Starting phenix.real_space_refine on Wed Feb 21 17:07:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmk_22925/02_2024/7kmk_22925.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmk_22925/02_2024/7kmk_22925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmk_22925/02_2024/7kmk_22925.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmk_22925/02_2024/7kmk_22925.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmk_22925/02_2024/7kmk_22925.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmk_22925/02_2024/7kmk_22925.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 142 5.16 5 C 19841 2.51 5 N 5148 2.21 5 O 6120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 187": "OD1" <-> "OD2" Residue "L TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 187": "OD1" <-> "OD2" Residue "M TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31251 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 8039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8039 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 54, 'TRANS': 973} Chain breaks: 7 Chain: "B" Number of atoms: 8018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8018 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 54, 'TRANS': 970} Chain breaks: 7 Chain: "C" Number of atoms: 8018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8018 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 54, 'TRANS': 970} Chain breaks: 7 Chain: "L" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "H" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1635 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "M" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "I" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1635 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 16.30, per 1000 atoms: 0.52 Number of scatterers: 31251 At special positions: 0 Unit cell: (147.29, 144.2, 223.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 142 16.00 O 6120 8.00 N 5148 7.00 C 19841 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=52, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.10 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.06 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.08 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.08 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.10 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.09 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.05 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.02 Simple disulfide: pdb=" SG CYS L 154 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS L 234 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.02 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 104 " distance=2.02 Simple disulfide: pdb=" SG CYS M 154 " - pdb=" SG CYS M 214 " distance=2.03 Simple disulfide: pdb=" SG CYS M 234 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 104 " distance=2.03 Simple disulfide: pdb=" SG CYS I 155 " - pdb=" SG CYS I 211 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 717 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B1134 " " NAG C1301 " - " ASN C 165 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN B 331 " " NAG G 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1074 " " NAG N 1 " - " ASN C 122 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " Time building additional restraints: 13.18 Conformation dependent library (CDL) restraints added in 6.1 seconds 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7374 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 68 sheets defined 21.1% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.776A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.688A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.716A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.571A pdb=" N GLY A 744 " --> pdb=" O MET A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 801 through 805 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.614A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.268A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1032 Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.611A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.592A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.811A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.683A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.767A pdb=" N GLY B 744 " --> pdb=" O MET B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.985A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.907A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 344 Processing helix chain 'C' and resid 364 through 372 Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 removed outlier: 3.837A pdb=" N GLY C 744 " --> pdb=" O MET C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 885 through 889 removed outlier: 3.982A pdb=" N PHE C 888 " --> pdb=" O GLY C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 941 through 944 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.303A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 981 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'L' and resid 95 through 99 Processing helix chain 'L' and resid 143 through 147 Processing helix chain 'L' and resid 203 through 207 Processing helix chain 'H' and resid 69 through 72 Processing helix chain 'H' and resid 95 through 99 Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 202 through 206 Processing helix chain 'H' and resid 216 through 219 Processing helix chain 'M' and resid 95 through 99 Processing helix chain 'M' and resid 143 through 147 Processing helix chain 'M' and resid 203 through 207 Processing helix chain 'I' and resid 69 through 72 Processing helix chain 'I' and resid 95 through 99 Processing helix chain 'I' and resid 146 through 148 No H-bonds generated for 'chain 'I' and resid 146 through 148' Processing helix chain 'I' and resid 171 through 173 No H-bonds generated for 'chain 'I' and resid 171 through 173' Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 216 through 219 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.820A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.792A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.194A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 230 removed outlier: 7.032A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.409A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 5.750A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.564A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.784A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 676 through 677 Processing sheet with id=AB6, first strand: chain 'A' and resid 703 through 704 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 715 removed outlier: 5.679A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.950A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 29 through 30 Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.374A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.300A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC6, first strand: chain 'B' and resid 224 through 230 removed outlier: 4.026A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.496A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.511A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.541A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.710A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.553A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.553A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL B1104 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLU B1111 " --> pdb=" O VAL B1104 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.568A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 29 through 30 removed outlier: 9.009A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.500A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.251A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.369A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.767A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 355 through 358 removed outlier: 3.534A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE8, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 653 through 660 removed outlier: 6.905A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.992A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.808A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1123 Processing sheet with id=AF5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.017A pdb=" N VAL L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR L 55 " --> pdb=" O VAL L 39 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 134 through 138 removed outlier: 5.361A pdb=" N TYR L 193 " --> pdb=" O ASN L 158 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 173 through 174 Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'H' and resid 11 through 13 removed outlier: 7.135A pdb=" N TYR H 37 " --> pdb=" O TYR H 57 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TYR H 57 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N MET H 39 " --> pdb=" O GLY H 55 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY H 55 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP H 41 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 135 through 139 removed outlier: 5.462A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 135 through 139 removed outlier: 5.462A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 166 through 169 Processing sheet with id=AG5, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AG6, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.576A pdb=" N LEU M 11 " --> pdb=" O GLU M 125 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL M 39 " --> pdb=" O TYR M 55 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TYR M 55 " --> pdb=" O VAL M 39 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TRP M 41 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 134 through 138 removed outlier: 5.541A pdb=" N TYR M 193 " --> pdb=" O ASN M 158 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 173 through 174 Processing sheet with id=AG9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AH1, first strand: chain 'I' and resid 11 through 13 removed outlier: 7.142A pdb=" N TYR I 37 " --> pdb=" O TYR I 57 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TYR I 57 " --> pdb=" O TYR I 37 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N MET I 39 " --> pdb=" O GLY I 55 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY I 55 " --> pdb=" O MET I 39 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP I 41 " --> pdb=" O VAL I 53 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 11 through 13 removed outlier: 4.098A pdb=" N TYR I 117 " --> pdb=" O ARG I 106 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 135 through 139 removed outlier: 5.218A pdb=" N ALA I 152 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL I 199 " --> pdb=" O ALA I 152 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLY I 154 " --> pdb=" O VAL I 197 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL I 197 " --> pdb=" O GLY I 154 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU I 156 " --> pdb=" O SER I 195 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N SER I 195 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LYS I 158 " --> pdb=" O LEU I 193 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU I 193 " --> pdb=" O LYS I 158 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 135 through 139 removed outlier: 5.218A pdb=" N ALA I 152 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL I 199 " --> pdb=" O ALA I 152 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLY I 154 " --> pdb=" O VAL I 197 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL I 197 " --> pdb=" O GLY I 154 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU I 156 " --> pdb=" O SER I 195 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N SER I 195 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LYS I 158 " --> pdb=" O LEU I 193 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU I 193 " --> pdb=" O LYS I 158 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 166 through 169 1323 hydrogen bonds defined for protein. 3510 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: 16.45 Time building geometry restraints manager: 14.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 6693 1.32 - 1.47: 11666 1.47 - 1.62: 13407 1.62 - 1.76: 38 1.76 - 1.91: 149 Bond restraints: 31953 Sorted by residual: bond pdb=" CB ILE C 692 " pdb=" CG1 ILE C 692 " ideal model delta sigma weight residual 1.530 1.413 0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" NE1 TRP C 64 " pdb=" CE2 TRP C 64 " ideal model delta sigma weight residual 1.370 1.307 0.063 1.10e-02 8.26e+03 3.33e+01 bond pdb=" C CYS A 15 " pdb=" O CYS A 15 " ideal model delta sigma weight residual 1.233 1.306 -0.073 1.30e-02 5.92e+03 3.12e+01 bond pdb=" CG GLU B1072 " pdb=" CD GLU B1072 " ideal model delta sigma weight residual 1.516 1.377 0.139 2.50e-02 1.60e+03 3.11e+01 bond pdb=" CG TYR A1138 " pdb=" CD2 TYR A1138 " ideal model delta sigma weight residual 1.389 1.498 -0.109 2.10e-02 2.27e+03 2.67e+01 ... (remaining 31948 not shown) Histogram of bond angle deviations from ideal: 93.63 - 101.94: 152 101.94 - 110.25: 8808 110.25 - 118.56: 16540 118.56 - 126.87: 17717 126.87 - 135.18: 263 Bond angle restraints: 43480 Sorted by residual: angle pdb=" C GLY A 526 " pdb=" N PRO A 527 " pdb=" CA PRO A 527 " ideal model delta sigma weight residual 119.56 129.03 -9.47 1.02e+00 9.61e-01 8.63e+01 angle pdb=" C PHE L 138 " pdb=" N PRO L 139 " pdb=" CA PRO L 139 " ideal model delta sigma weight residual 119.66 126.30 -6.64 7.30e-01 1.88e+00 8.28e+01 angle pdb=" N THR B 333 " pdb=" CA THR B 333 " pdb=" C THR B 333 " ideal model delta sigma weight residual 114.31 102.89 11.42 1.29e+00 6.01e-01 7.83e+01 angle pdb=" C LEU C 560 " pdb=" N