Starting phenix.real_space_refine on Sat Apr 13 11:59:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xcn_22128/04_2024/6xcn_22128.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xcn_22128/04_2024/6xcn_22128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xcn_22128/04_2024/6xcn_22128.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xcn_22128/04_2024/6xcn_22128.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xcn_22128/04_2024/6xcn_22128.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xcn_22128/04_2024/6xcn_22128.pdb" } resolution = 3.66 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= 0.004 sd= 0.024 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 123 5.16 5 C 18228 2.51 5 N 4680 2.21 5 O 5631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "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 TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A GLU 990": "OE1" <-> "OE2" 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 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "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 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1118": "OD1" <-> "OD2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 191": "OE1" <-> "OE2" Residue "E TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 346": "NH1" <-> "NH2" Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 408": "NH1" <-> "NH2" Residue "E TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 454": "NH1" <-> "NH2" Residue "E ARG 457": "NH1" <-> "NH2" Residue "E ARG 466": "NH1" <-> "NH2" Residue "E GLU 471": "OE1" <-> "OE2" Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 868": "OE1" <-> "OE2" Residue "E PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 985": "OD1" <-> "OD2" Residue "E GLU 990": "OE1" <-> "OE2" Residue "E TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1118": "OD1" <-> "OD2" Residue "E PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 61": "OD1" <-> "OD2" Residue "B ASP 72": "OD1" <-> "OD2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 61": "OD1" <-> "OD2" Residue "F ASP 72": "OD1" <-> "OD2" Residue "F ASP 86": "OD1" <-> "OD2" Residue "F TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 61": "OD1" <-> "OD2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 27": "OD1" <-> "OD2" Residue "D TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 50": "OE1" <-> "OE2" Residue "D ASP 82": "OD1" <-> "OD2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 27": "OD1" <-> "OD2" Residue "G TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 50": "OE1" <-> "OE2" Residue "G ASP 82": "OD1" <-> "OD2" Residue "G TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 27": "OD1" <-> "OD2" Residue "L TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 50": "OE1" <-> "OE2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 28662 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7581 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 985, 7578 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 936} Chain breaks: 11 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 84 Conformer: "B" Number of residues, atoms: 985, 7578 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 936} Chain breaks: 11 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 84 bond proxies already assigned to first conformer: 7742 Chain: "C" Number of atoms: 7581 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 985, 7578 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 936} Chain breaks: 11 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 84 Conformer: "B" Number of residues, atoms: 985, 7578 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 936} Chain breaks: 11 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 84 bond proxies already assigned to first conformer: 7742 Chain: "E" Number of atoms: 7581 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 985, 7578 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 936} Chain breaks: 11 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 84 Conformer: "B" Number of residues, atoms: 985, 7578 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 936} Chain breaks: 11 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 84 bond proxies already assigned to first conformer: 7742 Chain: "B" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 890 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "F" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 890 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "H" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 890 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "D" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 810 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "G" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 810 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 810 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "I" 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: 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: "M" 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "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: "Q" 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: "R" 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: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "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: "C" 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: "E" 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 