Starting phenix.real_space_refine on Wed Jul 24 03:29:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpt_21865/07_2024/6wpt_21865.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpt_21865/07_2024/6wpt_21865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpt_21865/07_2024/6wpt_21865.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpt_21865/07_2024/6wpt_21865.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpt_21865/07_2024/6wpt_21865.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpt_21865/07_2024/6wpt_21865.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.048 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 107 5.16 5 C 15472 2.51 5 N 4080 2.21 5 O 4667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "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 TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1019": "NH1" <-> "NH2" 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 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 24326 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 7049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 945, 7049 Classifications: {'peptide': 945} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 44, 'TRANS': 900} Chain breaks: 13 Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 446 Unresolved non-hydrogen dihedrals: 287 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 22, 'PHE:plan': 7, 'GLU:plan': 21, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 259 Chain: "B" Number of atoms: 6561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 937, 6561 Classifications: {'peptide': 937} Incomplete info: {'truncation_to_alanine': 213} Link IDs: {'PTRANS': 45, 'TRANS': 891} Chain breaks: 13 Unresolved non-hydrogen bonds: 787 Unresolved non-hydrogen angles: 1014 Unresolved non-hydrogen dihedrals: 647 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 15, 'ASN:plan1': 22, 'TRP:plan': 2, 'ASP:plan': 27, 'PHE:plan': 14, 'GLU:plan': 17, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 509 Chain: "C" Number of atoms: 6997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 6997 Classifications: {'peptide': 952} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 46, 'TRANS': 905} Chain breaks: 12 Unresolved non-hydrogen bonds: 458 Unresolved non-hydrogen angles: 584 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 11, 'ASP:plan': 21, 'PHE:plan': 7, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 291 Chain: "H" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 876 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "L" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 590 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 2 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 5, 'PHE:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 79 Chain: "D" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 783 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 79 Chain: "E" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 580 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 4, 'PHE:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 76 Chain: "F" 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" 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: "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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 14.95, per 1000 atoms: 0.61 Number of scatterers: 24326 At special positions: 0 Unit cell: (139.65, 138.6, 179.55, 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 107 16.00 O 4667 8.00 N 4080 7.00 C 15472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.08 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.12 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 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.18 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 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.07 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " 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=0, symmetry=0 Links applied ALPHA1-3 " BMA S 3 " - " MAN S 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " 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 R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " BETA1-6 " NAG J 1 " - " FUC J 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 6 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1314 " - " ASN A1074 " " NAG A1317 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 717 " " NAG B1314 " - " ASN B1074 " " NAG B1319 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1314 " - " ASN C1074 " " NAG C1319 " - " ASN C 165 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A 343 " " NAG K 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " " NAG S 1 " - " ASN C 343 " Time building additional restraints: 10.05 Conformation dependent library (CDL) restraints added in 4.6 seconds 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6104 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 55 sheets defined 23.5% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.75 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.791A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.508A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.749A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 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: 4.977A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.199A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.651A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.906A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.099A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.371A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 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 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.503A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 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: 4.731A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.772A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.742A pdb=" N SER D 31 " --> pdb=" O PRO D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.867A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.035A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.690A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.006A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.768A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.267A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.163A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.435A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.163A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.435A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.397A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.950A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.596A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.525A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.525A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 