PRO C 561 " pdb=" CA PRO C 561 " ideal model delta sigma weight residual 119.56 128.06 -8.50 1.02e+00 9.61e-01 6.94e+01 angle pdb=" N VAL C 341 " pdb=" CA VAL C 341 " pdb=" C VAL C 341 " ideal model delta sigma weight residual 110.53 102.96 7.57 9.40e-01 1.13e+00 6.49e+01 ... (remaining 43475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 18998 21.29 - 42.58: 435 42.58 - 63.88: 160 63.88 - 85.17: 50 85.17 - 106.46: 25 Dihedral angle restraints: 19668 sinusoidal: 8192 harmonic: 11476 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -39.64 -46.36 1 1.00e+01 1.00e-02 2.97e+01 dihedral pdb=" C PHE A 201 " pdb=" N PHE A 201 " pdb=" CA PHE A 201 " pdb=" CB PHE A 201 " ideal model delta harmonic sigma weight residual -122.60 -136.17 13.57 0 2.50e+00 1.60e-01 2.94e+01 dihedral pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " pdb=" SG CYS B 749 " pdb=" CB CYS B 749 " ideal model delta sinusoidal sigma weight residual 93.00 47.33 45.67 1 1.00e+01 1.00e-02 2.89e+01 ... (remaining 19665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3252 0.087 - 0.174: 1410 0.174 - 0.261: 350 0.261 - 0.348: 49 0.348 - 0.435: 8 Chirality restraints: 5069 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.05e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.42e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.00e+01 ... (remaining 5066 not shown) Planarity restraints: 5591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 489 " -0.103 2.00e-02 2.50e+03 6.05e-02 7.33e+01 pdb=" CG TYR B 489 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 489 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR B 489 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 TYR B 489 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR B 489 " 0.047 2.00e-02 2.50e+03 pdb=" CZ TYR B 489 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR B 489 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 707 " -0.072 2.00e-02 2.50e+03 3.89e-02 3.03e+01 pdb=" CG TYR C 707 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR C 707 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR C 707 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR C 707 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR C 707 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR C 707 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR C 707 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 453 " -0.072 2.00e-02 2.50e+03 3.88e-02 3.01e+01 pdb=" CG TYR C 453 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR C 453 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR C 453 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR C 453 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR C 453 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR C 453 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR C 453 " -0.051 2.00e-02 2.50e+03 ... (remaining 5588 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 11811 2.88 - 3.39: 29438 3.39 - 3.89: 55887 3.89 - 4.40: 64987 4.40 - 4.90: 103719 Nonbonded interactions: 265842 Sorted by model distance: nonbonded pdb=" N THR B 333 " pdb=" N ASN B 334 " model vdw 2.381 2.560 nonbonded pdb=" O ASN B 603 " pdb=" OD1 ASN B 603 " model vdw 2.397 3.040 nonbonded pdb=" N PRO B 600 " pdb=" O PRO B 600 " model vdw 2.398 2.496 nonbonded pdb=" N PRO C 600 " pdb=" O PRO C 600 " model vdw 2.422 2.496 nonbonded pdb=" N ASN C1125 " pdb=" O ASN C1125 " model vdw 2.423 2.496 ... (remaining 265837 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 14 through 676 or resid 689 through 1138 or resid 1301 thr \ ough 1308)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 1138 or resid 1301 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 5.190 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: 0.030 Extract box with map and model: 15.350 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 88.970 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.019 0.139 31953 Z= 1.250 Angle : 1.835 12.113 43480 Z= 1.240 Chirality : 0.098 0.435 5069 Planarity : 0.009 0.061 5557 Dihedral : 11.497 106.460 12138 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.98 % Favored : 97.95 % Rotamer: Outliers : 0.20 % Allowed : 0.93 % Favored : 98.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.59 (0.13), residues: 3896 helix: -0.20 (0.18), residues: 661 sheet: 0.67 (0.15), residues: 1050 loop : 0.61 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.010 TRP I 52 HIS 0.019 0.003 HIS L 218 PHE 0.056 0.008 PHE C 374 TYR 0.103 0.010 TYR B 489 ARG 0.009 0.001 ARG M 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 465 time to evaluate : 3.359 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASN cc_start: 0.7726 (m-40) cc_final: 0.7477 (p0) REVERT: A 308 VAL cc_start: 0.8932 (t) cc_final: 0.8565 (t) REVERT: A 709 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.7904 (p0) REVERT: A 763 LEU cc_start: 0.9620 (mt) cc_final: 0.9414 (mp) REVERT: A 797 PHE cc_start: 0.8170 (m-10) cc_final: 0.7884 (m-10) REVERT: A 801 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8297 (m-40) REVERT: A 927 PHE cc_start: 0.9418 (t80) cc_final: 0.9163 (t80) REVERT: A 933 LYS cc_start: 0.9801 (mttt) cc_final: 0.9521 (mmtp) REVERT: A 1018 ILE cc_start: 0.9597 (mm) cc_final: 0.9132 (tp) REVERT: A 1063 LEU cc_start: 0.9563 (mt) cc_final: 0.9309 (mt) REVERT: A 1065 VAL cc_start: 0.9341 (t) cc_final: 0.7815 (t) REVERT: A 1108 ASN cc_start: 0.9189 (m-40) cc_final: 0.8972 (m-40) REVERT: B 88 ASP cc_start: 0.9546 (m-30) cc_final: 0.9251 (t0) REVERT: B 104 TRP cc_start: 0.8882 (m-90) cc_final: 0.8172 (m-90) REVERT: B 170 TYR cc_start: 0.9393 (t80) cc_final: 0.9066 (t80) REVERT: B 640 SER cc_start: 0.8813 (m) cc_final: 0.8613 (p) REVERT: B 657 ASN cc_start: 0.8875 (OUTLIER) cc_final: 0.8226 (p0) REVERT: B 755 GLN cc_start: 0.9111 (mt0) cc_final: 0.8614 (mt0) REVERT: B 756 TYR cc_start: 0.7128 (m-80) cc_final: 0.6747 (m-80) REVERT: B 779 GLN cc_start: 0.9609 (mt0) cc_final: 0.9297 (tm-30) REVERT: B 782 PHE cc_start: 0.9610 (m-80) cc_final: 0.9316 (m-80) REVERT: B 927 PHE cc_start: 0.9501 (t80) cc_final: 0.8765 (t80) REVERT: B 1049 LEU cc_start: 0.9508 (mt) cc_final: 0.9136 (mm) REVERT: B 1065 VAL cc_start: 0.9617 (t) cc_final: 0.8444 (t) REVERT: B 1108 ASN cc_start: 0.8210 (m-40) cc_final: 0.7359 (m-40) REVERT: C 118 LEU cc_start: 0.9721 (tp) cc_final: 0.9400 (mt) REVERT: C 201 PHE cc_start: 0.8939 (m-80) cc_final: 0.8368 (m-80) REVERT: C 266 TYR cc_start: 0.8089 (t80) cc_final: 0.7476 (t80) REVERT: C 365 TYR cc_start: 0.6810 (t80) cc_final: 0.6148 (t80) REVERT: C 654 GLU cc_start: 0.9491 (mt-10) cc_final: 0.9279 (mp0) REVERT: C 697 MET cc_start: 0.8070 (mtp) cc_final: 0.7822 (tpt) REVERT: C 702 GLU cc_start: 0.9410 (mt-10) cc_final: 0.9172 (mm-30) REVERT: C 708 SER cc_start: 0.9253 (m) cc_final: 0.8879 (t) REVERT: C 714 ILE cc_start: 0.9010 (mt) cc_final: 0.8751 (mp) REVERT: C 781 VAL cc_start: 0.9646 (t) cc_final: 0.9055 (m) REVERT: C 786 LYS cc_start: 0.9429 (tttt) cc_final: 0.9148 (mtmt) REVERT: C 865 LEU cc_start: 0.9235 (tp) cc_final: 0.8802 (tt) REVERT: C 927 PHE cc_start: 0.9321 (t80) cc_final: 0.8919 (t80) REVERT: C 1038 LYS cc_start: 0.9609 (mttt) cc_final: 0.9382 (mmmt) REVERT: C 1047 TYR cc_start: 0.8788 (m-80) cc_final: 0.8576 (m-10) REVERT: C 1108 ASN cc_start: 0.8197 (m-40) cc_final: 0.7476 (m-40) REVERT: C 1111 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8938 (mp0) REVERT: L 162 ARG cc_start: 0.9483 (tpt90) cc_final: 0.8763 (tpp80) REVERT: L 172 ASN cc_start: 0.9812 (m-40) cc_final: 0.9464 (t0) REVERT: M 4 MET cc_start: 0.8341 (tpp) cc_final: 0.7951 (tpp) REVERT: M 203 LYS cc_start: 0.9332 (tttt) cc_final: 0.9062 (mtmm) REVERT: M 219 GLN cc_start: 0.8979 (tt0) cc_final: 0.8779 (tt0) outliers start: 7 outliers final: 1 residues processed: 472 average time/residue: 0.4987 time to fit residues: 356.4734 Evaluate side-chains 239 residues out of total 3437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 235 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 10.0000 chunk 297 optimal weight: 7.9990 chunk 164 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 chunk 200 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 307 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 186 optimal weight: 0.8980 chunk 228 optimal weight: 2.9990 chunk 355 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A1005 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1005 GLN B1011 GLN B1054 GLN B1119 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN C 914 ASN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN L 144 GLN L 180 GLN ** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 167 GLN I 186 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.124 31953 Z= 0.388 Angle : 0.794 11.242 43480 Z= 0.422 Chirality : 0.049 0.719 5069 Planarity : 0.005 0.085 5557 Dihedral : 7.998 89.825 5172 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.82 % Favored : 98.13 % Rotamer: Outliers : 0.15 % Allowed : 1.54 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.13), residues: 3896 helix: 0.56 (0.19), residues: 688 sheet: 0.51 (0.15), residues: 1063 loop : 0.49 (0.14), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 104 HIS 0.009 0.002 HIS A 655 PHE 0.032 0.003 PHE A 377 TYR 0.028 0.003 TYR C 421 ARG 0.011 0.001 ARG I 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 252 time to evaluate : 3.642 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: A 211 ASN cc_start: 0.7986 (m-40) cc_final: 0.7640 (p0) REVERT: A 598 ILE cc_start: 0.9850 (mp) cc_final: 0.9358 (tt) REVERT: A 855 PHE cc_start: 0.8691 (p90) cc_final: 0.7985 (t80) REVERT: A 869 MET cc_start: 0.9679 (mtp) cc_final: 0.9467 (mtp) REVERT: A 927 PHE cc_start: 0.9517 (t80) cc_final: 0.9219 (t80) REVERT: A 1038 LYS cc_start: 0.9043 (mmpt) cc_final: 0.8664 (mmmt) REVERT: A 1041 ASP cc_start: 0.9158 (t0) cc_final: 0.8954 (t0) REVERT: A 1063 LEU cc_start: 0.9512 (mt) cc_final: 0.9276 (mt) REVERT: A 1065 VAL cc_start: 0.9415 (t) cc_final: 0.8869 (t) REVERT: B 88 ASP cc_start: 0.9500 (m-30) cc_final: 0.9214 (t0) REVERT: B 170 TYR cc_start: 0.9346 (t80) cc_final: 0.8866 (t80) REVERT: B 710 ASN cc_start: 0.9366 (m-40) cc_final: 0.9056 (m-40) REVERT: B 755 GLN cc_start: 0.9198 (mt0) cc_final: 0.8656 (mt0) REVERT: B 902 MET cc_start: 0.9519 (mmp) cc_final: 0.9141 (mmm) REVERT: B 927 PHE cc_start: 0.9509 (t80) cc_final: 0.8925 (t80) REVERT: B 990 GLU cc_start: 0.9765 (mt-10) cc_final: 0.9548 (tm-30) REVERT: B 1010 GLN cc_start: 0.9661 (mt0) cc_final: 0.9431 (pt0) REVERT: B 1040 VAL cc_start: 0.8866 (t) cc_final: 0.8448 (t) REVERT: B 1052 PHE cc_start: 0.9590 (m-10) cc_final: 0.9316 (m-10) REVERT: B 1065 VAL cc_start: 0.9700 (t) cc_final: 0.9091 (t) REVERT: B 1108 ASN cc_start: 0.8592 (m-40) cc_final: 0.8180 (m-40) REVERT: B 1113 GLN cc_start: 0.9489 (mm-40) cc_final: 0.9144 (mp10) REVERT: C 118 LEU cc_start: 0.9810 (tp) cc_final: 0.9482 (mp) REVERT: C 266 TYR cc_start: 0.8395 (t80) cc_final: 0.7848 (t80) REVERT: C 304 LYS cc_start: 0.9745 (mttt) cc_final: 0.9531 (tmtt) REVERT: C 365 TYR cc_start: 0.6848 (t80) cc_final: 0.6073 (t80) REVERT: C 740 MET cc_start: 0.9283 (mtp) cc_final: 0.8900 (ttm) REVERT: C 797 PHE cc_start: 0.8841 (m-80) cc_final: 0.8140 (m-10) REVERT: C 855 PHE cc_start: 0.8602 (p90) cc_final: 0.8094 (t80) REVERT: C 927 PHE cc_start: 0.9282 (t80) cc_final: 0.8821 (t80) REVERT: C 1101 HIS cc_start: 0.9484 (m90) cc_final: 0.9184 (m90) REVERT: C 1108 ASN cc_start: 0.8626 (m-40) cc_final: 0.8303 (m-40) REVERT: L 172 ASN cc_start: 0.9813 (m-40) cc_final: 0.9476 (t0) REVERT: I 115 MET cc_start: 0.8971 (mmm) cc_final: 0.8639 (tmm) outliers start: 5 outliers final: 1 residues processed: 257 average time/residue: 0.4760 time to fit residues: 192.3535 Evaluate side-chains 170 residues out of total 3437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 3.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 296 optimal weight: 2.9990 chunk 242 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 356 optimal weight: 20.0000 chunk 385 optimal weight: 5.9990 chunk 317 optimal weight: 3.9990 chunk 353 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 286 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1005 GLN B1119 ASN C 66 HIS C 125 ASN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 167 GLN ** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 31953 Z= 0.227 Angle : 0.618 7.866 43480 Z= 0.329 Chirality : 0.045 0.443 5069 Planarity : 0.004 0.060 5557 Dihedral : 6.921 80.754 5172 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.17 % Allowed : 1.75 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 3896 helix: 0.77 (0.19), residues: 688 sheet: 0.40 (0.15), residues: 1065 loop : 0.32 (0.14), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 41 HIS 0.005 0.001 HIS C1048 PHE 0.022 0.002 PHE A 201 TYR 0.025 0.002 TYR C 421 ARG 0.025 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 218 time to evaluate : 3.450 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.9309 (m-90) cc_final: 0.9094 (m-90) REVERT: A 855 PHE cc_start: 0.8672 (p90) cc_final: 0.7868 (t80) REVERT: A 869 MET cc_start: 0.9675 (mtp) cc_final: 0.9472 (mtp) REVERT: A 900 MET cc_start: 0.8780 (tpt) cc_final: 0.8446 (tpp) REVERT: A 1038 LYS cc_start: 0.9045 (mmpt) cc_final: 0.8705 (mmmt) REVERT: A 1063 LEU cc_start: 0.9517 (mt) cc_final: 0.9289 (mt) REVERT: A 1065 VAL cc_start: 0.9424 (t) cc_final: 0.8933 (t) REVERT: A 1118 ASP cc_start: 0.9114 (t70) cc_final: 0.8798 (p0) REVERT: B 170 TYR cc_start: 0.9418 (t80) cc_final: 0.8999 (t80) REVERT: B 710 ASN cc_start: 0.9229 (m-40) cc_final: 0.9002 (m110) REVERT: B 718 PHE cc_start: 0.9604 (p90) cc_final: 0.8966 (p90) REVERT: B 869 MET cc_start: 0.9581 (mtp) cc_final: 0.9282 (mtp) REVERT: B 927 PHE cc_start: 0.9437 (t80) cc_final: 0.8808 (t80) REVERT: B 1017 GLU cc_start: 0.9400 (tm-30) cc_final: 0.9195 (tm-30) REVERT: B 1052 PHE cc_start: 0.9555 (m-10) cc_final: 0.9284 (m-10) REVERT: B 1065 VAL