Time building chain proxies: 25.69, per 1000 atoms: 0.90 Number of scatterers: 28662 At special positions: 0 Unit cell: (133.76, 139.612, 219.868, 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 123 16.00 O 5631 8.00 N 4680 7.00 C 18228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.02 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.02 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.02 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " BETA1-6 " NAG N 1 " - " FUC N 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG X 1 " - " FUC X 3 " NAG-ASN " NAG A1305 " - " ASN A 61 " " NAG A1306 " - " ASN A 122 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 234 " " NAG A1309 " - " ASN A 282 " " NAG A1310 " - " ASN A 603 " " NAG A1311 " - " ASN A 616 " " NAG A1312 " - " ASN A 709 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 122 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 234 " " NAG C1309 " - " ASN C 282 " " NAG C1310 " - " ASN C 603 " " NAG C1311 " - " ASN C 616 " " NAG C1312 " - " ASN C 709 " " NAG E1305 " - " ASN E 61 " " NAG E1306 " - " ASN E 122 " " NAG E1307 " - " ASN E 165 " " NAG E1308 " - " ASN E 234 " " NAG E1309 " - " ASN E 282 " " NAG E1310 " - " ASN E 603 " " NAG E1311 " - " ASN E 616 " " NAG E1312 " - " ASN E 709 " " NAG I 1 " - " ASN A 331 " " NAG J 1 " - " ASN A 343 " " NAG K 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN C 331 " " NAG P 1 " - " ASN C 343 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1134 " " NAG T 1 " - " ASN E 331 " " NAG U 1 " - " ASN E 343 " " NAG V 1 " - " ASN E 717 " " NAG W 1 " - " ASN E 801 " " NAG X 1 " - " ASN E1134 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.77 Conformation dependent library (CDL) restraints added in 9.6 seconds 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6732 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 69 sheets defined 21.9% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.746A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.397A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.581A pdb=" N VAL A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 737 through 743 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 758 through 783 removed outlier: 4.128A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.154A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (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 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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.171A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.539A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.745A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.399A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.581A pdb=" N VAL C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 743 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 758 through 783 removed outlier: 4.128A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.154A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 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 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.171A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.539A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.745A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 370 removed outlier: 4.398A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.581A pdb=" N VAL E 407 " --> pdb=" O ARG E 403 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG E 408 " --> pdb=" O GLY E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 506 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 removed outlier: 4.128A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 825 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 890 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.154A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 965 Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 5.171A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1147 removed outlier: 4.539A pdb=" N GLU E1144 " --> pdb=" O PRO E1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'H' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.563A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.271A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.769A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.795A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 52 through 55 removed outlier: 3.853A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.783A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.765A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.209A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.983A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.466A 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 654 through 655 removed outlier: 6.270A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 719 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 719 removed outlier: 7.024A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.803A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1123 Processing sheet with id=AC2, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.563A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.272A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.769A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 48 through 49 removed outlier: 6.795A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 52 through 55 removed