removed outlier: 3.551A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.545A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.738A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.520A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.336A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.415A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.270A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.995A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.496A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.496A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.749A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.844A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.509A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.385A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.716A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.181A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.181A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.618A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.366A pdb=" N TYR C 660 " --> pdb=" O SER C 698 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.641A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.787A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.121A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.324A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.548A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.107A pdb=" N GLU H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.107A pdb=" N GLU H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN H 116 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF4, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.520A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.520A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AF7, first strand: chain 'D' and resid 10 through 11 removed outlier: 7.122A pdb=" N GLU D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 10 through 11 removed outlier: 7.122A pdb=" N GLU D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN D 116 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AG1, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.597A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) 1172 hydrogen bonds defined for protein. 3153 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: 11.58 Time building geometry restraints manager: 11.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 6533 1.33 - 1.47: 7772 1.47 - 1.61: 10369 1.61 - 1.75: 6 1.75 - 1.89: 134 Bond restraints: 24814 Sorted by residual: bond pdb=" NE ARG C 454 " pdb=" CZ ARG C 454 " ideal model delta sigma weight residual 1.326 1.380 -0.054 1.10e-02 8.26e+03 2.43e+01 bond pdb=" CB ILE B 210 " pdb=" CG1 ILE B 210 " ideal model delta sigma weight residual 1.530 1.626 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" CB LEU C 212 " pdb=" CG LEU C 212 " ideal model delta sigma weight residual 1.530 1.616 -0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" CB ILE A 68 " pdb=" CG1 ILE A 68 " ideal model delta sigma weight residual 1.530 1.616 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" CB ILE L 2 " pdb=" CG1 ILE L 2 " ideal model delta sigma weight residual 1.530 1.615 -0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 24809 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.51: 716 106.51 - 113.40: 13494 113.40 - 120.29: 9081 120.29 - 127.18: 10498 127.18 - 134.07: 115 Bond angle restraints: 33904 Sorted by residual: angle pdb=" C THR C 599 " pdb=" N PRO C 600 " pdb=" CA PRO C 600 " ideal model delta sigma weight residual 119.56 127.03 -7.47 1.02e+00 9.61e-01 5.37e+01 angle pdb=" C PRO C 792 " pdb=" N PRO C 793 " pdb=" CA PRO C 793 " ideal model delta sigma weight residual 119.56 126.91 -7.35 1.02e+00 9.61e-01 5.20e+01 angle pdb=" C GLN B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 119.56 126.77 -7.21 1.01e+00 9.80e-01 5.09e+01 angle pdb=" C PRO A 862 " pdb=" N PRO A 863 " pdb=" CA PRO A 863 " ideal model delta sigma weight residual 120.03 127.05 -7.02 9.90e-01 1.02e+00 5.03e+01 angle pdb=" C PHE A 490 " pdb=" N PRO A 491 " pdb=" CA PRO A 491 " ideal model delta sigma weight residual 119.87 127.22 -7.35 1.04e+00 9.25e-01 4.99e+01 ... (remaining 33899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 15014 21.47 - 42.95: 294 42.95 - 64.42: 69 64.42 - 85.90: 36 85.90 - 107.37: 12 Dihedral angle restraints: 15425 sinusoidal: 5969 harmonic: 9456 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 171.61 -78.61 1 1.00e+01 1.00e-02 7.70e+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 93.00 169.91 -76.91 1 1.00e+01 1.00e-02 7.43e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 161.68 -68.68 1 1.00e+01 1.00e-02 6.11e+01 ... (remaining 15422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3058 0.089 - 0.177: 818 0.177 - 0.266: 250 0.266 - 0.354: 51 0.354 - 0.443: 7 Chirality restraints: 4184 Sorted by residual: chirality pdb=" C1 BMA S 3 " pdb=" O4 NAG S 2 " pdb=" C2 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.37e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.36e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.19e+01 ... (remaining 4181 not shown) Planarity restraints: 4351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " -0.037 2.00e-02 2.50e+03 3.73e-02 1.74e+01 pdb=" CG ASN B 331 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " 0.056 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 266 " 0.044 2.00e-02 2.50e+03 2.46e-02 1.21e+01 pdb=" CG TYR A 266 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR A 266 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 266 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 266 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 266 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 266 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 266 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 200 " -0.040 2.00e-02 2.50e+03 2.21e-02 9.78e+00 pdb=" CG TYR A 200 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 200 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 200 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 200 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 200 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 200 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 200 " -0.036 2.00e-02 2.50e+03 ... (remaining 4348 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 12 2.52 - 3.12: 17482 3.12 - 3.71: 35194 3.71 - 4.31: 