cc_start: 0.9747 (t) cc_final: 0.9156 (t) REVERT: B 1108 ASN cc_start: 0.8573 (m-40) cc_final: 0.8188 (m-40) REVERT: C 118 LEU cc_start: 0.9800 (tp) cc_final: 0.9451 (mp) REVERT: C 201 PHE cc_start: 0.8996 (m-80) cc_final: 0.8449 (m-80) REVERT: C 304 LYS cc_start: 0.9724 (mttt) cc_final: 0.9429 (tmtt) REVERT: C 365 TYR cc_start: 0.7110 (t80) cc_final: 0.6448 (t80) REVERT: C 740 MET cc_start: 0.9203 (mtp) cc_final: 0.8942 (ttm) REVERT: C 855 PHE cc_start: 0.8576 (p90) cc_final: 0.7960 (t80) REVERT: C 869 MET cc_start: 0.9378 (ptp) cc_final: 0.9085 (ptp) REVERT: C 927 PHE cc_start: 0.9248 (t80) cc_final: 0.8647 (t80) REVERT: C 1038 LYS cc_start: 0.8783 (mmpt) cc_final: 0.8428 (mmmt) REVERT: C 1101 HIS cc_start: 0.9505 (m90) cc_final: 0.9255 (m90) REVERT: L 172 ASN cc_start: 0.9800 (m-40) cc_final: 0.9451 (t0) REVERT: M 4 MET cc_start: 0.9090 (tpt) cc_final: 0.7951 (ttm) REVERT: I 115 MET cc_start: 0.8860 (mmm) cc_final: 0.8500 (tmm) outliers start: 6 outliers final: 1 residues processed: 224 average time/residue: 0.4759 time to fit residues: 169.7111 Evaluate side-chains 164 residues out of total 3437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 3.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 6.9990 chunk 268 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 239 optimal weight: 5.9990 chunk 357 optimal weight: 5.9990 chunk 378 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 339 optimal weight: 20.0000 chunk 102 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN A 804 GLN A 935 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN A1135 ASN B 66 HIS B 87 ASN B 134 GLN B 188 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN C 66 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 GLN ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 209 HIS ** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.139 31953 Z= 0.437 Angle : 0.815 13.345 43480 Z= 0.427 Chirality : 0.046 0.366 5069 Planarity : 0.005 0.060 5557 Dihedral : 7.062 80.002 5172 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 30.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.06 % Allowed : 2.44 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.09 (0.13), residues: 3896 helix: 0.17 (0.18), residues: 700 sheet: -0.08 (0.15), residues: 1107 loop : 0.01 (0.14), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 41 HIS 0.010 0.002 HIS B 207 PHE 0.027 0.003 PHE A 377 TYR 0.054 0.003 TYR B 91 ARG 0.010 0.001 ARG I 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 181 time to evaluate : 3.597 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: A 104 TRP cc_start: 0.9466 (m-90) cc_final: 0.9264 (m-90) REVERT: A 598 ILE cc_start: 0.9838 (mp) cc_final: 0.9529 (tt) REVERT: A 927 PHE cc_start: 0.9597 (t80) cc_final: 0.9372 (t80) REVERT: A 1038 LYS cc_start: 0.9059 (mmpt) cc_final: 0.8786 (mmmt) REVERT: A 1063 LEU cc_start: 0.9557 (mt) cc_final: 0.9357 (mt) REVERT: A 1118 ASP cc_start: 0.9160 (t70) cc_final: 0.8884 (p0) REVERT: B 710 ASN cc_start: 0.9265 (m-40) cc_final: 0.9048 (m-40) REVERT: B 718 PHE cc_start: 0.9694 (p90) cc_final: 0.9214 (p90) REVERT: B 869 MET cc_start: 0.9525 (mtp) cc_final: 0.9266 (mtp) REVERT: B 927 PHE cc_start: 0.9467 (t80) cc_final: 0.8946 (t80) REVERT: B 1029 MET cc_start: 0.9011 (mtm) cc_final: 0.8809 (mtm) REVERT: C 118 LEU cc_start: 0.9800 (tp) cc_final: 0.9463 (mp) REVERT: C 201 PHE cc_start: 0.8977 (m-80) cc_final: 0.8660 (m-10) REVERT: C 266 TYR cc_start: 0.8470 (t80) cc_final: 0.7811 (t80) REVERT: C 365 TYR cc_start: 0.7200 (t80) cc_final: 0.6558 (t80) REVERT: C 697 MET cc_start: 0.8960 (tpp) cc_final: 0.8669 (mmp) REVERT: C 759 PHE cc_start: 0.9047 (t80) cc_final: 0.8421 (t80) REVERT: C 782 PHE cc_start: 0.9778 (m-10) cc_final: 0.9492 (m-80) REVERT: C 927 PHE cc_start: 0.9376 (t80) cc_final: 0.8837 (t80) REVERT: C 1038 LYS cc_start: 0.8887 (mmpt) cc_final: 0.8596 (mmmt) REVERT: C 1101 HIS cc_start: 0.9438 (m90) cc_final: 0.9224 (m90) REVERT: L 172 ASN cc_start: 0.9815 (m-40) cc_final: 0.9487 (t0) REVERT: H 115 MET cc_start: 0.8753 (tpp) cc_final: 0.8496 (tpp) REVERT: M 162 ARG cc_start: 0.9502 (tpt90) cc_final: 0.8934 (mmp80) REVERT: I 115 MET cc_start: 0.8902 (mmm) cc_final: 0.8614 (tmm) outliers start: 2 outliers final: 1 residues processed: 183 average time/residue: 0.4698 time to fit residues: 137.6069 Evaluate side-chains 131 residues out of total 3437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 3.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 282 optimal weight: 0.6980 chunk 156 optimal weight: 7.9990 chunk 323 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 193 optimal weight: 3.9990 chunk 340 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 762 GLN A1005 GLN A1023 ASN B 66 HIS ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1002 GLN B1005 GLN C 134 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 690 GLN C 762 GLN C 779 GLN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 GLN ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31953 Z= 0.235 Angle : 0.614 11.641 43480 Z= 0.324 Chirality : 0.046 0.551 5069 Planarity : 0.004 0.040 5557 Dihedral : 6.504 74.782 5172 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.15 % Allowed : 1.54 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.10 (0.13), residues: 3896 helix: 0.66 (0.19), residues: 705 sheet: -0.12 (0.15), residues: 1092 loop : 0.10 (0.14), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.005 0.001 HIS C1088 PHE 0.049 0.002 PHE B1109 TYR 0.028 0.002 TYR B 453 ARG 0.003 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 189 time to evaluate : 3.688 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: A 104 TRP cc_start: 0.9389 (m-90) cc_final: 0.9171 (m-90) REVERT: A 598 ILE cc_start: 0.9888 (mp) cc_final: 0.9485 (tt) REVERT: A 900 MET cc_start: 0.8724 (tpp) cc_final: 0.8282 (tpp) REVERT: A 1038 LYS cc_start: 0.9079 (mmpt) cc_final: 0.8692 (mmmt) REVERT: A 1062 PHE cc_start: 0.9531 (m-80) cc_final: 0.8798 (m-10) REVERT: A 1063 LEU cc_start: 0.9540 (mt) cc_final: 0.9332 (mt) REVERT: A 1110 TYR cc_start: 0.9394 (t80) cc_final: 0.8914 (t80) REVERT: A 1111 GLU cc_start: 0.9671 (mp0) cc_final: 0.9467 (pm20) REVERT: A 1118 ASP cc_start: 0.9155 (t70) cc_final: 0.8834 (p0) REVERT: B 170 TYR cc_start: 0.9545 (t80) cc_final: 0.9133 (t80) REVERT: B 710 ASN cc_start: 0.9188 (m-40) cc_final: 0.8978 (m110) REVERT: B 718 PHE cc_start: 0.9734 (p90) cc_final: 0.9086 (p90) REVERT: B 721 SER cc_start: 0.9347 (t) cc_final: 0.9098 (p) REVERT: B 773 GLU cc_start: 0.9612 (mm-30) cc_final: 0.8923 (tp30) REVERT: B 869 MET cc_start: 0.9609 (mtp) cc_final: 0.9307 (mtp) REVERT: B 927 PHE cc_start: 0.9438 (t80) cc_final: 0.8662 (t80) REVERT: C 118 LEU cc_start: 0.9815 (tp) cc_final: 0.9463 (mp) REVERT: C 201 PHE cc_start: 0.9021 (m-80) cc_final: 0.8595 (m-80) REVERT: C 266 TYR cc_start: 0.8477 (t80) cc_final: 0.7861 (t80) REVERT: C 365 TYR cc_start: 0.7243 (t80) cc_final: 0.6631 (t80) REVERT: C 718 PHE cc_start: 0.9623 (p90) cc_final: 0.9124 (p90) REVERT: C 782 PHE cc_start: 0.9796 (m-10) cc_final: 0.9468 (m-80) REVERT: C 927 PHE cc_start: 0.9381 (t80) cc_final: 0.8822 (t80) REVERT: C 1038 LYS cc_start: 0.8914 (mmpt) cc_final: 0.8602 (mmmt) REVERT: C 1101 HIS cc_start: 0.9419 (m90) cc_final: 0.9194 (m90) REVERT: L 172 ASN cc_start: 0.9815 (m-40) cc_final: 0.9481 (t0) REVERT: H 115 MET cc_start: 0.8679 (tpp) cc_final: 0.8431 (tpp) REVERT: I 115 MET cc_start: 0.8864 (mmm) cc_final: 0.8614 (tmm) outliers start: 5 outliers final: 2 residues processed: 194 average time/residue: 0.4594 time to fit residues: 144.3817 Evaluate side-chains 138 residues out of total 3437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 3.