Starting phenix.real_space_refine on Thu Apr 11 16:05:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzl_22532/04_2024/7jzl_22532.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzl_22532/04_2024/7jzl_22532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzl_22532/04_2024/7jzl_22532.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzl_22532/04_2024/7jzl_22532.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzl_22532/04_2024/7jzl_22532.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzl_22532/04_2024/7jzl_22532.pdb" } resolution = 2.7 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= 0.079 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 102 5.16 5 C 14661 2.51 5 N 3858 2.21 5 O 4502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "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 ASP 287": "OD1" <-> "OD2" 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 PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "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 PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 408": "NH1" <-> "NH2" 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 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 796": "OD1" <-> "OD2" 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 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1150": "OE1" <-> "OE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "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 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "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 PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 646": "NH1" <-> "NH2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "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 GLU 1017": "OE1" <-> "OE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C 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 PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "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 ARG 355": "NH1" <-> "NH2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 574": "OD1" <-> "OD2" 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 PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" 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 TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1017": "OE1" <-> "OE2" 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 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 23123 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 7420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 980, 7420 Classifications: {'peptide': 980} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 53, 'TRANS': 926} Chain breaks: 10 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 10, 'PHE:plan': 5, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 172 Chain: "E" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 273 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'TRANS': 54} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "C" Number of atoms: 6978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 6978 Classifications: {'peptide': 984} Incomplete info: {'truncation_to_alanine': 211} Link IDs: {'PTRANS': 53, 'TRANS': 930} Chain breaks: 8 Unresolved non-hydrogen bonds: 736 Unresolved non-hydrogen angles: 947 Unresolved non-hydrogen dihedrals: 605 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 15, 'ASN:plan1': 19, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 13, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 445 Chain: "G" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 273 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'TRANS': 54} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "B" Number of atoms: 7080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7080 Classifications: {'peptide': 976} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PTRANS': 52, 'TRANS': 923} Chain breaks: 9 Unresolved non-hydrogen bonds: 566 Unresolved non-hydrogen angles: 730 Unresolved non-hydrogen dihedrals: 470 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 13, 'ASN:plan1': 19, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 11, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 371 Chain: "F" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 273 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'TRANS': 54} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: "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 Chain: "B" 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: 11.95, per 1000 atoms: 0.52 Number of scatterers: 23123 At special positions: 0 Unit cell: (129.15, 133.35, 200.55, 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 102 16.00 O 4502 8.00 N 3858 7.00 C 14661 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.09 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.01 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=2.08 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.13 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.10 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.06 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 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 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.08 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.11 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 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-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 122 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C1074 " " NAG D 1 " - " ASN A 717 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN C 717 " " NAG L 1 " - " ASN C1098 " " NAG M 1 " - " ASN C1134 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN B 801 " Time building additional restraints: 9.74 Conformation dependent library (CDL) restraints added in 4.4 seconds 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5824 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 48 sheets defined 29.0% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 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 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.187A 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 502 through 505 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.667A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.771A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.763A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.085A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.889A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.161A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'E' and resid 2 through 19 Processing helix chain 'E' and resid 21 through 36 Processing helix chain 'E' and resid 41 through 55 removed outlier: 4.063A pdb=" N GLU E 45 " --> pdb=" O GLU E 41 " (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 365 through 370 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.800A 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 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.976A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.886A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.995A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.248A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'G' and resid 2 through 19 Processing helix chain 'G' and resid 21 through 36 Processing helix chain 'G' and resid 41 through 55 removed outlier: 4.168A pdb=" N GLU G 45 " --> pdb=" O GLU G 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.390A 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 removed outlier: 3.694A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) 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: 3.817A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 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 