53789 4.31 - 4.90: 85514 Nonbonded interactions: 191991 Sorted by model distance: nonbonded pdb=" CD2 PHE B 817 " pdb=" NE2 GLN B 935 " model vdw 1.930 3.420 nonbonded pdb=" CD2 PHE C 817 " pdb=" NE2 GLN C 935 " model vdw 2.027 3.420 nonbonded pdb=" NZ LYS C1028 " pdb=" O PHE C1042 " model vdw 2.410 2.520 nonbonded pdb=" CE2 PHE B 817 " pdb=" NE2 GLN B 935 " model vdw 2.413 3.420 nonbonded pdb=" N ALA C 520 " pdb=" O ALA C 520 " model vdw 2.441 2.496 ... (remaining 191986 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 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 44 or (resid 45 through 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 50 or (res \ id 51 and (name N or name CA or name C or name O or name CB )) or resid 52 or (r \ esid 53 and (name N or name CA or name C or name O or name CB )) or resid 54 thr \ ough 59 or (resid 60 and (name N or name CA or name C or name O or name CB )) or \ resid 61 through 66 or resid 82 through 94 or (resid 95 through 102 and (name N \ or name CA or name C or name O or name CB )) or resid 103 through 104 or (resid \ 105 and (name N or name CA or name C or name O or name CB )) or resid 106 throu \ gh 107 or (resid 108 through 118 and (name N or name CA or name C or name O or n \ ame CB )) or resid 119 through 120 or (resid 121 and (name N or name CA or name \ C or name O or name CB )) or resid 122 through 123 or (resid 124 through 130 and \ (name N or name CA or name C or name O or name CB )) or resid 131 through 139 o \ r (resid 140 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 66 through 169 or (resid 170 through 172 and (name N or name CA or name C or nam \ e O or name CB )) or resid 188 through 189 or (resid 190 through 191 and (name N \ or name CA or name C or name O or name CB )) or resid 192 through 196 or (resid \ 200 through 203 and (name N or name CA or name C or name O or name CB )) or res \ id 204 through 209 or (resid 210 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 216 and (name N or name CA or name C or name O or name CB )) \ or resid 217 through 223 or (resid 224 and (name N or name CA or name C or name \ O or name CB )) or resid 225 through 226 or (resid 227 through 229 and (name N \ or name CA or name C or name O or name CB )) or resid 230 or (resid 231 and (nam \ e N or name CA or name C or name O or name CB )) or resid 232 through 235 or (re \ sid 236 through 237 and (name N or name CA or name C or name O or name CB )) or \ resid 238 or (resid 239 through 264 and (name N or name CA or name C or name O o \ r name CB )) or resid 265 through 273 or (resid 274 and (name N or name CA or na \ me C or name O or name CB )) or resid 275 through 279 or (resid 280 through 281 \ and (name N or name CA or name C or name O or name CB )) or resid 282 through 28 \ 3 or (resid 284 and (name N or name CA or name C or name O or name CB )) or resi \ d 285 through 286 or (resid 287 through 288 and (name N or name CA or name C or \ name O or name CB )) or resid 289 through 316 or (resid 317 and (name N or name \ CA or name C or name O or name CB )) or resid 318 through 323 or (resid 324 and \ (name N or name CA or name C or name O or name CB )) or resid 325 through 332 or \ (resid 333 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 4 through 344 or (resid 345 through 360 and (name N or name CA or name C or name \ O or name CB )) or resid 361 or (resid 362 through 378 and (name N or name CA o \ r name C or name O or name CB )) or resid 379 or (resid 380 and (name N or name \ CA or name C or name O or name CB )) or resid 381 or (resid 382 through 383 and \ (name N or name CA or name C or name O or name CB )) or resid 384 or (resid 385 \ through 390 and (name N or name CA or name C or name O or name CB )) or resid 39 \ 1 or (resid 392 through 403 and (name N or name CA or name C or name O or name C \ B )) or (resid 404 through 411 and (name N or name CA or name C or name O or nam \ e CB )) or resid 412 through 413 or (resid 414 through 415 and (name N or name C \ A or name C or name O or name CB )) or (resid 416 through 425 and (name N or nam \ e CA or name C or name O or name CB )) or resid 426 through 427 or (resid 428 th \ rough 430 and (name N or name CA or name C or name O or name CB )) or resid 431 \ through 432 or (resid 433 through 442 and (name N or name CA or name C or name O \ or name CB )) or resid 463 or (resid 464 through 466 and (name N or name CA or \ name C or name O or name CB )) or resid 491 through 494 or (resid 495 and (name \ N or name CA or name C or name O or name CB )) or resid 496 or (resid 497 throug \ h 498 and (name N or name CA or name C or name O or name CB )) or resid 504 thro \ ugh 507 or (resid 508 through 515 and (name N or name CA or name C or name O or \ name CB )) or (resid 522 through 524 and (name N or name CA or name C or name O \ or name CB )) or resid 525 through 527 or (resid 528 through 537 and (name N or \ name CA or name C or name O or name CB )) or resid 538 through 553 or (resid 554 \ through 557 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 58 through 564 or (resid 565 and (name N or name CA or name C or name O or name \ CB )) or resid 566 through 570 or (resid 571 and (name N or name CA or name C or \ name O or name CB )) or resid 572 through 573 or (resid 574 through 575 and (na \ me N or name CA or name C or name O or name CB )) or resid 576 through 577 or (r \ esid 578 and (name N or name CA or name C or name O or name CB )) or resid 579 t \ hrough 582 or (resid 583 and (name N or name CA or name C or name O or name CB ) \ ) or resid 584 through 658 or (resid 659 and (name N or name CA or name C or nam \ e O or name CB )) or resid 660 through 675 or (resid 676 and (name N or name CA \ or name C or name O or name CB )) or resid 690 through 724 or (resid 725 and (na \ me N or name CA or name C or name O or name CB )) or resid 726 through 775 or (r \ esid 776 and (name N or name CA or name C or name O or name CB )) or resid 777 t \ hrough 779 or (resid 780 and (name N or name CA or name C or name O or name CB ) \ ) or resid 781 through 810 or (resid 811 and (name N or name CA or name C or nam \ e O or name CB )) or resid 813 through 827 or (resid 856 and (name N or name CA \ or name C or name O or name CB )) or resid 857 through 871 or (resid 872 and (na \ me N or name CA or name C or name O or name CB )) or resid 873 through 903 or (r \ esid 904 and (name N or name CA or name C or name O or name CB )) or resid 905 t \ hrough 939 or (resid 940 and (name N or name CA or name C or name O or name CB ) \ ) or resid 941 through 942 or (resid 943 through 944 and (name N or name CA or n \ ame C or name O or name CB )) or resid 945 through 984 or (resid 985 and (name N \ or name CA or name C or name O or