 Processing helix chain 'G' and resid 157 through 169 removed outlier: 4.239A pdb=" N ALA G 161 " --> pdb=" O PRO G 158 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG G 162 " --> pdb=" O MET G 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 107 Processing helix chain 'H' and resid 110 through 130 Processing helix chain 'H' and resid 132 through 165 removed outlier: 4.994A pdb=" N GLU H 136 " --> pdb=" O SER H 133 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE H 139 " --> pdb=" O GLU H 136 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR H 141 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU H 143 " --> pdb=" O THR H 140 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLU H 150 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N MET H 159 " --> pdb=" O CYS H 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 130 removed outlier: 3.700A pdb=" N MET I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N SER I 109 " --> pdb=" O ILE I 105 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL I 110 " --> pdb=" O ALA I 106 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLY I 111 " --> pdb=" O LEU I 107 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLY I 112 " --> pdb=" O MET I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 163 removed outlier: 5.261A pdb=" N GLU I 136 " --> pdb=" O SER I 133 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE I 139 " --> pdb=" O GLU I 136 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLU I 150 " --> pdb=" O GLY I 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 130 removed outlier: 4.381A pdb=" N SER J 109 " --> pdb=" O ILE J 105 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL J 110 " --> pdb=" O ALA J 106 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLY J 111 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLY J 112 " --> pdb=" O MET J 108 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL J 113 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 164 removed outlier: 5.541A pdb=" N GLU J 136 " --> pdb=" O SER J 133 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE J 139 " --> pdb=" O GLU J 136 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR J 140 " --> pdb=" O ASP J 137 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLU J 150 " --> pdb=" O GLY J 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 108 removed outlier: 3.834A pdb=" N LEU K 107 " --> pdb=" O ALA K 103 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N MET K 108 " --> pdb=" O ALA K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 130 Processing helix chain 'K' and resid 132 through 165 removed outlier: 5.560A pdb=" N GLU K 136 " --> pdb=" O SER K 133 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP K 137 " --> pdb=" O ILE K 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 106 Processing helix chain 'L' and resid 113 through 130 Processing helix chain 'L' and resid 132 through 162 removed outlier: 5.615A pdb=" N GLU L 136 " --> pdb=" O SER L 133 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE L 139 " --> pdb=" O GLU L 136 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N MET L 146 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU L 149 " --> pdb=" O MET L 146 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLU L 150 " --> pdb=" O GLY L 147 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY L 153 " --> pdb=" O GLU L 150 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE L 155 " --> pdb=" O LEU L 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 130 removed outlier: 3.779A pdb=" N SER M 102 " --> pdb=" O ALA M 99 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER M 126 " --> pdb=" O ALA M 123 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR M 128 " --> pdb=" O VAL M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 165 Processing helix chain 'N' and resid 98 through 130 removed outlier: 3.817A pdb=" N MET N 108 " --> pdb=" O ALA N 104 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N SER N 109 " --> pdb=" O ILE N 105 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL N 110 " --> pdb=" O ALA N 106 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLY N 111 " --> pdb=" O LEU N 107 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLY N 112 " --> pdb=" O MET N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 164 Processing helix chain 'O' and resid 98 through 130 removed outlier: 4.037A pdb=" N LEU O 107 " --> pdb=" O ALA O 103 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N SER O 109 " --> pdb=" O ILE O 105 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL O 110 " --> pdb=" O ALA O 106 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY O 111 " --> pdb=" O LEU O 107 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY O 112 " --> pdb=" O MET O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 132 through 164 removed outlier: 5.892A pdb=" N GLU O 136 " --> pdb=" O SER O 133 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE O 139 " --> pdb=" O GLU O 136 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLU O 150 " --> pdb=" O GLY O 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 130 removed outlier: 4.341A pdb=" N MET P 108 " --> pdb=" O ALA P 104 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N SER P 109 " --> pdb=" O ILE P 105 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N VAL P 110 " --> pdb=" O ALA P 106 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY P 111 " --> pdb=" O LEU P 107 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY P 116 " --> pdb=" O GLY P 112 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N SER P 119 " --> pdb=" O GLN P 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 139 through 164 Processing helix chain 'Q' and resid 97 through 130 removed outlier: 3.567A pdb=" N LEU Q 101 " --> pdb=" O GLY Q 97 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA Q 104 " --> pdb=" O SER Q 100 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER Q 109 " --> pdb=" O ILE Q 105 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL Q 110 " --> pdb=" O ALA Q 106 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLY Q 111 " --> pdb=" O LEU Q 107 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY Q 112 " --> pdb=" O MET Q 108 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN Q 115 " --> pdb=" O GLY Q 111 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY Q 116 " --> pdb=" O GLY Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 132 through 165 removed outlier: 5.511A pdb=" N GLU Q 136 " --> pdb=" O SER Q 133 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE Q 139 " --> pdb=" O GLU Q 136 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU Q 150 " --> pdb=" O GLY Q 147 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N MET Q 159 " --> pdb=" O CYS Q 156 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.361A pdb=" N GLY A 123 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N PHE A 93 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL A 82 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 147 through 150 removed outlier: 4.238A pdb=" N GLU A 176 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 218 through 220 Processing sheet with id= D, first strand: chain 'A' and resid 281 through 286 removed outlier: 6.816A pdb=" N CYS A 253 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N VAL A 284 " --> pdb=" O CYS A 253 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR A 255 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ALA A 286 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA A 257 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER A 372 " --> pdb=" O CYS A 316 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE A 318 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR A 374 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N TYR A 320 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU A 376 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 138 through 140 removed outlier: 6.644A pdb=" N ARG E 91 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL E 85 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE E 89 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL E 125 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ALA E 114 " --> pdb=" O VAL E 125 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 218 through 220 Processing sheet with id= G, first strand: chain 'E' and resid 281 through 286 removed outlier: 9.507A pdb=" N THR E 282 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N CYS E 253 " --> pdb=" O THR E 282 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N VAL E 284 " --> pdb=" O CYS E 253 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR E 255 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ALA E 286 " --> pdb=" O TYR E 255 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA E 257 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N HIS E 315 " --> pdb=" O TYR E 252 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ILE E 254 " --> pdb=" O HIS E 315 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL E 317 " --> pdb=" O ILE E 254 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL E 256 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE E 319 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL E 258 " --> pdb=" O ILE E 319 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ASP E 321 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER E 372 " --> pdb=" O CYS E 316 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE E 318 " --> pdb=" O SER E 372 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR E 374 " --> pdb=" O ILE E 318 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N TYR E 320 " --> pdb=" O THR E 374 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU E 376 " --> pdb=" O TYR E 320 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 79 through 81 removed outlier: 6.435A pdb=" N GLY C 123 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N PHE C 93 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL C 82 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 147 through 149 Processing sheet with id= J, first strand: chain 'C' and resid 401 through 404 removed outlier: 6.942A pdb=" N LEU C 217 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU C 404 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE C 219 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 281 through 286 removed outlier: 9.139A pdb=" N THR C 282 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS C 253 " --> pdb=" O THR C 282 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N VAL C 284 " --> pdb=" O CYS C 253 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TYR C 255 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ALA C 286 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA C 257 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N HIS C 315 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE C 254 " --> pdb=" O HIS C 315 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL C 317 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL C 256 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C 319 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL C 258 " --> pdb=" O ILE C 319 