outlier: 3.854A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.783A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 128 through 129 Processing sheet with id=AC8, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.765A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.209A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.983A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.466A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.270A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 702 through 704 Processing sheet with id=AD6, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AD7, first strand: chain 'C' and resid 718 through 719 Processing sheet with id=AD8, first strand: chain 'C' and resid 718 through 719 removed outlier: 7.025A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'C' and resid 1120 through 1123 Processing sheet with id=AE2, first strand: chain 'E' and resid 29 through 31 removed outlier: 3.563A pdb=" N SER E 60 " --> pdb=" O SER E 31 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 36 through 37 removed outlier: 7.271A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 10.768A pdb=" N LEU E 223 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N HIS E 207 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL E 227 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN E 188 " --> pdb=" O GLU E 96 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 48 through 49 removed outlier: 6.795A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 52 through 55 removed outlier: 3.853A pdb=" N ASP E 53 " --> pdb=" O ARG E 273 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.783A pdb=" N ILE E 105 " --> pdb=" O GLN E 239 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AE8, first strand: chain 'E' and resid 311 through 319 removed outlier: 3.765A pdb=" N TYR E 313 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 324 through 328 removed outlier: 4.209A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR E 553 " --> pdb=" O ASP E 586 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY E 566 " --> pdb=" O ASP E 574 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 357 through 358 removed outlier: 3.984A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.466A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.270A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY E 667 " --> pdb=" O ILE E 670 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ALA E 672 " --> pdb=" O PRO E 665 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 711 through 715 Processing sheet with id=AF6, first strand: chain 'E' and resid 718 through 719 Processing sheet with id=AF7, first strand: chain 'E' and resid 718 through 719 removed outlier: 7.025A pdb=" N GLY E1059 " --> pdb=" O SER E1055 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N SER E1055 " --> pdb=" O GLY E1059 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL E1061 " --> pdb=" O PRO E1053 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU E1063 " --> pdb=" O SER E1051 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER E1051 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL E1065 " --> pdb=" O LEU E1049 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AF9, first strand: chain 'E' and resid 1120 through 1123 Processing sheet with id=AG1, first strand: chain 'B' and resid 57 through 58 removed outlier: 3.580A pdb=" N TYR B 58 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR B 102 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 68 through 70 Processing sheet with id=AG3, first strand: chain 'F' and resid 57 through 58 removed outlier: 3.581A pdb=" N TYR F 58 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TYR F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 68 through 70 Processing sheet with id=AG5, first strand: chain 'H' and resid 57 through 58 removed outlier: 3.580A pdb=" N TYR H 58 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 68 through 70 Processing sheet with id=AG7, first strand: chain 'D' and resid 9 through 11 removed outlier: 5.733A pdb=" N TRP D 35 " --> pdb=" O MET D 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 9 through 11 Processing sheet with id=AG9, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AH1, first strand: chain 'G' and resid 9 through 11 removed outlier: 5.733A pdb=" N TRP G 35 " --> pdb=" O MET G 47 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 9 through 11 Processing sheet with id=AH3, first strand: chain 'G' and resid 19 through 24 Processing sheet with id=AH4, first strand: chain 'L' and resid 9 through 11 removed outlier: 5.734A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AH6, first strand: chain 'L' and resid 19 through 24 1006 hydrogen bonds defined for protein. 2676 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: 14.79 Time building geometry restraints manager: 13.