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 7.9990 chunk 341 optimal weight: 20.0000 chunk 74 optimal weight: 0.0570 chunk 222 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 379 optimal weight: 6.9990 chunk 314 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 199 optimal weight: 5.9990 overall best weight: 4.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A 913 GLN A 965 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS B1071 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.5440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 31953 Z= 0.365 Angle : 0.701 12.512 43480 Z= 0.371 Chirality : 0.045 0.349 5069 Planarity : 0.005 0.051 5557 Dihedral : 6.660 71.675 5172 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 29.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.18 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.16 (0.13), residues: 3896 helix: 0.37 (0.19), residues: 709 sheet: -0.27 (0.15), residues: 1104 loop : -0.04 (0.14), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 52 HIS 0.007 0.002 HIS B 655 PHE 0.021 0.002 PHE H 161 TYR 0.023 0.002 TYR B 453 ARG 0.012 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 3.602 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: A 104 TRP cc_start: 0.9432 (m-90) cc_final: 0.9190 (m-90) REVERT: A 731 MET cc_start: 0.9068 (tpp) cc_final: 0.8335 (tpp) REVERT: A 900 MET cc_start: 0.8827 (tpp) cc_final: 0.8373 (tpp) REVERT: A 927 PHE cc_start: 0.9614 (t80) cc_final: 0.9410 (t80) REVERT: A 933 LYS cc_start: 0.9804 (mttt) cc_final: 0.9478 (ptpp) REVERT: A 1038 LYS cc_start: 0.9088 (mmpt) cc_final: 0.8825 (mmmt) REVERT: A 1110 TYR cc_start: 0.9366 (t80) cc_final: 0.9142 (t80) REVERT: A 1118 ASP cc_start: 0.9265 (t70) cc_final: 0.8990 (p0) REVERT: B 170 TYR cc_start: 0.9592 (t80) cc_final: 0.9216 (t80) REVERT: B 194 PHE cc_start: 0.9027 (m-80) cc_final: 0.8769 (m-80) REVERT: B 718 PHE cc_start: 0.9690 (p90) cc_final: 0.9097 (p90) REVERT: B 721 SER cc_start: 0.9311 (t) cc_final: 0.9054 (p) REVERT: B 927 PHE cc_start: 0.9478 (t80) cc_final: 0.8753 (t80) REVERT: C 118 LEU cc_start: 0.9824 (tp) cc_final: 0.9488 (mp) REVERT: C 201 PHE cc_start: 0.9025 (m-80) cc_final: 0.8768 (m-10) REVERT: C 266 TYR cc_start: 0.8558 (t80) cc_final: 0.7930 (t80) REVERT: C 365 TYR cc_start: 0.7293 (t80) cc_final: 0.6816 (t80) REVERT: C 718 PHE cc_start: 0.9732 (p90) cc_final: 0.9251 (p90) REVERT: C 721 SER cc_start: 0.8611 (t) cc_final: 0.8324 (p) REVERT: C 740 MET cc_start: 0.9422 (ttm) cc_final: 0.9091 (ttm) REVERT: C 759 PHE cc_start: 0.8999 (t80) cc_final: 0.8609 (t80) REVERT: C 782 PHE cc_start: 0.9806 (m-10) cc_final: 0.9488 (m-80) REVERT: C 927 PHE cc_start: 0.9417 (t80) cc_final: 0.8866 (t80) REVERT: C 1038 LYS cc_start: 0.8824 (mmpt) cc_final: 0.8540 (mmmt) REVERT: C 1101 HIS cc_start: 0.9432 (m90) cc_final: 0.9199 (m90) REVERT: L 172 ASN cc_start: 0.9834 (m-40) cc_final: 0.9544 (t0) REVERT: H 115 MET cc_start: 0.8895 (tpp) cc_final: 0.8617 (tpp) REVERT: M 4 MET cc_start: 0.8765 (tpt) cc_final: 0.8518 (tpt) REVERT: I 115 MET cc_start: 0.8848 (mmm) cc_final: 0.8627 (tmm) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.4477 time to fit residues: 126.0244 Evaluate side-chains 122 residues out of total 3437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 3.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 216 optimal weight: 0.2980 chunk 276 optimal weight: 0.7980 chunk 214 optimal weight: 5.9990 chunk 319 optimal weight: 5.9990 chunk 211 optimal weight: 0.2980 chunk 377 optimal weight: 20.0000 chunk 236 optimal weight: 0.9990 chunk 230 optimal weight: 20.0000 chunk 174 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 907 ASN A 913 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31953 Z= 0.184 Angle : 0.584 8.754 43480 Z= 0.307 Chirality : 0.046 0.359 5069 Planarity : 0.004 0.049 5557 Dihedral : 6.131 67.029 5172 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.03 % Allowed : 0.61 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.09 (0.14), residues: 3896 helix: 0.82 (0.20), residues: 708 sheet: -0.12 (0.15), residues: 1077 loop : 0.02 (0.14), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.004 0.001 HIS L 218 PHE 0.015 0.001 PHE L 159 TYR 0.019 0.002 TYR B 453 ARG 0.010 0.001 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 3.845 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: A 104 TRP cc_start: 0.9331 (m-90) cc_final: 0.9097 (m-90) REVERT: A 731 MET cc_start: 0.8838 (tpp) cc_final: 0.8419 (tpp) REVERT: A 855 PHE cc_start: 0.8276 (p90) cc_final: 0.7387 (t80) REVERT: A 869 MET cc_start: 0.9643 (mtp) cc_final: 0.9440 (mtp) REVERT: A 900 MET cc_start: 0.8712 (tpp) cc_final: 0.8259 (tpp) REVERT: A 927 PHE cc_start: 0.9565 (t80) cc_final: 0.9347 (t80) REVERT: A 933 LYS cc_start: 0.9783 (mttt) cc_final: 0.9500 (ptpt) REVERT: A 1038 LYS cc_start: 0.9080 (mmpt) cc_final: 0.8762 (mmmt) REVERT: A 1062 PHE cc_start: 0.9547 (m-80) cc_final: 0.8765 (m-10) REVERT: A 1063 LEU cc_start: 0.9555 (mt) cc_final: 0.9304 (mt) REVERT: A 1118 ASP cc_start: 0.9214 (t70) cc_final: 0.8920 (p0) REVERT: B 170 TYR cc_start: 0.9579 (t80) cc_final: 0.9161 (t80) REVERT: B 194 PHE cc_start: 0.8991 (m-80) cc_final: 0.8724 (m-80) REVERT: B 710 ASN cc_start: 0.9187 (m-40) cc_final: 0.8948 (m-40) REVERT: B 718 PHE cc_start: 0.9752 (p90) cc_final: 0.9201 (p90) REVERT: B 721 SER cc_start: 0.9339 (t) cc_final: 0.9132 (p) REVERT: B 773 GLU cc_start: 0.9644 (mm-30) cc_final: 0.9068 (tp30) REVERT: B 869 MET cc_start: 0.9643 (mtp) cc_final: 0.9412 (mtp) REVERT: B 927 PHE cc_start: 0.9417 (t80) cc_final: 0.8632 (t80) REVERT: B 1065 VAL cc_start: 0.9849 (t) cc_final: 0.9590 (t) REVERT: C 118 LEU cc_start: 0.9816 (tp) cc_final: 0.9481 (mp) REVERT: C 201 PHE cc_start: 0.8996 (m-80) cc_final: 0.8675 (m-80) REVERT: C 266 TYR cc_start: 0.8443 (t80) cc_final: 0.7898 (t80) REVERT: C 365 TYR cc_start: 0.7323 (t80) cc_final: 0.6746 (t80) REVERT: C 718 PHE cc_start: 0.9707 (p90) cc_final: 0.9109 (p90) REVERT: C 721 SER cc_start: 0.8533 (t) cc_final: 0.8278 (p) REVERT: C 740 MET cc_start: 0.9437 (ttm) cc_final: 0.9094 (ttp) REVERT: C 759 PHE cc_start: 0.8912 (t80) cc_final: 0.8677 (t80) REVERT: C 776 LYS cc_start: 0.9751 (mtmm) cc_final: 0.9534 (ptpp) REVERT: C 782 PHE cc_start: 0.9813 (m-10) cc_final: 0.9412 (m-80) REVERT: C 927 PHE cc_start: 0.9421 (t80) cc_final: 0.8847 (t80) REVERT: C 1038 LYS cc_start: 0.8911 (mmpt) cc_final: 0.8566 (mmmt) REVERT: C 1101 HIS cc_start: 0.9501 (m90) cc_final: 0.9288 (m90) REVERT: C 1108 ASN cc_start: 0.8802 (m-40) cc_final: 0.8308 (p0) REVERT: L 172 ASN cc_start: 0.9831 (m-40) cc_final: 0.9522 (t0) REVERT: H 115 MET cc_start: 0.8868 (tpp) cc_final: 0.8666 (tpp) REVERT: I 115 MET cc_start: 0.8846 (mmm) cc_final: 0.8616 (tmm) outliers start: 1 outliers final: 1 residues processed: 185 average time/residue: 0.4604 time to fit residues: 138.0200 Evaluate side-chains 138 residues out of total 3437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 3.