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ASP C 321 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C 320 " --> pdb=" O LEU C 376 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 82 through 88 removed outlier: 6.769A pdb=" N ASP B 93 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL B 87 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE B 132 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL B 120 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS B 145 " --> pdb=" O GLN B 110 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 154 through 156 Processing sheet with id= N, first strand: chain 'B' and resid 410 through 413 removed outlier: 7.703A pdb=" N ILE B 223 " --> pdb=" O ILE B 383 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N SER B 385 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU B 225 " --> pdb=" O SER B 385 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN B 387 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLY B 227 " --> pdb=" O GLN B 387 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL B 389 " --> pdb=" O GLY B 227 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 330 " --> pdb=" O THR B 384 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL B 386 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 332 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ALA B 388 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE B 334 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N TYR B 390 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N PHE B 251 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N PHE B 333 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 253 " --> pdb=" O PHE B 333 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ASP B 335 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA B 255 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA B 295 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY B 256 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B 297 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 81 through 83 removed outlier: 6.720A pdb=" N ARG F 130 " --> pdb=" O ALA F 121 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N HIS F 123 " --> pdb=" O THR F 128 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N THR F 128 " --> pdb=" O HIS F 123 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N HIS F 95 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ILE F 84 " --> pdb=" O HIS F 95 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 154 through 156 Processing sheet with id= Q, first strand: chain 'F' and resid 410 through 413 removed outlier: 3.752A pdb=" N ALA F 410 " --> pdb=" O LYS F 222 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY F 224 " --> pdb=" O ALA F 410 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ILE F 223 " --> pdb=" O ILE F 383 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER F 385 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU F 225 " --> pdb=" O SER F 385 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN F 387 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL F 330 " --> pdb=" O THR F 384 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL F 386 " --> pdb=" O VAL F 330 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU F 332 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ALA F 388 " --> pdb=" O LEU F 332 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE F 334 " --> pdb=" O ALA F 388 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA F 295 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N GLY F 256 " --> pdb=" O ALA F 295 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL F 297 " --> pdb=" O GLY F 256 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLY F 258 " --> pdb=" O VAL F 297 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLY F 299 " --> pdb=" O GLY F 258 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 279 through 281 removed outlier: 3.696A pdb=" N LYS F 280 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 81 through 83 removed outlier: 6.837A pdb=" N ARG D 130 " --> pdb=" O ALA D 121 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N HIS D 123 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N THR D 128 " --> pdb=" O HIS D 123 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N HIS D 95 " --> pdb=" O ILE D 84 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE D 84 " --> pdb=" O HIS D 95 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 154 through 157 removed outlier: 4.368A pdb=" N LYS D 183 " --> pdb=" O VAL D 157 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 410 through 413 removed outlier: 7.712A pdb=" N ILE D 223 " --> pdb=" O ILE D 383 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER D 385 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU D 225 " --> pdb=" O SER D 385 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLN D 387 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY D 227 " --> pdb=" O GLN D 387 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL D 389 " --> pdb=" O GLY D 227 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL D 330 " --> pdb=" O THR D 384 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N VAL D 386 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU D 332 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA D 388 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE D 334 " --> pdb=" O ALA D 388 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N TYR D 390 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N PHE D 251 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N PHE D 333 " --> pdb=" O PHE D 251 