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9050 1.34 - 1.46: 7505 1.46 - 1.58: 12575 1.58 - 1.70: 3 1.70 - 1.83: 156 Bond restraints: 29289 Sorted by residual: bond pdb=" CA LEU A 189 " pdb=" CB LEU A 189 " ideal model delta sigma weight residual 1.528 1.486 0.041 1.39e-02 5.18e+03 8.83e+00 bond pdb=" CA LEU C 189 " pdb=" CB LEU C 189 " ideal model delta sigma weight residual 1.528 1.486 0.041 1.39e-02 5.18e+03 8.71e+00 bond pdb=" CA LEU E 189 " pdb=" CB LEU E 189 " ideal model delta sigma weight residual 1.528 1.487 0.041 1.39e-02 5.18e+03 8.59e+00 bond pdb=" C PHE C 559 " pdb=" N LEU C 560 " ideal model delta sigma weight residual 1.329 1.243 0.086 3.03e-02 1.09e+03 8.08e+00 bond pdb=" C PHE E 559 " pdb=" N LEU E 560 " ideal model delta sigma weight residual 1.329 1.243 0.086 3.03e-02 1.09e+03 8.05e+00 ... (remaining 29284 not shown) Histogram of bond angle deviations from ideal: 97.30 - 104.64: 500 104.64 - 111.99: 14697 111.99 - 119.34: 9230 119.34 - 126.69: 15112 126.69 - 134.04: 325 Bond angle restraints: 39864 Sorted by residual: angle pdb=" CA GLU F 85 " pdb=" CB GLU F 85 " pdb=" CG GLU F 85 " ideal model delta sigma weight residual 114.10 127.20 -13.10 2.00e+00 2.50e-01 4.29e+01 angle pdb=" CA GLU H 85 " pdb=" CB GLU H 85 " pdb=" CG GLU H 85 " ideal model delta sigma weight residual 114.10 127.18 -13.08 2.00e+00 2.50e-01 4.28e+01 angle pdb=" CA GLU B 85 " pdb=" CB GLU B 85 " pdb=" CG GLU B 85 " ideal model delta sigma weight residual 114.10 127.17 -13.07 2.00e+00 2.50e-01 4.27e+01 angle pdb=" N PHE A 133 " pdb=" CA PHE A 133 " pdb=" C PHE A 133 " ideal model delta sigma weight residual 110.33 115.75 -5.42 1.29e+00 6.01e-01 1.76e+01 angle pdb=" N PHE C 133 " pdb=" CA PHE C 133 " pdb=" C PHE C 133 " ideal model delta sigma weight residual 110.33 115.72 -5.39 1.29e+00 6.01e-01 1.75e+01 ... (remaining 39859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.76: 16489 19.76 - 39.52: 1280 39.52 - 59.28: 195 59.28 - 79.05: 50 79.05 - 98.81: 73 Dihedral angle restraints: 18087 sinusoidal: 7578 harmonic: 10509 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.32 -86.32 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS E1032 " pdb=" SG CYS E1032 " pdb=" SG CYS E1043 " pdb=" CB CYS E1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.31 -86.31 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.31 -86.31 1 1.00e+01 1.00e-02 8.98e+01 ... (remaining 18084 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3252 0.052 - 0.103: 1237 0.103 - 0.155: 189 0.155 - 0.207: 20 0.207 - 0.258: 12 Chirality restraints: 4710 Sorted by residual: chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C5 BMA V 3 " pdb=" C4 BMA V 3 " pdb=" C6 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 4707 not shown) Planarity restraints: 5094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 58 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO G 59 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO G 59 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 59 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 58 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO D 59 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO D 59 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 59 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " 0.037 5.00e-02 4.00e+02 5.60e-02 5.01e+00 pdb=" N PRO L 59 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " 0.031 5.00e-02 4.00e+02 ... (remaining 5091 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 1073 2.67 - 3.23: 29269 3.23 - 3.79: 44394 3.79 - 4.34: 57411 4.34 - 4.90: 96041 Nonbonded interactions: 228188 Sorted by model distance: nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.117 2.440 nonbonded pdb=" OH TYR E 91 " pdb=" OE1 GLU E 191 " model vdw 2.118 2.440 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.118 2.440 nonbonded pdb=" O ARG E 457 " pdb=" OG SER F 53 " model vdw 2.136 2.440 nonbonded pdb=" O ARG A 457 " pdb=" OG SER B 53 " model vdw 2.138 2.440 ... (remaining 228183 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 27 through 476 or resid 478 through 1147 or resid 1305 thr \ ough 1312)) selection = (chain 'C' and (resid 27 through 476 or resid 478 through 1147 or resid 1305 thr \ ough 1312)) selection = (chain 'E' and (resid 27 through 476 or resid 478 through 1147 or resid 1305 thr \ ough 1312)) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' } ncs_group { reference = (chain 'K' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) } 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=0.33 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 10.880 Check model and map are aligned: 0.470 Set scattering table: 0.270 Process input model: 98.130 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.086 29289 Z= 0.724 Angle : 0.931 13.095 39864 Z= 0.506 Chirality : 0.053 0.258 4710 Planarity : 0.005 0.056 5055 Dihedral : 15.407 98.808 11229 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 1.08 % Allowed : 7.92 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.12), residues: 3555 helix: -0.97 (0.18), residues: 669 sheet: -3.09 (0.15), residues: 825 loop : -3.30 (0.11), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 103 HIS 0.010 0.002 HIS A1048 PHE 0.022 0.003 PHE A 275 TYR 0.021 0.002 TYR A 91 ARG 0.005 0.001 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 210 time to evaluate : 3.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7960 (m-10) cc_final: 0.7736 (t80) REVERT: A 390 LEU cc_start: 0.8105 (mm) cc_final: 0.7745 (mm) REVERT: A 869 MET cc_start: 0.9086 (mtp) cc_final: 0.8285 (mtm) REVERT: C 390 LEU cc_start: 0.7963 (mm) cc_final: 0.7570 (mm) REVERT: C 451 TYR cc_start: 0.7416 (m-80) cc_final: 0.6902 (m-80) REVERT: E 133 PHE cc_start: 0.7950 (m-10) cc_final: 0.7651 (t80) REVERT: E 390 LEU cc_start: 0.8005 (mm) cc_final: 0.7658 (mm) REVERT: E 869 MET cc_start: 0.9051 (mtp) cc_final: 0.8783 (mtt) REVERT: E 902 MET cc_start: 0.9364 (mmm) cc_final: 0.9059 (tpt) REVERT: B 20 LEU cc_start: 0.5118 (mm) cc_final: 0.4870 (mm) REVERT: D 49 TYR cc_start: 0.6466 (p90) cc_final: 0.6246 (t80) REVERT: D 95 PHE cc_start: 0.7545 (t80) cc_final: 0.7264 (t80) REVERT: L 53 LYS cc_start: 0.7077 (ttpt) cc_final: 0.6704 (tttm) outliers start: 33 outliers final: 14 residues processed: 243 average time/residue: 0.4350 time to fit residues: 166.2184 Evaluate side-chains 150 residues out of total 3138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 time to evaluate : 3.