name CB )) or resid 986 through 1030 or (resi \ d 1031 and (name N or name CA or name C or name O or name CB )) or resid 1032 th \ rough 1040 or (resid 1041 and (name N or name CA or name C or name O or name CB \ )) or resid 1042 through 1044 or (resid 1045 and (name N or name CA or name C or \ name O or name CB )) or resid 1046 through 1082 or (resid 1083 through 1084 and \ (name N or name CA or name C or name O or name CB )) or resid 1085 through 1096 \ or (resid 1097 and (name N or name CA or name C or name O or name CB )) or resi \ d 1098 through 1099 or (resid 1100 and (name N or name CA or name C or name O or \ name CB )) or resid 1101 through 1134 or (resid 1135 and (name N or name CA or \ name C or name O or name CB )) or resid 1136 through 1137 or resid 1301 through \ 1317)) selection = (chain 'B' and (resid 27 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 44 or (resid 45 through 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 50 or (res \ id 51 and (name N or name CA or name C or name O or name CB )) or resid 52 throu \ gh 59 or (resid 60 and (name N or name CA or name C or name O or name CB )) or r \ esid 61 through 66 or resid 82 through 94 or (resid 95 through 102 and (name N o \ r name CA or name C or name O or name CB )) or resid 103 through 104 or (resid 1 \ 05 and (name N or name CA or name C or name O or name CB )) or resid 106 through \ 110 or (resid 116 through 118 and (name N or name CA or name C or name O or nam \ e CB )) or resid 119 through 120 or (resid 121 and (name N or name CA or name C \ or name O or name CB )) or resid 122 through 129 or (resid 130 and (name N or na \ me CA or name C or name O or name CB )) or resid 131 through 136 or resid 138 th \ rough 139 or (resid 140 and (name N or name CA or name C or name O or name CB )) \ or resid 166 through 167 or (resid 168 through 188 and (name N or name CA or na \ me C or name O or name CB )) or resid 189 or (resid 190 through 191 and (name N \ or name CA or name C or name O or name CB )) or resid 192 through 209 or (resid \ 210 through 216 and (name N or name CA or name C or name O or name CB )) or resi \ d 217 through 232 or (resid 233 and (name N or name CA or name C or name O or na \ me CB )) or resid 234 through 238 or (resid 239 through 263 and (name N or name \ CA or name C or name O or name CB )) or resid 265 through 280 or (resid 281 and \ (name N or name CA or name C or name O or name CB )) or resid 282 through 286 or \ (resid 287 through 288 and (name N or name CA or name C or name O or name CB )) \ or resid 289 or (resid 290 and (name N or name CA or name C or name O or name C \ B )) or resid 291 through 293 or (resid 294 and (name N or name CA or name C or \ name O or name CB )) or resid 295 through 316 or (resid 317 and (name N or name \ CA or name C or name O or name CB )) or resid 318 through 320 or (resid 321 and \ (name N or name CA or name C or name O or name CB )) or resid 322 through 323 or \ (resid 324 and (name N or name CA or name C or name O or name CB )) or resid 32 \ 5 through 442 or resid 463 through 498 or resid 504 through 568 or (resid 569 th \ rough 571 and (name N or name CA or name C or name O or name CB )) or resid 572 \ through 581 or (resid 582 through 583 and (name N or name CA or name C or name O \ or name CB )) or resid 584 through 591 or (resid 592 and (name N or name CA or \ name C or name O or name CB )) or resid 593 through 618 or (resid 619 and (name \ N or name CA or name C or name O or name CB )) or resid 620 through 645 or (resi \ d 646 through 647 and (name N or name CA or name C or name O or name CB )) or re \ sid 648 through 658 or (resid 659 and (name N or name CA or name C or name O or \ name CB )) or resid 660 through 662 or (resid 663 and (name N or name CA or name \ C or name O or name CB )) or resid 664 through 675 or (resid 676 and (name N or \ name CA or name C or name O or name CB )) or resid 690 through 724 or (resid 72 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 726 through \ 736 or (resid 737 and (name N or name CA or name C or name O or name CB )) or re \ sid 738 through 772 or (resid 773 and (name N or name CA or name C or name O or \ name CB )) or resid 774 through 775 or (resid 776 and (name N or name CA or name \ C or name O or name CB )) or resid 777 through 789 or (resid 790 and (name N or \ name CA or name C or name O or name CB )) or resid 791 through 827 or (resid 85 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 857 through \ 871 or (resid 872 and (name N or name CA or name C or name O or name CB )) or re \ sid 873 through 903 or (resid 904 and (name N or name CA or name C or name O or \ name CB )) or resid 905 through 917 or (resid 918 and (name N or name CA or name \ C or name O or name CB )) or resid 919 through 920 or (resid 921 and (name N or \ name CA or name C or name O or name CB )) or resid 922 through 932 or (resid 93 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 934 through \ 935 or (resid 936 and (name N or name CA or name C or name O or name CB )) or re \ sid 937 through 939 or (resid 940 and (name N or name CA or name C or name O or \ name CB )) or resid 941 through 942 or (resid 943 through 944 and (name N or nam \ e CA or name C or name O or name CB )) or resid 945 through 984 or (resid 985 an \ d (name N or name CA or name C or name O or name CB )) or resid 986 through 987 \ or (resid 988 through 990 and (name N or name CA or name C or name O or name CB \ )) or resid 991 through 1016 or (resid 1017 and (name N or name CA or name C or \ name O or name CB )) or resid 1018 through 1082 or (resid 1083 through 1084 and \ (name N or name CA or name C or name O or name CB )) or resid 1085 through 1096 \ or (resid 1097 and (name N or name CA or name C or name O or name CB )) or resid \ 1098 through 1110 or (resid 1111 and (name N or name CA or name C or name O or \ name CB )) or resid 1112 through 1137 or resid 1303 through 1319)) selection = (chain 'C' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 97 or (resi \ d 98 through 102 and (name N or name CA or name C or name O or name CB )) or res \ id 103 through 110 or (resid 116 through 118 and (name N or name CA or name C or \ name O or name CB )) or resid 119 through 136 or resid 138 through 140 or resid \ 166 through 172 or resid 188 through 190 or (resid 191 and (name N or name CA o \ r name C or name O or name CB )) or resid 192 through 196 or (resid 200 through \ 203 and (name N or name CA or name C or name O or name CB )) or resid 204 throug \ h 210 or resid 216 through 223 or (resid 224 and (name N or name CA or name C or \ name O or name CB )) or resid 225 through 230 or (resid 231 and (name N or name \ CA or name C or name O or name CB )) or resid 232 or (resid 233 and (name N or \ name CA or name C or name O or name CB )) or resid 234 through 273 or (resid 274 \ and (name N or name CA or name C or name O or name CB )) or resid 275 through 2 \ 79 or (resid 280 through 281 and (name N or name CA or name C or name O or name \ CB )) or resid 282 through 283 or (resid 284 and (name N or name CA or name C or \ name O or name CB )) or resid 285 through 293 or (resid 294 and (name N or name \ CA or name C or name O or name CB )) or resid 295 through 320 or (resid 321 and \ (name N or name CA or name C or name O or name CB )) or resid 322 through 339 o \ r (resid 340 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 41 through 344 or (resid 345 through 360 and (name N or name CA or name C or nam \ e O or name CB )) or resid 361 or (resid 362 through 378 and (name N or name CA \ or name C or name O or name CB )) or resid 379 or (resid 380 and (name N or name \ CA or name C or name O or name CB )) or resid 381 or (resid 382 through 383 and \ (name N or name CA or name C or name O or name CB )) or resid 384 or (resid 385 \ through 390 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 91 or (resid 392 through 403 and (name N or name CA or name C or name O or name \ CB )) or (resid 404 through 411 and (name N or name CA or name C or name O or na \ me CB )) or resid 412 through 413 or (resid 414 through 415 and (name N or name \ CA or name C or name O or name CB )) or (resid 416 through 425 and (name N or na \ me CA or name C or name O or name CB )) or resid 426 or (resid 427 through 430 a \ nd (name N or name CA or name C or name O or name CB )) or resid 431 through 432 \ or (resid 433 through 442 and (name N or name CA or name C or name O or name CB \ )) or resid 463 or (resid 464 through 466 and (name N or name CA or name C or n \ ame O or name CB )) or resid 491 or (resid 492 through 495 and (name N or name C \ A or name C or name O or name CB )) or resid 496 or (resid 497 through 498 and ( \ name N or name CA or name C or name O or name CB )) or (resid 504 through 506 an \ d (name N or name CA or name C or name O or name CB )) or resid 507 or (resid 50 \ 8 through 515 and (name N or name CA or name C or name O or name CB )) or (resid \ 522 through 524 and (name N or name CA or name C or name O or name CB )) or res \ id 525 through 527 or (resid 528 through 537 and (name N or name CA or name C or \ name O or name CB )) or resid 538 through 554 or (resid 555 through 557 and (na \ me N or name CA or name C or name O or name CB )) or resid 558 through 563 or (r \ esid 564 through 565 and (name N or name CA or name C or name O or name CB )) or \ resid 566 through 567 or (resid 568 through 571 and (name N or name CA or name \ C or name O or name CB )) or resid 572 through 573 or (resid 574 through 575 and \ (name N or name CA or name C or name O or name CB )) or resid 576 through 581 o \ r (resid 582 through 583 and (name N or name CA or name C or name O or name CB ) \ ) or resid 584 through 591 or (resid 592 and (name N or name CA or name C or nam \ e O or name CB )) or resid 593 through 645 or (resid 646 through 647 and (name N \ or name CA or name C or name O or name CB )) or resid 648 through 657 or (resid \ 658 through 659 and (name N or name CA or name C or name O or name CB )) or res \ id 660 or (resid 661 and (name N or name CA or name C or name O or name CB )) or \ resid 662 or (resid 663 and (name N or name CA or name C or name O or name CB ) \ ) or resid 664 through 674 or (resid 675 through 676 and (name N or name CA or n \ ame C or name O or name CB )) or resid 690 through 701 or (resid 702 and (name N \ or name CA or name C or name O or name CB )) or resid 703 through 736 or (resid \ 737 and (name N or name CA or name C or name O or name CB )) or resid 738 throu \ gh 747 or (resid 748 and (name N or name CA or name C or name O or name CB )) or \ resid 749 through 772 or (resid 773 and (name N or name CA or name C or name O \ or name CB )) or resid 774 through 779 or (resid 780 and (name N or name CA or n \ ame C or name O or name CB )) or resid 781 through 793 or (resid 794 and (name N \ or name CA or name C or name O or name CB )) or resid 795 or (resid 796 and (na \ me N or name CA or name C or name O or name CB )) or resid 797 through 810 or (r \ esid 811 and (name N or name CA or name C or name O or name CB )) or resid 813 t \ hrough 866 or (resid 867 and (name N or name CA or name C or name O or name CB ) \ ) or resid 868 through 917 or (resid 918 and (name N or name CA or name C or nam \ e O or name CB )) or resid 919 through 920 or (resid 921 and (name N or name CA \ or name C or name O or name CB )) or resid 922 through 932 or (resid 933 and (na \ me N or name CA or name C or name O or name CB )) or resid 934 through 935 or (r \ esid 936 and (name N or name CA or name C or name O or name CB )) or resid 937 t \ hrough 978 or (resid 979 and (name N or name CA or name C or name O or name CB ) \ ) or resid 980 through 987 or (resid 988 through 990 and (name N or name CA or n \ ame C or name O or name CB )) or resid 991 through 1016 or (resid 1017 and (name \ N or name CA or name C or name O or name CB )) or resid 1018 through 1030 or (r \ esid 1031 and (name N or name CA or name C or name O or name CB )) or resid 1032 \ through 1040 or (resid 1041 and (name N or name CA or name C or name O or name \ CB )) or resid 1042 through 1110 or (resid 1111 and (name N or name CA or name C \ or name O or name CB )) or resid 1112 through 1134 or (resid 1135 and (name N o \ r name CA or name C or name O or name CB )) or resid 1136 through 1137 or resid \ 1301 through 1319)) } ncs_group { reference = (chain 'D' and (resid 2 through 30 or (resid 31 and (name N or name CA or name C \ or name O or name CB )) or resid 32 through 83 or (resid 84 through 93 and (nam \ e N or name CA or name C or name O or name CB )) or resid 94 through 124)) selection = (chain 'H' and ((resid 2 through 7 and (name N or name CA or name C or name O or \ name CB )) or (resid 8 through 13 and (name N or name CA or name C or name O or \ name CB )) or resid 14 through 17 or (resid 18 through 21 and (name N or name C \ A or name C or name O or name CB )) or resid 22 through 36 or (resid 37 and (nam \ e N or name CA or name C or name O or name CB )) or resid 38 through 47 or (resi \ d 48 and (name N or name CA or name C or name O or name CB )) or resid 49 throug \ h 52 or (resid 53 and (name N or name CA or name C or name O or name CB )) or re \ sid 54 or (resid 55 and (name N or name CA or name C or name O or name CB )) or \ resid 56 through 57 or (resid 58 and (name N or name CA or name C or name O or n \ ame CB )) or resid 59 through 64 or (resid 65 and (name N or name CA or name C o \ r name O or name CB )) or resid 66 or (resid 67 through 71 and (name N or name C \ A or name C or name O or name CB )) or resid 72 through 73 or (resid 74 through \ 78 and (name N or name CA or name C or name O or name CB )) or resid 79 or (resi \ d 80 through 93 and (name N or name CA or name C or name O or name CB )) or resi \ d 94 through 98 or (resid 99 and (name N or name CA or name C or name O or name \ CB )) or resid 100 or (resid 101 and (name N or name CA or name C or name O or n \ ame CB )) or resid 102 through 107 or (resid 108 through 109 and (name N or name \ CA or name C or name O or name CB )) or resid 110 or (resid 111 and (name N or \ name CA or name C or name O or name CB )) or resid 112 through 114 or (resid 115 \ through 116 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 17 through 124)) } ncs_group { reference = (chain 'E' and (resid 2 through 7 or (resid 11 through 12 and (name N or name CA \ or name C or name O or name CB )) or resid 13 through 19 or (resid 20 through 2 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 23 through 2 \ 6 or (resid 27 through 35 and (name N or name CA or name C or name O or name CB \ )) or resid 36 through 45 or (resid 46 and (name N or name CA or name C or name \ O or name CB )) or resid 47 through 59 or resid 62 through 90 or (resid 91 and ( \ name N or name CA or name C or name O or name CB )) or resid 92 through 101)) selection = (chain 'L' and ((resid 2 through 12 and (name N or name CA or name C or name O o \ r name CB )) or resid 13 through 28 or (resid 29 through 35 and (name N or name \ CA or name C or name O or name CB )) or resid 36 through 38 or (resid 39 through \ 40 and (name N or name CA or name C or name O or name CB )) or resid 41 through \ 47 or (resid 48 through 49 and (name N or name CA or name C or name O or name C \ B )) or resid 50 through 82 or (resid 83 through 86 and (name N or name CA or na \ me C or name O or name CB )) or resid 87 through 89 or (resid 90 through 91 and \ (name N or name CA or name C or name O or name CB )) or resid 92 through 94 or ( \ resid 95 through 97 and (name N or name CA or name C or name O or name CB )) or \ resid 98 through 101)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.010 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 72.290 Find NCS groups from input model: 3.340 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 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 : 0.012 0.096 24814 Z= 0.815 Angle : 1.347 8.273 33904 Z= 0.909 Chirality : 0.091 0.443 4184 Planarity : 0.005 0.025 4304 Dihedral : 10.414 107.371 9201 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.95 % Favored : 97.96 % Rotamer: Outliers : 0.09 % Allowed : 0.59 % Favored : 99.32 % 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: 0.62 (0.14), residues: 3181 helix: 0.17 (0.18), residues: 691 sheet: 1.21 (0.17), residues: 767 loop : 0.26 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.007 TRP C 886 HIS 0.004 0.001 HIS C 655 PHE 0.024 0.004 PHE L 98 TYR 0.044 0.005 TYR A 266 ARG 0.005 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 438 time to evaluate : 2.705 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 418 ILE cc_start: 0.8326 (mm) cc_final: 0.7984 (mp) REVERT: A 758 SER cc_start: 0.8248 (m) cc_final: 0.7917 (t) REVERT: C 423 TYR cc_start: 0.7001 (t80) cc_final: 0.6668 (t80) REVERT: C 740 MET cc_start: 0.7590 (ttt) cc_final: 0.7354 (ttt) REVERT: C 751 ASN cc_start: 0.7777 (m-40) cc_final: 0.7400 (t0) REVERT: C 778 THR cc_start: 0.9036 (m) cc_final: 0.8788 (p) REVERT: C 870 ILE cc_start: 0.8962 (mm) cc_final: 0.8682 (mt) REVERT: H 34 ILE cc_start: 0.8951 (mt) cc_final: 0.8564 (tt) REVERT: H 47 TRP cc_start: 0.8182 (t60) cc_final: 0.7964 (t60) REVERT: H 48 MET cc_start: 0.8100 (mtp) cc_final: 0.7604 (mtp) REVERT: H 117 TRP cc_start: 0.8369 (m100) cc_final: 0.8045 (m100) REVERT: D 57 ASN cc_start: 0.8411 (t0) cc_final: 0.8198 (p0) outliers start: 2 outliers final: 0 residues processed: 440 average time/residue: 0.3454 time to fit residues: 240.9424 Evaluate side-chains 161 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 0.5980 chunk 245 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 131 optimal weight: 20.0000 chunk 253 optimal weight: 1.9990 chunk 98 optimal weight: 0.0870 chunk 154 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 294 optimal weight: 9.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A 978 ASN A1010 GLN A1048 HIS A1119 ASN B 542 ASN B 914 ASN B1002 GLN B1113 GLN C 87 ASN C 804 GLN C 914 ASN C 926 GLN C 935 GLN C 955 ASN C1005 GLN C1135 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24814 Z= 0.208 Angle : 0.598 6.805 33904 Z= 0.320 Chirality : 0.045 0.188 4184 Planarity : 0.004 0.047 4304 Dihedral : 6.315 75.047 4787 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.41 % Favored : 98.49 % Rotamer: Outliers : 1.95 % Allowed : 7.17 % Favored : 90.88 % 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: 0.89 (0.14), residues: 3181 helix: 1.45 (0.20), residues: 695 sheet: 0.85 (0.16), residues: 867 loop : 0.17 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 36 HIS 0.004 0.001 HIS A1058 PHE 0.024 0.002 PHE C 565 TYR 0.027 0.002 TYR B1067 ARG 0.005 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 189 time to evaluate : 2.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1029 MET cc_start: 0.7704 (ttm) cc_final: 0.7318 (mtt) REVERT: C 423 TYR cc_start: 0.6924 (t80) cc_final: 0.6450 (t80) REVERT: C 870 ILE cc_start: 0.8749 (mm) cc_final: 0.8523 (mt) REVERT: H 101 THR cc_start: 0.8685 (p) cc_final: 0.8292 (p) outliers start: 43 outliers final: 21 residues processed: 222 average time/residue: 0.3296 time to fit residues: 120.6154 Evaluate side-chains 147 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain H residue 37 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 294 optimal weight: 20.0000 chunk 318 optimal weight: 10.0000 chunk 262 optimal weight: 0.8980 chunk 292 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 236 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN B 606 ASN B 804 GLN B 901 GLN C 271 GLN C 655 HIS C1005 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1064 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 24814 Z= 0.429 Angle : 0.694 10.618 33904 Z= 0.360 Chirality : 0.048 0.303 4184 Planarity : 0.004 0.039 4304 Dihedral : 5.641 58.108 4787 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.83 % Favored : 97.11 % Rotamer: Outliers : 2.86 % Allowed : 7.89 % Favored : 89.25 % 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: 0.46 (0.14), residues: 3181 helix: 1.42 (0.20), residues: 674 sheet: 0.37 (0.16), residues: 856 loop : -0.11 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP L 36 HIS 0.010 0.002 HIS C1048 PHE 0.031 0.003 PHE C 906 TYR 0.029 0.002 TYR B1067 ARG 0.006 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 132 time to evaluate : 3.