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL D 253 " --> pdb=" O PHE D 333 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ASP D 335 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA D 255 " --> pdb=" O ASP D 335 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA D 295 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N GLY D 256 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL D 297 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'g' and resid 207 through 215 removed outlier: 7.033A pdb=" N ASP g 209 " --> pdb=" O PHE g 202 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N PHE g 202 " --> pdb=" O ASP g 209 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU g 211 " --> pdb=" O ASN g 200 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASN g 200 " --> pdb=" O LEU g 211 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU g 213 " --> pdb=" O ILE g 198 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE g 198 " --> pdb=" O LEU g 213 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL g 215 " --> pdb=" O MET g 196 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N MET g 196 " --> pdb=" O VAL g 215 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASN g 200 " --> pdb=" O LEU g 110 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLY g 146 " --> pdb=" O LYS g 164 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE g 166 " --> pdb=" O GLY g 146 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'd' and resid 83 through 87 removed outlier: 3.786A pdb=" N GLY d 111 " --> pdb=" O LEU d 87 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ARG d 95 " --> pdb=" O ARG d 63 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL d 65 " --> pdb=" O ILE d 93 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE d 93 " --> pdb=" O VAL d 65 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'd' and resid 65 through 68 Processing sheet with id= Y, first strand: chain 'e' and resid 40 through 44 removed outlier: 3.829A pdb=" N THR e 52 " --> pdb=" O VAL e 44 " (cutoff:3.500A) 1553 hydrogen bonds defined for protein. 3816 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: 22.60 Time building geometry restraints manager: 46.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 32904 1.03 - 1.23: 47 1.23 - 1.42: 13082 1.42 - 1.62: 19496 1.62 - 1.81: 310 Bond restraints: 65839 Sorted by residual: bond pdb=" C1' ATP A 601 " pdb=" C2' ATP A 601 " ideal model delta sigma weight residual 1.531 1.299 0.232 1.20e-02 6.94e+03 3.74e+02 bond pdb=" C1' ATP E 601 " pdb=" C2' ATP E 601 " ideal model delta sigma weight residual 1.531 1.301 0.230 1.20e-02 6.94e+03 3.68e+02 bond pdb=" C1' ATP C 601 " pdb=" C2' ATP C 601 " ideal model delta sigma weight residual 1.531 1.301 0.230 1.20e-02 6.94e+03 3.67e+02 bond pdb=" C1' ATP A 601 " pdb=" O4' ATP A 601 " ideal model delta sigma weight residual 1.416 1.616 -0.200 1.30e-02 5.92e+03 2.37e+02 bond pdb=" C1' ATP E 601 " pdb=" O4' ATP E 601 " ideal model delta sigma weight residual 1.416 1.614 -0.198 1.30e-02 5.92e+03 2.32e+02 ... (remaining 65834 not shown) Histogram of bond angle deviations from ideal: 84.80 - 94.65: 3 94.65 - 104.50: 535 104.50 - 114.34: 83353 114.34 - 124.19: 31825 124.19 - 134.04: 3664 Bond angle restraints: 119380 Sorted by residual: angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 122.37 17.50 1.00e+00 1.00e+00 3.06e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 123.19 16.68 1.00e+00 1.00e+00 2.78e+02 angle pdb=" PB ATP E 601 " pdb=" O3B ATP E 601 " pdb=" PG ATP E 601 " ideal model delta sigma weight residual 139.87 123.49 16.38 1.00e+00 1.00e+00 2.68e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 123.47 13.36 1.00e+00 1.00e+00 1.78e+02 angle pdb=" PA ATP E 601 " pdb=" O3A ATP E 601 " pdb=" PB ATP E 601 " ideal model delta sigma weight residual 136.83 123.66 13.17 1.00e+00 1.00e+00 1.74e+02 ... (remaining 119375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.17: 25171 28.17 - 56.34: 690 56.34 - 84.51: 48 84.51 - 112.68: 20 112.68 - 140.85: 4 Dihedral angle restraints: 25933 sinusoidal: 12384 harmonic: 13549 Sorted by residual: dihedral pdb=" CA ASP F 335 " pdb=" C ASP F 335 " pdb=" N ASN F 336 " pdb=" CA ASN F 336 " ideal model delta harmonic sigma weight residual 180.00 57.76 122.24 0 5.00e+00 4.00e-02 5.98e+02 dihedral pdb=" CA ASP D 335 " pdb=" C ASP D 335 " pdb=" N ASN D 336 " pdb=" CA ASN D 336 " ideal model delta harmonic sigma weight residual -180.00 -74.87 -105.13 0 5.00e+00 4.00e-02 4.42e+02 dihedral pdb=" CA ASP B 335 " pdb=" C ASP B 335 " pdb=" N ASN B 336 " pdb=" CA ASN B 336 " ideal model delta harmonic sigma weight residual -180.00 -74.95 -105.05 0 5.00e+00 4.00e-02 4.41e+02 ... (remaining 25930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.352: 5224 0.352 - 0.704: 0 0.704 - 1.056: 0 1.056 - 1.408: 0 1.408 - 1.760: 1 Chirality restraints: 5225 Sorted by residual: chirality pdb=" CG LEU C 462 " pdb=" CB LEU C 462 " pdb=" CD1 LEU C 462 " pdb=" CD2 LEU C 462 " both_signs ideal model delta sigma weight residual False -2.59 -0.83 -1.76 2.00e-01 2.50e+01 7.74e+01 chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.37 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C2' ATP E 601 " pdb=" C1' ATP E 601 " pdb=" C3' ATP E 601 " pdb=" O2' ATP E 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.40 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 5222 not shown) Planarity restraints: 9797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 336 " -0.024 2.00e-02 2.50e+03 3.93e-02 2.31e+01 pdb=" CG ASN D 336 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN D 336 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN D 336 " -0.065 2.00e-02 2.50e+03 pdb="HD21 ASN D 336 " -0.002 2.00e-02 2.50e+03 pdb="HD22 ASN D 336 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 336 " 0.022 2.00e-02 2.50e+03 3.88e-02 2.25e+01 pdb=" CG ASN F 336 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN F 336 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN F 336 " 0.068 2.00e-02 2.50e+03 pdb="HD21 ASN F 336 " 0.001 2.00e-02 2.50e+03 pdb="HD22 ASN F 336 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 458 " -0.006 2.00e-02 2.50e+03 2.37e-02 1.69e+01 pdb=" CG PHE C 458 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE C 458 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 458 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 PHE C 458 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE C 458 " -0.045 2.00e-02 2.50e+03 pdb=" CZ PHE C 458 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 PHE C 458 " 0.006 2.00e-02 2.50e+03 pdb=" HD2 PHE C 458 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE C 458 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 PHE C 458 " 0.043 2.00e-02 2.50e+03 pdb=" HZ PHE C 458 " 0.006 2.00e-02 2.50e+03 ... (remaining 9794 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1609 2.13 - 2.74: 124469 2.74 - 3.36: 183959 3.36 - 3.98: 239218 3.98 - 4.60: 393047 Nonbonded interactions: 942302 Sorted by model distance: nonbonded pdb=" OG SER D 348 " pdb="HH21 ARG D 353 " model vdw 1.507 1.850 nonbonded pdb=" O ALA C 388 " pdb=" HG1 THR C 392 " model vdw 1.546 1.850 nonbonded pdb=" O VAL J 157 " pdb=" HG SER J 160 " model vdw 1.565 1.850 nonbonded pdb=" H VAL A 158 " pdb=" OD2 ASP A 167 " model vdw 1.565 1.850 nonbonded pdb=" OE2 GLU i 68 " pdb=" H MET B 472 " model vdw 1.569 1.850 ... (remaining 942297 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 78 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 79 through 564 or resid 601 through 602)) selection = chain 'C' selection = (chain 'E' and ((resid 78 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 79 through 226 or (resid 227 and (name N or \ name CA or name C or name O or name CB or name OG1 or name CG2 or name H or name \ HA or name HB or name HG21 or name HG22 or name HG23)) or resid 228 through 564 \ or resid 601 through 602)) } ncs_group { reference = (chain 'B' and ((resid 80 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name ND2 or name HA or name HB2 or name HB3 or name HD \ 21 or name HD22)) or resid 81 through 554)) selection = (chain 'D' and resid 80 through 554) selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 166 5.16 5 C 20479 2.51 5 N 5547 2.21 5 O 6200 1.98 5 H 32948 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic 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: 8.180 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: 0.740 Extract box with map and model: 35.760 Check model and map are aligned: 0.780 Process input model: 162.790 Find NCS groups from input model: 2.600 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Set scattering table: 0.460 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 213.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 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 : 0.009 0.232 32891 Z= 0.612 Angle : 0.697 17.503 44510 Z= 0.417 Chirality : 0.051 1.760 5225 Planarity : 0.004 0.059 5718 Dihedral : 14.391 140.847 12164 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.12), residues: 4221 helix: -0.54 (0.11), residues: 2123 sheet: -1.60 (0.20), residues: 556 loop : -2.07 (0.15), residues: 1542 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 227 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Evaluate side-chains 763 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 753 time to evaluate : 5.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 759 average time/residue: 1.0600 time to fit residues: 1194.0543 Evaluate side-chains 471 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 469 time to evaluate : 4.081 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.7131 time to fit residues: 7.4553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 354 optimal weight: 2.9990 chunk 318 optimal weight: 0.6980 chunk 176 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 329 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 245 optimal weight: 0.9990 chunk 381 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN E 121 ASN E 528 HIS C 223 GLN C 525 ASN C 529 GLN B 464 GLN D 242 ASN D 361 GLN g 261 ASN e 36 ASN e 47 GLN G 92 GLN M 131 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 32891 Z= 0.226 Angle : 0.520 9.832 44510 Z= 0.269 Chirality : 0.046 1.705 5225 Planarity : 0.004 0.055 5718 Dihedral : 6.240 147.245 4611 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.27 % Favored : 96.71 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.13), residues: 4221 helix: 0.21 (0.11), residues: 2131 sheet: -1.17 (0.21), residues: 554 loop : -1.49 (0.16), residues: 1536 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 227 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Evaluate side-chains 529 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 497 time to evaluate : 4.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 26 residues processed: 513 average time/residue: 1.0346 time to fit residues: 810.5677 Evaluate side-chains 469 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 443 time to evaluate : 4.089 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 26 outliers final: 1 residues processed: 26 average time/residue: 0.6557 time to fit residues: 36.9052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 211 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 317 optimal weight: 3.9990 chunk 259 optimal weight: 0.0060 chunk 105 optimal weight: 2.9990 chunk 382 optimal weight: 1.9990 chunk 412 optimal weight: 7.9990 chunk 340 optimal weight: 3.9990 chunk 378 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 306 optimal weight: 3.