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 27 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 50.0000 chunk 272 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 282 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 326 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 690 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN A1106 GLN C 487 ASN C 690 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN C1106 GLN E 388 ASN E 690 GLN E 784 GLN E1071 GLN E1106 GLN B 32 ASN F 32 ASN H 32 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29289 Z= 0.190 Angle : 0.628 8.687 39864 Z= 0.320 Chirality : 0.044 0.177 4710 Planarity : 0.005 0.054 5055 Dihedral : 9.860 120.925 5155 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.62 % Allowed : 11.05 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.13), residues: 3555 helix: 1.25 (0.20), residues: 645 sheet: -2.54 (0.16), residues: 789 loop : -2.60 (0.11), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 98 HIS 0.002 0.001 HIS A1083 PHE 0.016 0.002 PHE A 140 TYR 0.021 0.002 TYR L 87 ARG 0.005 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 174 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8001 (mm) cc_final: 0.7728 (mm) REVERT: C 210 ILE cc_start: 0.8608 (pt) cc_final: 0.8407 (tp) REVERT: C 390 LEU cc_start: 0.7998 (mm) cc_final: 0.7709 (mm) REVERT: E 133 PHE cc_start: 0.7852 (m-10) cc_final: 0.7643 (t80) REVERT: E 390 LEU cc_start: 0.7882 (mm) cc_final: 0.7599 (mm) REVERT: E 427 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7211 (p0) REVERT: B 58 TYR cc_start: 0.6590 (m-80) cc_final: 0.6375 (m-80) REVERT: H 59 TYR cc_start: 0.4665 (m-80) cc_final: 0.4269 (m-80) REVERT: D 95 PHE cc_start: 0.7576 (t80) cc_final: 0.7110 (t80) REVERT: L 35 TRP cc_start: 0.5273 (m100) cc_final: 0.4983 (m100) REVERT: L 95 PHE cc_start: 0.7668 (t80) cc_final: 0.6979 (t80) outliers start: 19 outliers final: 14 residues processed: 187 average time/residue: 0.4296 time to fit residues: 128.2215 Evaluate side-chains 148 residues out of total 3138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 75 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 272 optimal weight: 4.9990 chunk 222 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 327 optimal weight: 20.0000 chunk 353 optimal weight: 10.0000 chunk 291 optimal weight: 4.9990 chunk 324 optimal weight: 50.0000 chunk 111 optimal weight: 7.9990 chunk 262 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 901 GLN A 955 ASN A1071 GLN C 388 ASN E 784 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29289 Z= 0.252 Angle : 0.603 13.056 39864 Z= 0.300 Chirality : 0.043 0.180 4710 Planarity : 0.004 0.053 5055 Dihedral : 7.399 57.743 5139 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.58 % Allowed : 12.52 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.09 (0.13), residues: 3555 helix: 1.73 (0.20), residues: 645 sheet: -2.23 (0.17), residues: 795 loop : -2.14 (0.12), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 98 HIS 0.003 0.001 HIS A1083 PHE 0.015 0.002 PHE C 377 TYR 0.031 0.001 TYR C 423 ARG 0.007 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 151 time to evaluate : 3.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8034 (mm) cc_final: 0.7676 (mm) REVERT: A 427 ASP cc_start: 0.7467 (m-30) cc_final: 0.7245 (p0) REVERT: A 449 TYR cc_start: 0.5795 (m-80) cc_final: 0.5450 (m-80) REVERT: C 451 TYR cc_start: 0.7516 (m-80) cc_final: 0.7164 (m-80) REVERT: E 390 LEU cc_start: 0.7931 (mm) cc_final: 0.7601 (mm) REVERT: F 51 ILE cc_start: 0.7436 (tt) cc_final: 0.7165 (tt) REVERT: D 46 LEU cc_start: 0.4280 (pt) cc_final: 0.3429 (tp) REVERT: D 95 PHE cc_start: 0.7544 (t80) cc_final: 0.7060 (t80) REVERT: L 35 TRP cc_start: 0.5148 (m100) cc_final: 0.4678 (m100) outliers start: 48 outliers final: 34 residues processed: 190 average time/residue: 0.4142 time to fit residues: 127.6012 Evaluate side-chains 171 residues out of total 3138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 137 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 30.0000 chunk 246 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 36 optimal weight: 30.0000 chunk 156 optimal weight: 3.9990 chunk 219 optimal weight: 0.0040 chunk 328 optimal weight: 0.0270 chunk 347 optimal weight: 50.0000 chunk 171 optimal weight: 2.9990 chunk 311 optimal weight: 20.0000 chunk 93 optimal weight: 0.9980 overall best weight: 1.2054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A1071 GLN E 437 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29289 Z= 0.164 Angle : 0.551 12.144 39864 Z= 0.275 Chirality : 0.042 0.179 4710 Planarity : 0.004 0.050 5055 Dihedral : 6.776 55.576 5139 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.41 % Allowed : 13.48 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.69 (0.14), residues: 3555 helix: 2.03 (0.20), residues: 657 sheet: -2.09 (0.17), residues: 819 loop : -1.81 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 98 HIS 0.002 0.001 HIS A1083 PHE 0.013 0.001 PHE A 133 TYR 0.017 0.001 TYR F 52 ARG 0.006 