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 73 optimal weight: 0.5980 chunk 240 optimal weight: 7.9990 chunk 257 optimal weight: 10.0000 chunk 186 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 296 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31953 Z= 0.177 Angle : 0.555 8.434 43480 Z= 0.293 Chirality : 0.045 0.468 5069 Planarity : 0.004 0.054 5557 Dihedral : 5.747 60.837 5172 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.06 % Allowed : 0.49 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.19 (0.14), residues: 3896 helix: 1.03 (0.20), residues: 695 sheet: -0.03 (0.16), residues: 1058 loop : 0.02 (0.14), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 104 HIS 0.005 0.001 HIS M 218 PHE 0.016 0.001 PHE A 782 TYR 0.036 0.001 TYR B 37 ARG 0.012 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 183 time to evaluate : 3.496 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: A 104 TRP cc_start: 0.9395 (m-90) cc_final: 0.9192 (m-90) REVERT: A 697 MET cc_start: 0.9601 (tpp) cc_final: 0.8931 (mmm) REVERT: A 731 MET cc_start: 0.8909 (tpp) cc_final: 0.8405 (tpp) REVERT: A 855 PHE cc_start: 0.8327 (p90) cc_final: 0.7548 (t80) REVERT: A 900 MET cc_start: 0.8660 (tpp) cc_final: 0.8168 (tpp) REVERT: A 933 LYS cc_start: 0.9791 (mttt) cc_final: 0.9477 (ptpp) REVERT: A 1018 ILE cc_start: 0.9696 (mm) cc_final: 0.9490 (tt) REVERT: A 1038 LYS cc_start: 0.9039 (mmpt) cc_final: 0.8797 (mmmt) REVERT: A 1062 PHE cc_start: 0.9542 (m-80) cc_final: 0.8785 (m-10) REVERT: A 1063 LEU cc_start: 0.9534 (mt) cc_final: 0.9283 (mt) REVERT: A 1118 ASP cc_start: 0.9214 (t70) cc_final: 0.8948 (p0) REVERT: B 104 TRP cc_start: 0.9029 (m-90) cc_final: 0.8763 (m-10) REVERT: B 170 TYR cc_start: 0.9616 (t80) cc_final: 0.9245 (t80) REVERT: B 194 PHE cc_start: 0.9069 (m-80) cc_final: 0.7689 (m-80) REVERT: B 710 ASN cc_start: 0.9190 (m-40) cc_final: 0.8924 (m110) REVERT: B 718 PHE cc_start: 0.9754 (p90) cc_final: 0.9125 (p90) REVERT: B 721 SER cc_start: 0.9325 (t) cc_final: 0.9095 (p) REVERT: B 773 GLU cc_start: 0.9639 (mm-30) cc_final: 0.9033 (tp30) REVERT: B 775 ASP cc_start: 0.9298 (m-30) cc_final: 0.9049 (m-30) REVERT: B 858 LEU cc_start: 0.9384 (pp) cc_final: 0.9127 (pt) REVERT: B 869 MET cc_start: 0.9660 (mtp) cc_final: 0.9436 (mtp) REVERT: B 927 PHE cc_start: 0.9406 (t80) cc_final: 0.8663 (t80) REVERT: B 1019 ARG cc_start: 0.9709 (ptm-80) cc_final: 0.9241 (ptm-80) REVERT: B 1065 VAL cc_start: 0.9833 (t) cc_final: 0.9611 (t) REVERT: C 118 LEU cc_start: 0.9796 (tp) cc_final: 0.9452 (mp) REVERT: C 201 PHE cc_start: 0.9074 (m-80) cc_final: 0.8739 (m-80) REVERT: C 266 TYR cc_start: 0.8397 (t80) cc_final: 0.7882 (t80) REVERT: C 365 TYR cc_start: 0.7308 (t80) cc_final: 0.6707 (t80) REVERT: C 718 PHE cc_start: 0.9703 (p90) cc_final: 0.8882 (p90) REVERT: C 721 SER cc_start: 0.8543 (t) cc_final: 0.8306 (p) REVERT: C 740 MET cc_start: 0.9471 (ttm) cc_final: 0.9146 (ttm) REVERT: C 759 PHE cc_start: 0.8927 (t80) cc_final: 0.8397 (t80) REVERT: C 782 PHE cc_start: 0.9806 (m-10) cc_final: 0.9408 (m-80) REVERT: C 869 MET cc_start: 0.9336 (ptp) cc_final: 0.9112 (ptp) REVERT: C 927 PHE cc_start: 0.9438 (t80) cc_final: 0.8841 (t80) REVERT: C 1038 LYS cc_start: 0.8979 (mmpt) cc_final: 0.8634 (mmmt) REVERT: C 1101 HIS cc_start: 0.9523 (m90) cc_final: 0.9319 (m90) REVERT: L 172 ASN cc_start: 0.9833 (m-40) cc_final: 0.9527 (t0) REVERT: H 115 MET cc_start: 0.8967 (tpp) cc_final: 0.8766 (tpp) REVERT: I 91 MET cc_start: 0.8985 (mpp) cc_final: 0.8746 (mpp) REVERT: I 115 MET cc_start: 0.8819 (mmm) cc_final: 0.8606 (tmm) outliers start: 2 outliers final: 0 residues processed: 185 average time/residue: 0.4516 time to fit residues: 134.6386 Evaluate side-chains 138 residues out of total 3437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 3.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 4.9990 chunk 361 optimal weight: 7.9990 chunk 330 optimal weight: 20.0000 chunk 352 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 276 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 318 optimal weight: 0.7980 chunk 332 optimal weight: 0.5980 chunk 350 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A1005 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1005 GLN C 23 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31953 Z= 0.189 Angle : 0.550 8.448 43480 Z= 0.291 Chirality : 0.044 0.371 5069 Planarity : 0.004 0.056 5557 Dihedral : 5.605 56.311 5172 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.09 % Allowed : 0.32 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.19 (0.14), residues: 3896 helix: 1.05 (0.20), residues: 696 sheet: -0.05 (0.16), residues: 1086 loop : 0.03 (0.14), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1102 HIS 0.003 0.001 HIS C 66 PHE 0.013 0.001 PHE C 374 TYR 0.020 0.001 TYR A 789 ARG 0.013 0.000 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 177 time to evaluate : 3.325 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: A 104 TRP cc_start: 0.9343 (m-90) cc_final: 0.9135 (m-90) REVERT: A 697 MET cc_start: 0.9557 (tpp) cc_final: 0.8809 (mmp) REVERT: A 731 MET cc_start: 0.8819 (tpp) cc_final: 0.8351 (tpp) REVERT: A 855 PHE cc_start: 0.8321 (p90) cc_final: 0.7626 (t80) REVERT: A 900 MET cc_start: 0.8637 (tpp) cc_final: 0.8162 (tpp) REVERT: A 927 PHE cc_start: 0.9579 (t80) cc_final: 0.9353 (t80) REVERT: A 933 LYS cc_start: 0.9791 (mttt) cc_final: 0.9476 (ptpp) REVERT: A 1038 LYS cc_start: 0.9037 (mmpt) cc_final: 0.8795 (mmmt) REVERT: A 1062 PHE cc_start: 0.9524 (m-80) cc_final: 0.8696 (m-10) REVERT: A 1063 LEU cc_start: 0.9527 (mt) cc_final: 0.9280 (mt) REVERT: A 1118 ASP cc_start: 0.9216 (t70) cc_final: 0.8959 (p0) REVERT: B 104 TRP cc_start: 0.9048 (m-90) cc_final: 0.8770 (m-10) REVERT: B 170 TYR cc_start: 0.9626 (t80) cc_final: 0.9252 (t80) REVERT: B 194 PHE cc_start: 0.9181 (m-80) cc_final: 0.7605 (m-80) REVERT: B 710 ASN cc_start: 0.9188 (m-40) cc_final: 0.8919 (m110) REVERT: B 718 PHE cc_start: 0.9753 (p90) cc_final: 0.9112 (p90) REVERT: B 721 SER cc_start: 0.9326 (t) cc_final: 0.9086 (p) REVERT: B 773 GLU cc_start: 0.9640 (mm-30) cc_final: 0.8995 (tp30) REVERT: B 775 ASP cc_start: 0.9330 (m-30) cc_final: 0.9081 (m-30) REVERT: B 869 MET cc_start: 0.9660 (mtp) cc_final: 0.9441 (mtp) REVERT: B 927 PHE cc_start: 