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 527 ASN B 114 ASN B 123 HIS ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN e 34 GLN e 37 GLN H 131 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 32891 Z= 0.378 Angle : 0.572 10.031 44510 Z= 0.299 Chirality : 0.048 1.685 5225 Planarity : 0.004 0.043 5718 Dihedral : 5.974 127.744 4611 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.13), residues: 4221 helix: 0.43 (0.12), residues: 2136 sheet: -0.90 (0.21), residues: 565 loop : -1.11 (0.16), residues: 1520 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 227 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Evaluate side-chains 522 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 489 time to evaluate : 5.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 20 residues processed: 507 average time/residue: 1.0162 time to fit residues: 779.2514 Evaluate side-chains 455 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 435 time to evaluate : 4.109 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.5815 time to fit residues: 26.6441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 377 optimal weight: 4.9990 chunk 287 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 182 optimal weight: 0.5980 chunk 256 optimal weight: 0.9980 chunk 383 optimal weight: 7.9990 chunk 405 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 363 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 525 ASN C 529 GLN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 32891 Z= 0.228 Angle : 0.505 9.895 44510 Z= 0.261 Chirality : 0.046 1.676 5225 Planarity : 0.004 0.044 5718 Dihedral : 5.612 117.258 4611 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.13), residues: 4221 helix: 0.72 (0.12), residues: 2130 sheet: -0.75 (0.21), residues: 572 loop : -0.87 (0.17), residues: 1519 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 227 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Evaluate side-chains 490 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 461 time to evaluate : 4.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 26 residues processed: 476 average time/residue: 1.0817 time to fit residues: 783.7600 Evaluate side-chains 460 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 434 time to evaluate : 4.088 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.6692 time to fit residues: 37.6367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 338 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 302 optimal weight: 0.5980 chunk 167 optimal weight: 1.9990 chunk 346 optimal weight: 0.9980 chunk 280 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 364 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 200 ASN e 31 GLN e 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 32891 Z= 0.278 Angle : 0.514 9.968 44510 Z= 0.267 Chirality : 0.046 1.679 5225 Planarity : 0.004 0.059 5718 Dihedral : 5.465 106.480 4611 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.13), residues: 4221 helix: 0.83 (0.12), residues: 2138 sheet: -0.67 (0.21), residues: 577 loop : -0.81 (0.17), residues: 1506 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 227 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Evaluate side-chains 467 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 448 time to evaluate : 4.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 457 average time/residue: 1.1243 time to fit residues: 784.2822 Evaluate side-chains 433 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 421 time to evaluate : 4.070 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.6505 time to fit residues: 19.7833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 136 optimal weight: 0.9980 chunk 365 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 238 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 406 optimal weight: 6.9990 chunk 337 optimal weight: 2.9990 chunk 188 optimal weight: 0.1980 chunk 33 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 32891 Z= 0.255 Angle : 0.504 9.827 44510 Z= 0.261 Chirality : 0.046 1.680 5225 Planarity : 0.004 0.046 5718 Dihedral : 5.362 101.979 4611 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.13), residues: 4221 helix: 0.93 (0.12), residues: 2137 sheet: -0.61 (0.21), residues: 578 loop : -0.74 (0.17), residues: 1506 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 227 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Evaluate side-chains 473 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 450 time to evaluate : 4.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 466 average time/residue: 1.0814 time to fit residues: 765.2155 Evaluate side-chains 442 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 426 time to evaluate : 4.091 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.5831 time to fit residues: 22.7732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 391 optimal weight: 8.9990 chunk 45 optimal weight: 0.0030 chunk 231 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 chunk 229 optimal weight: 0.6980 chunk 342 optimal weight: 6.9990 chunk 226 optimal weight: 0.9990 chunk 404 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 246 optimal weight: 0.9980 chunk 186 optimal weight: 0.6980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 32891 Z= 0.175 Angle : 0.488 9.870 44510 Z= 0.249 Chirality : 0.045 1.677 5225 Planarity : 0.003 0.055 5718 Dihedral : 5.119 90.311 4611 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.14), residues: 4221 helix: 1.09 (0.12), residues: 2135 sheet: -0.51 (0.21), residues: 577 loop : -0.58 (0.17), residues: 1509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 227 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Evaluate side-chains 459 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 446 time to evaluate : 4.