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 165 time to evaluate : 3.008 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: A 390 LEU cc_start: 0.8014 (mm) cc_final: 0.7686 (mm) REVERT: A 427 ASP cc_start: 0.7601 (m-30) cc_final: 0.7315 (p0) REVERT: A 449 TYR cc_start: 0.5852 (m-80) cc_final: 0.5468 (m-80) REVERT: C 427 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7269 (p0) REVERT: C 451 TYR cc_start: 0.7393 (m-80) cc_final: 0.7008 (m-80) REVERT: C 464 PHE cc_start: 0.6871 (m-80) cc_final: 0.6641 (m-80) REVERT: E 210 ILE cc_start: 0.8612 (pt) cc_final: 0.8224 (tp) REVERT: E 390 LEU cc_start: 0.7911 (mm) cc_final: 0.7601 (mm) REVERT: E 451 TYR cc_start: 0.7540 (m-80) cc_final: 0.7133 (m-80) REVERT: F 96 GLU cc_start: 0.4164 (OUTLIER) cc_final: 0.3654 (pm20) REVERT: D 46 LEU cc_start: 0.4453 (pt) cc_final: 0.3591 (tp) REVERT: D 95 PHE cc_start: 0.7518 (t80) cc_final: 0.7010 (t80) REVERT: G 46 LEU cc_start: 0.4288 (pt) cc_final: 0.3145 (tp) REVERT: L 46 LEU cc_start: 0.4029 (pt) cc_final: 0.2982 (tp) outliers start: 43 outliers final: 34 residues processed: 200 average time/residue: 0.3927 time to fit residues: 129.2557 Evaluate side-chains 183 residues out of total 3138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 147 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 75 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 259 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 296 optimal weight: 20.0000 chunk 240 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 312 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1071 GLN C 901 GLN C1071 GLN E 487 ASN E 901 GLN E1071 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 29289 Z= 0.375 Angle : 0.632 12.315 39864 Z= 0.313 Chirality : 0.044 0.190 4710 Planarity : 0.004 0.052 5055 Dihedral : 6.927 56.167 5138 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.47 % Allowed : 13.74 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.68 (0.14), residues: 3555 helix: 1.90 (0.20), residues: 648 sheet: -2.01 (0.17), residues: 840 loop : -1.77 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 98 HIS 0.004 0.001 HIS E1048 PHE 0.023 0.002 PHE A 168 TYR 0.035 0.002 TYR C 904 ARG 0.008 0.001 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 134 time to evaluate : 2.917 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: A 427 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7329 (p0) REVERT: A 449 TYR cc_start: 0.5900 (m-80) cc_final: 0.5474 (m-80) REVERT: A 451 TYR cc_start: 0.7356 (m-80) cc_final: 0.6818 (m-80) REVERT: C 427 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7344 (p0) REVERT: C 451 TYR cc_start: 0.7300 (m-80) cc_final: 0.6942 (m-80) REVERT: C 464 PHE cc_start: 0.6991 (m-80) cc_final: 0.6748 (m-80) REVERT: E 427 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7212 (p0) REVERT: E 451 TYR cc_start: 0.7507 (m-80) cc_final: 0.7043 (m-80) REVERT: B 82 MET cc_start: 0.4720 (ptp) cc_final: 0.4470 (pmm) REVERT: D 46 LEU cc_start: 0.4635 (pt) cc_final: 0.3786 (tp) REVERT: D 95 PHE cc_start: 0.7612 (t80) cc_final: 0.7276 (t80) REVERT: L 46 LEU cc_start: 0.4165 (pt) cc_final: 0.3183 (tp) outliers start: 75 outliers final: 55 residues processed: 191 average time/residue: 0.4229 time to fit residues: 133.5977 Evaluate side-chains 186 residues out of total 3138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 128 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 351 TYR Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 3.9990 chunk 313 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 204 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 348 optimal weight: 40.0000 chunk 289 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 28 optimal weight: 0.0070 chunk 115 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A1071 GLN C 437 ASN C 901 GLN C1071 GLN E1071 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29289 Z= 0.193 Angle : 0.557 12.265 39864 Z= 0.276 Chirality : 0.042 0.200 4710 Planarity : 0.004 0.049 5055 Dihedral : 6.640 55.372 5136 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.87 % Allowed : 14.89 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.43 (0.14), residues: 3555 helix: 2.13 (0.20), residues: 657 sheet: -1.86 (0.17), residues: 846 loop : -1.62 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 98 HIS 0.002 0.001 HIS A1083 PHE 0.024 0.001 PHE A 168 TYR 0.028 0.001 TYR C 904 ARG 0.006 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 133 time to evaluate : 3.208 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: A 427 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7365 (p0) REVERT: A 449 TYR cc_start: 0.5908 (m-80) cc_final: 0.5442 (m-80) REVERT: A 451 TYR cc_start: 0.7326 (m-80) cc_final: 0.6810 (m-80) REVERT: C 427 ASP cc_start: 0.7569 (m-30) cc_final: 0.7234 (p0) REVERT: C 451 TYR cc_start: 0.7154 (m-80) cc_final: 0.6749 (m-80) REVERT: E 390 LEU cc_start: 0.7923 (mm) cc_final: 0.7588 (mm) REVERT: E 451 TYR cc_start: 0.7461 (m-80) cc_final: 0.6898 (m-80) REVERT: E 779 GLN cc_start: 0.8340 (tp40) cc_final: 0.8140 (tp40) REVERT: E 1002 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7872 (mm-40) REVERT: B 82 MET cc_start: 0.4672 (ptp) cc_final: 0.4403 (pmm) REVERT: D 46 LEU cc_start: 0.4512 (pt) cc_final: 0.3708 (tp) REVERT: D 95 PHE cc_start: 0.7551 (t80) cc_final: 0.7189 (t80) REVERT: G 46 LEU cc_start: 0.4168 (pt) cc_final: 0.3002 (tp) REVERT: L 46 LEU cc_start: 0.4275 (pt) cc_final: 0.3238 (tp) outliers