0.9413 (t80) cc_final: 0.8666 (t80) REVERT: B 1065 VAL cc_start: 0.9834 (t) cc_final: 0.9609 (t) REVERT: C 118 LEU cc_start: 0.9799 (tp) cc_final: 0.9432 (mp) REVERT: C 177 MET cc_start: 0.9116 (mmt) cc_final: 0.8583 (mmm) REVERT: C 201 PHE cc_start: 0.9065 (m-80) cc_final: 0.8738 (m-80) REVERT: C 266 TYR cc_start: 0.8387 (t80) cc_final: 0.7865 (t80) REVERT: C 365 TYR cc_start: 0.7314 (t80) cc_final: 0.6727 (t80) REVERT: C 718 PHE cc_start: 0.9701 (p90) cc_final: 0.8935 (p90) REVERT: C 721 SER cc_start: 0.8550 (t) cc_final: 0.8296 (p) REVERT: C 740 MET cc_start: 0.9466 (ttm) cc_final: 0.9135 (ttm) REVERT: C 759 PHE cc_start: 0.8960 (t80) cc_final: 0.8402 (t80) REVERT: C 782 PHE cc_start: 0.9802 (m-10) cc_final: 0.9415 (m-80) REVERT: C 869 MET cc_start: 0.9342 (ptp) cc_final: 0.9096 (ptp) REVERT: C 925 ASN cc_start: 0.9419 (m110) cc_final: 0.9143 (p0) REVERT: C 927 PHE cc_start: 0.9423 (t80) cc_final: 0.8823 (t80) REVERT: C 1038 LYS cc_start: 0.8968 (mmpt) cc_final: 0.8609 (mmmt) REVERT: C 1101 HIS cc_start: 0.9518 (m90) cc_final: 0.9307 (m90) REVERT: L 172 ASN cc_start: 0.9837 (m-40) cc_final: 0.9539 (t0) REVERT: H 39 MET cc_start: 0.6871 (tmm) cc_final: 0.6644 (tmm) REVERT: H 115 MET cc_start: 0.8983 (tpp) cc_final: 0.8774 (tpp) REVERT: I 91 MET cc_start: 0.9008 (mpp) cc_final: 0.8803 (mpp) REVERT: I 115 MET cc_start: 0.8806 (mmm) cc_final: 0.8598 (tmm) outliers start: 3 outliers final: 0 residues processed: 180 average time/residue: 0.4423 time to fit residues: 129.5913 Evaluate side-chains 134 residues out of total 3437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 3.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 30.0000 chunk 372 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 258 optimal weight: 0.4980 chunk 390 optimal weight: 8.9990 chunk 359 optimal weight: 3.9990 chunk 310 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 240 optimal weight: 0.7980 chunk 190 optimal weight: 6.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 134 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31953 Z= 0.196 Angle : 0.550 8.377 43480 Z= 0.291 Chirality : 0.044 0.331 5069 Planarity : 0.004 0.056 5557 Dihedral : 5.510 52.109 5172 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.06 % Allowed : 0.23 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.18 (0.14), residues: 3896 helix: 1.09 (0.20), residues: 699 sheet: -0.08 (0.16), residues: 1076 loop : 0.01 (0.14), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C1102 HIS 0.005 0.001 HIS C 66 PHE 0.024 0.001 PHE C 92 TYR 0.025 0.001 TYR B 37 ARG 0.005 0.000 ARG C 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 174 time to evaluate : 3.508 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: A 104 TRP cc_start: 0.9331 (m-90) cc_final: 0.9129 (m-90) REVERT: A 598 ILE cc_start: 0.9887 (mp) cc_final: 0.9512 (tt) REVERT: A 697 MET cc_start: 0.9568 (tpp) cc_final: 0.8868 (mmm) REVERT: A 718 PHE cc_start: 0.9517 (p90) cc_final: 0.9116 (p90) REVERT: A 731 MET cc_start: 0.8875 (tpp) cc_final: 0.8608 (tpp) REVERT: A 855 PHE cc_start: 0.8471 (p90) cc_final: 0.7714 (t80) REVERT: A 900 MET cc_start: 0.8566 (tpp) cc_final: 0.8049 (tpp) REVERT: A 927 PHE cc_start: 0.9584 (t80) cc_final: 0.9355 (t80) REVERT: A 933 LYS cc_start: 0.9793 (mttt) cc_final: 0.9480 (ptpp) REVERT: A 1038 LYS cc_start: 0.9050 (mmpt) cc_final: 0.8812 (mmmt) REVERT: A 1062 PHE cc_start: 0.9506 (m-80) cc_final: 0.8675 (m-10) REVERT: A 1063 LEU cc_start: 0.9523 (mt) cc_final: 0.9282 (mt) REVERT: A 1118 ASP cc_start: 0.9225 (t70) cc_final: 0.8961 (p0) REVERT: B 104 TRP cc_start: 0.9085 (m-90) cc_final: 0.8768 (m-10) REVERT: B 170 TYR cc_start: 0.9621 (t80) cc_final: 0.9250 (t80) REVERT: B 194 PHE cc_start: 0.9205 (m-80) cc_final: 0.7642 (m-80) REVERT: B 710 ASN cc_start: 0.9233 (m-40) cc_final: 0.8998 (m-40) REVERT: B 721 SER cc_start: 0.9344 (t) cc_final: 0.9090 (p) REVERT: B 773 GLU cc_start: 0.9617 (mm-30) cc_final: 0.8866 (tp30) REVERT: B 775 ASP cc_start: 0.9348 (m-30) cc_final: 0.9119 (m-30) REVERT: B 858 LEU cc_start: 0.9371 (pp) cc_final: 0.9101 (pt) REVERT: B 869 MET cc_start: 0.9661 (mtp) cc_final: 0.9448 (mtp) REVERT: B 927 PHE cc_start: 0.9417 (t80) cc_final: 0.8718 (t80) REVERT: B 1065 VAL cc_start: 0.9840 (t) cc_final: 0.9620 (t) REVERT: C 118 LEU cc_start: 0.9800 (tp) cc_final: 0.9444 (mt) REVERT: C 177 MET cc_start: 0.9106 (mmt) cc_final: 0.8571 (mmm) REVERT: C 201 PHE cc_start: 0.9068 (m-80) cc_final: 0.8775 (m-80) REVERT: C 266 TYR cc_start: 0.8277 (t80) cc_final: 0.7762 (t80) REVERT: C 365 TYR cc_start: 0.7324 (t80) cc_final: 0.6686 (t80) REVERT: C 718 PHE cc_start: 0.9714 (p90) cc_final: 0.9108 (p90) REVERT: C 721 SER cc_start: 0.8560 (t) cc_final: 0.8312 (p) REVERT: C 740 MET cc_start: 0.9446 (ttm) cc_final: 0.9102 (ttm) REVERT: C 759 PHE cc_start: 0.8976 (t80) cc_final: 0.8432 (t80) REVERT: C 782 PHE cc_start: 0.9796 (m-10) cc_final: 0.9438 (m-80) REVERT: C 869 MET cc_start: 0.9327 (ptp) cc_final: 0.9077 (ptp) REVERT: C 925 ASN cc_start: 0.9422 (m110) cc_final: 0.9144 (p0) REVERT: C 927 PHE cc_start: 0.9426 (t80) cc_final: 0.8846 (t80) REVERT: C 1038 LYS cc_start: 0.8996 (mmpt) cc_final: 0.8651 (mmmt) REVERT: C 1101 HIS cc_start: 0.9523 (m90) cc_final: 0.9313 (m90) REVERT: L 172 ASN cc_start: 0.9846 (m-40) cc_final: 0.9550 (t0) REVERT: I 115 MET cc_start: 0.8796 (mmm) cc_final: 0.8595 (tmm) outliers start: 2 outliers final: 0 residues processed: 176 average time/residue: 0.4707 time to fit residues: 133.8476 Evaluate side-chains 131 residues out of total 3437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 6.9990 chunk 331 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 286 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 311 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 319 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1005 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.040529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.032176 restraints weight = 429221.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.033055 restraints weight = 217431.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.033605 restraints weight = 137483.662| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 31953 Z= 0.381 Angle : 0.726 11.117 43480 Z= 0.386 Chirality : 0.045 0.310 5069 Planarity : 0.005 0.069 5557 Dihedral : 6.172 55.763 5172 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 32.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.90 % Favored : 95.07 % Rotamer: Outliers : 0.06 % Allowed : 0.12 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.13), residues: 3896 helix: 0.20 (0.19), residues: 715 sheet: -0.33 (0.16), residues: 1060 loop : -0.22 (0.14), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP B 152 HIS 0.006 0.002 HIS L 218 PHE 0.021 0.002 PHE B1052 TYR 0.027 0.002 TYR A 789 ARG 0.010 0.001 ARG A1014 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5381.23 seconds wall clock time: 102 minutes 4.61 seconds (6124.61 seconds total)