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 453 average time/residue: 1.0656 time to fit residues: 734.2398 Evaluate side-chains 434 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 428 time to evaluate : 4.138 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.6700 time to fit residues: 12.3749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 250 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 241 optimal weight: 0.2980 chunk 121 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 257 optimal weight: 0.0570 chunk 275 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 318 optimal weight: 1.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 32891 Z= 0.162 Angle : 0.477 9.917 44510 Z= 0.244 Chirality : 0.045 1.678 5225 Planarity : 0.003 0.056 5718 Dihedral : 4.976 81.175 4611 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.14), residues: 4221 helix: 1.21 (0.12), residues: 2137 sheet: -0.41 (0.21), residues: 577 loop : -0.48 (0.17), residues: 1507 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 227 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Evaluate side-chains 452 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 445 time to evaluate : 4.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 450 average time/residue: 1.0418 time to fit residues: 710.8768 Evaluate side-chains 430 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 425 time to evaluate : 4.107 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5918 time to fit residues: 10.5811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 368 optimal weight: 3.9990 chunk 387 optimal weight: 0.5980 chunk 353 optimal weight: 1.9990 chunk 377 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 296 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 340 optimal weight: 5.9990 chunk 356 optimal weight: 0.1980 chunk 375 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 32891 Z= 0.176 Angle : 0.478 9.973 44510 Z= 0.244 Chirality : 0.045 1.684 5225 Planarity : 0.003 0.061 5718 Dihedral : 4.915 78.331 4611 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.14), residues: 4221 helix: 1.29 (0.12), residues: 2138 sheet: -0.33 (0.21), residues: 576 loop : -0.41 (0.17), residues: 1507 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 227 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Evaluate side-chains 443 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 437 time to evaluate : 4.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 441 average time/residue: 1.0819 time to fit residues: 726.8957 Evaluate side-chains 432 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 431 time to evaluate : 4.279 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5959 time to fit residues: 6.1645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 247 optimal weight: 1.9990 chunk 398 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 277 optimal weight: 1.9990 chunk 418 optimal weight: 3.9990 chunk 385 optimal weight: 0.8980 chunk 333 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 257 optimal weight: 0.6980 chunk 204 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 32891 Z= 0.238 Angle : 0.499 9.970 44510 Z= 0.256 Chirality : 0.046 1.684 5225 Planarity : 0.004 0.054 5718 Dihedral : 5.073 84.340 4611 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.14), residues: 4221 helix: 1.22 (0.12), residues: 2145 sheet: -0.35 (0.21), residues: 578 loop : -0.45 (0.17), residues: 1498 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8442 Ramachandran restraints generated. 4221 Oldfield, 0 Emsley, 4221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 227 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Evaluate side-chains 439 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 436 time to evaluate : 4.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 437 average time/residue: 1.0388 time to fit residues: 685.8409 Evaluate side-chains 435 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 433 time to evaluate : 4.970 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.7575 time to fit residues: 7.5856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 264 optimal weight: 1.9990 chunk 354 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 307 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 333 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 342 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 0.0670 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.123676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.089393 restraints weight = 129410.948| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.89 r_work: 0.2813 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 32891 Z= 0.219 Angle : 0.496 9.892 44510 Z= 0.254 Chirality : 0.046 1.682 5225 Planarity : 0.004 0.066 5718 Dihedral : 5.038 79.279 4611 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.14), residues: 4221 helix: 1.24 (0.12), residues: 2145 sheet: -0.28 (0.21), residues: 577 loop : -0.40 (0.17), residues: 1499 =============================================================================== Job complete usr+sys time: 14708.36 seconds wall clock time: 254 minutes 30.67 seconds (15270.67 seconds total)