start: 57 outliers final: 48 residues processed: 174 average time/residue: 0.4207 time to fit residues: 118.7266 Evaluate side-chains 176 residues out of total 3138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 126 time to evaluate : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 351 TYR Chi-restraints excluded: chain E residue 449 TYR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1002 GLN Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 198 optimal weight: 10.0000 chunk 254 optimal weight: 0.7980 chunk 197 optimal weight: 5.9990 chunk 293 optimal weight: 0.6980 chunk 194 optimal weight: 5.9990 chunk 346 optimal weight: 6.9990 chunk 217 optimal weight: 0.5980 chunk 211 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A1071 GLN A1135 ASN C1071 GLN E 901 GLN E1071 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29289 Z= 0.140 Angle : 0.527 11.119 39864 Z= 0.261 Chirality : 0.042 0.170 4710 Planarity : 0.004 0.048 5055 Dihedral : 6.366 56.146 5136 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.51 % Allowed : 15.22 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.15 (0.14), residues: 3555 helix: 2.34 (0.21), residues: 660 sheet: -1.72 (0.18), residues: 825 loop : -1.42 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 98 HIS 0.003 0.001 HIS E1058 PHE 0.020 0.001 PHE A 168 TYR 0.015 0.001 TYR E 91 ARG 0.008 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 150 time to evaluate : 3.293 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: A 117 LEU cc_start: 0.8723 (tt) cc_final: 0.8406 (tt) REVERT: A 427 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7235 (p0) REVERT: A 449 TYR cc_start: 0.5951 (m-80) cc_final: 0.5452 (m-80) REVERT: A 451 TYR cc_start: 0.7379 (m-80) cc_final: 0.6886 (m-80) REVERT: A 1107 ARG cc_start: 0.7323 (mtt180) cc_final: 0.6934 (mtt90) REVERT: C 427 ASP cc_start: 0.7580 (m-30) cc_final: 0.7208 (p0) REVERT: C 451 TYR cc_start: 0.7113 (m-80) cc_final: 0.6706 (m-80) REVERT: E 427 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7295 (p0) REVERT: E 451 TYR cc_start: 0.7305 (m-80) cc_final: 0.6765 (m-80) REVERT: D 46 LEU cc_start: 0.4526 (pt) cc_final: 0.3776 (tp) REVERT: D 95 PHE cc_start: 0.7505 (t80) cc_final: 0.7088 (t80) REVERT: G 46 LEU cc_start: 0.4347 (pt) cc_final: 0.3178 (tp) REVERT: L 46 LEU cc_start: 0.4233 (pt) cc_final: 0.3299 (tp) outliers start: 46 outliers final: 40 residues processed: 183 average time/residue: 0.4217 time to fit residues: 126.5505 Evaluate side-chains 181 residues out of total 3138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 139 time to evaluate : 3.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 351 TYR Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 8.9990 chunk 138 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 68 optimal weight: 0.0270 chunk 67 optimal weight: 0.8980 chunk 220 optimal weight: 0.7980 chunk 236 optimal weight: 40.0000 chunk 171 optimal weight: 0.8980 chunk 32 optimal weight: 20.0000 chunk 272 optimal weight: 4.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 HIS C1048 HIS E 388 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29289 Z= 0.134 Angle : 0.521 11.275 39864 Z= 0.256 Chirality : 0.042 0.165 4710 Planarity : 0.004 0.048 5055 Dihedral : 6.250 57.144 5133 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.48 % Allowed : 15.71 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.99 (0.14), residues: 3555 helix: 2.41 (0.21), residues: 660 sheet: -1.55 (0.18), residues: 825 loop : -1.32 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 98 HIS 0.003 0.001 HIS E1083 PHE 0.024 0.001 PHE E 374 TYR 0.015 0.001 TYR C 904 ARG 0.007 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 147 time to evaluate : 3.128 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: A 427 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7173 (p0) REVERT: A 449 TYR cc_start: 0.5873 (m-80) cc_final: 0.5402 (m-80) REVERT: A 451 TYR cc_start: 0.7364 (m-80) cc_final: 0.6877 (m-80) REVERT: C 398 ASP cc_start: 0.6084 (OUTLIER) cc_final: 0.5731 (m-30) REVERT: C 427 ASP cc_start: 0.7558 (m-30) cc_final: 0.7198 (p0) REVERT: C 451 TYR cc_start: 0.7119 (m-80) cc_final: 0.6748 (m-80) REVERT: C 505 TYR cc_start: 0.6429 (t80) cc_final: 0.6119 (t80) REVERT: C 904 TYR cc_start: 0.7970 (m-10) cc_final: 0.7419 (m-10) REVERT: C 1029 MET cc_start: 0.9034 (tpp) cc_final: 0.8408 (ttm) REVERT: E 427 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7280 (p0) REVERT: E 451 TYR cc_start: 0.7255 (m-80) cc_final: 0.6701 (m-80) REVERT: D 46 LEU cc_start: 0.4492 (pt) cc_final: 0.3776 (tp) REVERT: D 95 PHE cc_start: 0.7494 (t80) cc_final: 0.7080 (t80) REVERT: G 46 LEU cc_start: 0.4456 (pt) cc_final: 0.3416 (tp) REVERT: L 46 LEU cc_start: 0.4457 (pt) cc_final: 0.3497 (tp) outliers start: 45 outliers final: 41 residues processed: 179 average time/residue: 0.4129 time to fit residues: 122.5799 Evaluate side-chains 184 residues out of total 3138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 140 time to evaluate : 3.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 351 TYR Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 449 TYR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 2.9990 chunk 332 optimal weight: 0.6980 chunk 303 optimal weight: 50.0000 chunk 323 optimal weight: 20.0000 chunk 194 optimal weight: 3.9990 chunk 140 optimal weight: 20.0000 chunk 253 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 292 optimal weight: 1.9990 chunk 305 optimal weight: 30.0000 chunk 322 optimal weight: 0.0670 overall best weight: 1.