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 996 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8983 (mp) REVERT: H 47 TRP cc_start: 0.8450 (t60) cc_final: 0.8026 (t60) REVERT: H 54 TYR cc_start: 0.8072 (t80) cc_final: 0.7598 (t80) outliers start: 63 outliers final: 37 residues processed: 179 average time/residue: 0.2983 time to fit residues: 91.8600 Evaluate side-chains 147 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 109 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain E residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 7.9990 chunk 221 optimal weight: 0.3980 chunk 152 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 197 optimal weight: 20.0000 chunk 295 optimal weight: 9.9990 chunk 313 optimal weight: 6.9990 chunk 154 optimal weight: 0.6980 chunk 280 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN B 239 GLN B 901 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 24814 Z= 0.173 Angle : 0.526 9.937 33904 Z= 0.275 Chirality : 0.044 0.388 4184 Planarity : 0.003 0.039 4304 Dihedral : 4.917 48.367 4787 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.82 % Favored : 98.11 % Rotamer: Outliers : 2.04 % Allowed : 9.48 % Favored : 88.48 % 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: 0.68 (0.14), residues: 3181 helix: 1.88 (0.20), residues: 680 sheet: 0.38 (0.16), residues: 858 loop : -0.04 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 36 HIS 0.003 0.001 HIS A1048 PHE 0.021 0.001 PHE A 140 TYR 0.021 0.001 TYR B1067 ARG 0.004 0.000 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 146 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8627 (ptm-80) cc_final: 0.8355 (ptp90) REVERT: B 223 LEU cc_start: 0.7820 (mp) cc_final: 0.7496 (mt) REVERT: C 870 ILE cc_start: 0.8965 (mm) cc_final: 0.8727 (mt) REVERT: C 873 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7504 (m-80) REVERT: H 29 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7528 (t80) REVERT: H 54 TYR cc_start: 0.7940 (t80) cc_final: 0.7417 (t80) REVERT: E 36 TRP cc_start: 0.7182 (OUTLIER) cc_final: 0.6882 (m-10) outliers start: 45 outliers final: 30 residues processed: 179 average time/residue: 0.3198 time to fit residues: 96.4323 Evaluate side-chains 151 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 118 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain E residue 36 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 233 optimal weight: 0.9980 chunk 129 optimal weight: 50.0000 chunk 267 optimal weight: 0.9980 chunk 216 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN B 955 ASN C1048 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 24814 Z= 0.291 Angle : 0.564 10.917 33904 Z= 0.290 Chirality : 0.045 0.404 4184 Planarity : 0.004 0.045 4304 Dihedral : 4.829 39.977 4787 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.96 % Favored : 96.98 % Rotamer: Outliers : 2.40 % Allowed : 10.57 % Favored : 87.02 % 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: 0.55 (0.15), residues: 3181 helix: 1.80 (0.20), residues: 681 sheet: 0.25 (0.16), residues: 867 loop : -0.12 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 117 HIS 0.006 0.001 HIS C1048 PHE 0.021 0.002 PHE A 140 TYR 0.023 0.002 TYR B1067 ARG 0.014 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 129 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8664 (ptm-80) cc_final: 0.8319 (ptp90) REVERT: C 873 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7716 (m-80) REVERT: H 54 TYR cc_start: 0.7993 (t80) cc_final: 0.7461 (t80) REVERT: E 36 TRP cc_start: 0.7311 (OUTLIER) cc_final: 0.7050 (m-10) outliers start: 53 outliers final: 35 residues processed: 165 average time/residue: 0.3285 time to fit residues: 92.8024 Evaluate side-chains 151 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 114 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain E residue 36 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 6.9990 chunk 282 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 183 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 313 optimal weight: 8.9990 chunk 260 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 103 optimal weight: 20.0000 chunk 164 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24814 Z= 0.212 Angle : 0.523 8.727 33904 Z= 0.268 Chirality : 0.044 0.253 4184 Planarity : 0.003 0.039 4304 Dihedral : 4.583 34.148 4787 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.48 % Favored : 97.45 % Rotamer: Outliers : 1.95 % Allowed : 11.48 % Favored : 86.57 % 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: 0.58 (0.15), residues: 3181 helix: 2.05 (0.21), residues: 668 sheet: 0.26 (0.17), residues: 862 loop : -0.17 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 36 HIS 0.004 0.001 HIS C1048 PHE 0.026 0.001 PHE A 140 TYR 0.021 0.001 TYR B1067 ARG 0.015 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 131 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8648 (ptm-80) cc_final: 0.8294 (ptp90) REVERT: B 223 LEU cc_start: 0.7793 (mp) cc_final: 0.7416 (mt) REVERT: C 869 MET cc_start: 0.7509 (mmm) cc_final: 0.7093 (mtt) REVERT: C 873 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.7636 (m-80) REVERT: H 47 TRP cc_start: 0.8602 (t60) cc_final: 0.8072 (t60) REVERT: H 54 TYR cc_start: 0.8027 (t80) cc_final: 0.7437 (t80) REVERT: E 36 TRP cc_start: 0.7293 (OUTLIER) cc_final: 0.7063 (m-10) outliers start: 43 outliers final: 32 residues processed: 162 average time/residue: 0.3126 time to fit residues: 86.7348 Evaluate side-chains 146 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 112 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain E residue 36 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 178 optimal weight: 0.6980 chunk 228 optimal weight: 0.9990 chunk 177 optimal weight: 0.6980 chunk 263 optimal weight: 3.9990 chunk 175 optimal weight: 0.7980 chunk 312 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24814 Z= 0.208 Angle : 0.516 9.663 33904 Z= 0.263 Chirality : 0.044 0.313 4184 Planarity : 0.003 0.040 4304 Dihedral : 4.465 38.896 4787 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.21 % Favored : 96.73 % Rotamer: Outliers : 1.91 % Allowed : 11.80 % Favored : 86.30 % 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: 0.59 (0.15), residues: 3181 helix: 2.16 (0.21), residues: 656 sheet: 0.20 (0.17), residues: 869 loop : -0.15 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 36 HIS 0.004 0.001 HIS B1058 PHE 0.028 0.001 PHE A 140 TYR 0.020 0.001 TYR B1067 ARG 0.011 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 121 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 223 