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29289 Z= 0.190 Angle : 0.531 10.286 39864 Z= 0.261 Chirality : 0.042 0.177 4710 Planarity : 0.004 0.049 5055 Dihedral : 6.267 56.938 5133 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.74 % Allowed : 15.84 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.93 (0.14), residues: 3555 helix: 2.38 (0.20), residues: 663 sheet: -1.46 (0.18), residues: 852 loop : -1.28 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 98 HIS 0.003 0.001 HIS E1083 PHE 0.030 0.001 PHE E 374 TYR 0.015 0.001 TYR A 91 ARG 0.008 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 144 time to evaluate : 3.141 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: A 427 ASP cc_start: 0.7665 (m-30) cc_final: 0.7228 (p0) REVERT: A 449 TYR cc_start: 0.5713 (m-80) cc_final: 0.5376 (m-80) REVERT: A 451 TYR cc_start: 0.7259 (m-80) cc_final: 0.6716 (m-80) REVERT: C 427 ASP cc_start: 0.7478 (m-30) cc_final: 0.7129 (p0) REVERT: C 451 TYR cc_start: 0.7082 (m-80) cc_final: 0.6651 (m-80) REVERT: C 505 TYR cc_start: 0.6483 (t80) cc_final: 0.6137 (t80) REVERT: C 1029 MET cc_start: 0.9126 (tpp) cc_final: 0.8488 (ttm) REVERT: E 427 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7291 (p0) REVERT: E 451 TYR cc_start: 0.7165 (m-80) cc_final: 0.6590 (m-80) REVERT: D 46 LEU cc_start: 0.4587 (pt) cc_final: 0.3850 (tp) REVERT: D 95 PHE cc_start: 0.7510 (t80) cc_final: 0.7085 (t80) REVERT: L 46 LEU cc_start: 0.4464 (pt) cc_final: 0.3456 (tp) outliers start: 53 outliers final: 49 residues processed: 180 average time/residue: 0.4169 time to fit residues: 120.4086 Evaluate side-chains 191 residues out of total 3138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 141 time to evaluate : 3.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 351 TYR Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 449 TYR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 7.9990 chunk 341 optimal weight: 40.0000 chunk 208 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 237 optimal weight: 2.9990 chunk 358 optimal weight: 10.0000 chunk 330 optimal weight: 40.0000 chunk 285 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 220 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1071 GLN E 901 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 29289 Z= 0.341 Angle : 0.599 10.771 39864 Z= 0.296 Chirality : 0.044 0.196 4710 Planarity : 0.004 0.052 5055 Dihedral : 6.569 57.280 5133 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.68 % Allowed : 16.04 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.06 (0.14), residues: 3555 helix: 1.97 (0.20), residues: 678 sheet: -1.39 (0.17), residues: 870 loop : -1.34 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 98 HIS 0.004 0.001 HIS C1058 PHE 0.034 0.002 PHE E 374 TYR 0.033 0.002 TYR C 904 ARG 0.008 0.001 ARG A1019 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 134 time to evaluate : 3.119 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: A 427 ASP cc_start: 0.7764 (m-30) cc_final: 0.7342 (p0) REVERT: A 449 TYR cc_start: 0.5749 (m-80) cc_final: 0.5338 (m-80) REVERT: A 451 TYR cc_start: 0.7197 (m-80) cc_final: 0.6617 (m-80) REVERT: C 398 ASP cc_start: 0.5956 (OUTLIER) cc_final: 0.5622 (m-30) REVERT: C 427 ASP cc_start: 0.7511 (m-30) cc_final: 0.7188 (p0) REVERT: C 451 TYR cc_start: 0.7123 (m-80) cc_final: 0.6655 (m-80) REVERT: C 505 TYR cc_start: 0.6589 (t80) cc_final: 0.6114 (t80) REVERT: E 427 ASP cc_start: 0.7625 (m-30) cc_final: 0.7338 (p0) REVERT: D 46 LEU cc_start: 0.4609 (pt) cc_final: 0.3853 (tp) REVERT: D 95 PHE cc_start: 0.7523 (t80) cc_final: 0.7100 (t80) REVERT: L 46 LEU cc_start: 0.4327 (pt) cc_final: 0.3301 (tp) outliers start: 51 outliers final: 44 residues processed: 170 average time/residue: 0.4054 time to fit residues: 112.7267 Evaluate side-chains 177 residues out of total 3138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 132 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 351 TYR Chi-restraints excluded: chain E residue 449 TYR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 8.9990 chunk 304 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 263 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 286 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 293 optimal weight: 0.0370 chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN E 901 GLN E1071 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.123112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.082034 restraints weight = 99274.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.081703 restraints weight = 53106.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.081819 restraints weight = 41258.209| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29289 Z= 0.188 Angle : 0.544 10.916 39864 Z= 0.267 Chirality : 0.042 0.201 4710 Planarity : 0.004 0.050 5055 Dihedral : 6.412 56.947 5133 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.78 % Allowed : 16.17 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.95 (0.14), residues: 3555 helix: 2.30 (0.20), residues: 663 sheet: -1.37 (0.17), residues: 882 loop : -1.31 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 98 HIS 0.004 0.001 HIS A1048 PHE 0.031 0.001 PHE E 374 TYR 0.026 0.001 TYR C 904 ARG 0.007 0.000 ARG C1019 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5389.81 seconds wall clock time: 100 minutes 12.80 seconds (6012.80 seconds total)