LEU cc_start: 0.7811 (mp) cc_final: 0.7450 (mt) REVERT: C 869 MET cc_start: 0.7409 (mmm) cc_final: 0.7189 (mtt) REVERT: C 873 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.7731 (m-80) REVERT: H 47 TRP cc_start: 0.8580 (t60) cc_final: 0.8076 (t60) REVERT: H 54 TYR cc_start: 0.7991 (t80) cc_final: 0.7428 (t80) outliers start: 42 outliers final: 35 residues processed: 152 average time/residue: 0.2973 time to fit residues: 78.2683 Evaluate side-chains 147 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 111 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 111 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 5.9990 chunk 124 optimal weight: 0.3980 chunk 186 optimal weight: 0.0670 chunk 94 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 245 optimal weight: 3.9990 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24814 Z= 0.207 Angle : 0.518 12.382 33904 Z= 0.265 Chirality : 0.044 0.269 4184 Planarity : 0.003 0.038 4304 Dihedral : 4.402 36.698 4787 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.73 % Favored : 97.20 % Rotamer: Outliers : 2.13 % Allowed : 11.93 % Favored : 85.93 % 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: 0.55 (0.15), residues: 3181 helix: 2.08 (0.21), residues: 665 sheet: 0.13 (0.17), residues: 863 loop : -0.14 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP L 36 HIS 0.003 0.001 HIS C1048 PHE 0.030 0.001 PHE A 140 TYR 0.020 0.001 TYR B1067 ARG 0.008 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 118 time to evaluate : 3.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1019 ARG cc_start: 0.8164 (tpt90) cc_final: 0.7891 (tpt90) REVERT: B 223 LEU cc_start: 0.7754 (mp) cc_final: 0.7411 (mt) REVERT: C 873 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.7727 (m-80) REVERT: C 916 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8000 (tp) REVERT: C 1126 CYS cc_start: 0.5464 (m) cc_final: 0.5111 (t) REVERT: H 54 TYR cc_start: 0.8038 (t80) cc_final: 0.7474 (t80) outliers start: 47 outliers final: 36 residues processed: 155 average time/residue: 0.3192 time to fit residues: 86.5289 Evaluate side-chains 150 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 112 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 111 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 5.9990 chunk 299 optimal weight: 40.0000 chunk 272 optimal weight: 0.9980 chunk 291 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 126 optimal weight: 30.0000 chunk 228 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 262 optimal weight: 0.6980 chunk 275 optimal weight: 0.6980 chunk 289 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 978 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24814 Z= 0.238 Angle : 0.530 11.948 33904 Z= 0.271 Chirality : 0.044 0.272 4184 Planarity : 0.003 0.038 4304 Dihedral : 4.438 34.975 4787 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.52 % Favored : 96.42 % Rotamer: Outliers : 2.22 % Allowed : 12.16 % Favored : 85.62 % 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: 0.51 (0.15), residues: 3181 helix: 2.03 (0.21), residues: 664 sheet: 0.13 (0.17), residues: 853 loop : -0.17 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 47 HIS 0.004 0.001 HIS B1058 PHE 0.030 0.001 PHE A 140 TYR 0.021 0.001 TYR B1067 ARG 0.004 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 112 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 873 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7837 (m-80) REVERT: C 916 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8012 (tp) REVERT: H 54 TYR cc_start: 0.8026 (t80) cc_final: 0.7477 (t80) outliers start: 49 outliers final: 40 residues processed: 148 average time/residue: 0.2820 time to fit residues: 73.1109 Evaluate side-chains 151 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 109 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 0.8980 chunk 307 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 145 optimal weight: 0.5980 chunk 213 optimal weight: 1.9990 chunk 322 optimal weight: 30.0000 chunk 297 optimal weight: 0.8980 chunk 257 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 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 978 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24814 Z= 0.171 Angle : 0.498 12.660 33904 Z= 0.255 Chirality : 0.043 0.317 4184 Planarity : 0.003 0.040 4304 Dihedral : 4.262 36.427 4787 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.52 % Rotamer: Outliers : 1.59 % Allowed : 12.84 % Favored : 85.57 % 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: 0.59 (0.15), residues: 3181 helix: 2.09 (0.21), residues: 671 sheet: 0.19 (0.17), residues: 864 loop : -0.15 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 47 HIS 0.003 0.001 HIS C1048 PHE 0.030 0.001 PHE A 140 TYR 0.019 0.001 TYR B1067 ARG 0.005 0.000 ARG H 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 120 time to evaluate : 2.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1019 ARG cc_start: 0.8198 (tpt90) cc_final: 0.7950 (tpt90) REVERT: B 902 MET cc_start: 0.8974 (tpp) cc_final: 0.8552 (tpp) REVERT: C 916 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7971 (tp) REVERT: H 54 TYR cc_start: 0.8014 (t80) cc_final: 0.7455 (t80) outliers start: 35 outliers final: 27 residues processed: 148 average time/residue: 0.3080 time to fit residues: 78.3187 Evaluate side-chains 137 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 4.9990 chunk 273 optimal weight: 0.1980 chunk 78 optimal weight: 2.9990 chunk 237 optimal weight: 0.0570 chunk 37 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 257 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.4504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.104173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.085586 restraints weight = 66336.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.086645 restraints weight = 53227.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.087123 restraints weight = 40334.215| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24814 Z= 0.264 Angle : 0.540 12.205 33904 Z= 0.276 Chirality : 0.044 0.276 4184 Planarity : 0.003 0.039 4304 Dihedral : 4.447 36.037 4787 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.74 % Favored : 96.20 % Rotamer: Outliers : 1.81 % Allowed : 12.79 % Favored : 85.39 % 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: 0.48 (0.15), residues: 3181 helix: 1.98 (0.21), residues: 668 sheet: 0.11 (0.17), residues: 880 loop : -0.19 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 47 HIS 0.005 0.001 HIS B1058 PHE 0.031 0.002 PHE A 140 TYR 0.023 0.001 TYR B1067 ARG 0.005 0.000 ARG H 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3795.11 seconds wall clock time: 69 minutes 42.44 seconds (4182.44 seconds total)