939 Processing helix chain 'B' and resid 941 through 944 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.883A 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 977 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.756A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'F' and resid 2 through 19 Processing helix chain 'F' and resid 21 through 36 removed outlier: 3.852A pdb=" N LEU F 31 " --> pdb=" O ARG F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 55 removed outlier: 4.242A pdb=" N GLU F 45 " --> pdb=" O GLU F 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.011A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.831A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.732A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.033A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.310A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.250A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.346A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.346A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.440A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.181A pdb=" N TYR A 660 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.601A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.704A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.806A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.852A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.426A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.673A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.927A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.833A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.338A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.500A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.258A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.558A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.439A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.584A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.704A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.929A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.414A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 787 through 790 Processing sheet with id=AD7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.437A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.687A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.437A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.705A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AE2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.376A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.078A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.078A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.523A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.573A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.378A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.876A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.453A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.818A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) 1135 hydrogen bonds defined for protein. 3114 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: 11.56 Time building geometry restraints manager: 10.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4955 1.32 - 1.46: 7470 1.46 - 1.59: 11018 1.59 - 1.73: 6 1.73 - 1.86: 126 Bond restraints: 23575 Sorted by residual: bond pdb=" N PRO C 600 " pdb=" CD PRO C 600 " ideal model delta sigma weight residual 1.473 1.543 -0.070 1.40e-02 5.10e+03 2.48e+01 bond pdb=" CB LEU C 242 " pdb=" CG LEU C 242 " ideal model delta sigma weight residual 1.530 1.614 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" CB LEU A 110 " pdb=" CG LEU A 110 " ideal model delta sigma weight residual 1.530 1.613 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" CB LEU B 242 " pdb=" CG LEU B 242 " ideal model delta sigma weight residual 1.530 1.613 -0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" CB LEU C 916 " pdb=" CG LEU C 916 " ideal model delta sigma weight residual 1.530 1.611 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 23570 not shown) Histogram of bond angle deviations from ideal: 92.22 - 100.59: 9 100.59 - 108.95: 2410 108.95 - 117.31: 15419 117.31 - 125.68: 14147 125.68 - 134.04: 235 Bond angle restraints: 32220 Sorted by residual: angle pdb=" CD1 LEU B 962 " pdb=" CG LEU B 962 " pdb=" CD2 LEU B 962 " ideal model delta sigma weight residual 110.80 133.93 -23.13 2.20e+00 2.07e-01 1.11e+02 angle pdb=" CD1 LEU C 916 " pdb=" CG LEU C 916 " pdb=" CD2 LEU C 916 " ideal model delta sigma weight residual 110.80 132.63 -21.83 2.20e+00 2.07e-01 9.85e+01 angle pdb=" CD1 LEU A 938 " pdb=" CG LEU A 938 " pdb=" CD2 LEU A 938 " ideal model delta sigma weight residual 110.80 132.25 -21.45 2.20e+00 2.07e-01 9.51e+01 angle pdb=" CD1 LEU B 966 " pdb=" CG LEU B 966 " pdb=" CD2 LEU B 966 " ideal model delta sigma weight residual 110.80 130.86 -20.06 2.20e+00 2.07e-01 8.31e+01 angle pdb=" CD1 LEU B1012 " pdb=" CG LEU B1012 " pdb=" CD2 LEU B1012 " ideal model delta sigma weight residual 110.80 92.22 18.58 2.20e+00 2.07e-01 7.13e+01 ... (remaining 32215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 14219 18.00 - 35.99: 447 35.99 - 53.99: 76 53.99 - 71.98: 41 71.98 - 89.98: 14 Dihedral angle restraints: 14797 sinusoidal: 5802 harmonic: 8995 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 151.05 -58.05 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 134.82 -41.82 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -50.88 -35.12 1 1.00e+01 1.00e-02 1.75e+01 ... (remaining 14794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 3741 0.208 - 0.416: 230 0.416 - 0.624: 4 0.624 - 0.833: 1 0.833 - 1.041: 1 Chirality restraints: 3977 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.08e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.56e+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 -2.56 0.16 2.00e-02 2.50e+03 6.36e+01 ... (remaining 3974 not shown) Planarity restraints: 4190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.053 2.00e-02 2.50e+03 5.41e-02 3.66e+01 pdb=" CG ASN C 331 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.083 2.00e-02 2.50e+03 pdb=" C1 NAG C1305 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.045 2.00e-02 2.50e+03 4.52e-02 2.55e+01 pdb=" CG ASN C 234 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " 0.067 2.00e-02 2.50e+03 pdb=" C1 NAG C1301 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " -0.041 2.00e-02 2.50e+03 4.36e-02 2.38e+01 pdb=" CG ASN B 709 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " 0.069 2.00e-02 2.50e+03 pdb=" C1 NAG B1309 " -0.053 2.00e-02 2.50e+03 ... (remaining 4187 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 7029 2.83 - 3.35: 20549 3.35 - 3.87: 38567 3.87 - 4.38: 44350 4.38 - 4.90: 73972 Nonbonded interactions: 184467 Sorted by model distance: nonbonded pdb=" ND2 ASN C 196 " pdb=" O ILE C 233 " model vdw 2.317 2.520 nonbonded pdb=" NZ LYS A 825 " pdb=" O LEU A 938 " model vdw 2.388 2.520 nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.396 2.520 nonbonded pdb=" N SER B 813 " pdb=" N LYS B 814 " model vdw 2.398 2.560 nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 2.407 2.520 ... (remaining 184462 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 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 93 or (resid 94 through 100 and (n \ ame N or name CA or name C or name O or name CB )) or resid 101 through 107 or ( \ resid 108 through 116 and (name N or name CA or name C or name O or name CB )) o \ r resid 117 through 119 or (resid 120 and (name N or name CA or name C or name O \ or name CB )) or resid 121 through 135 or (resid 138 and (name N or name CA or \ name C or name O or name CB )) or resid 139 through 140 or resid 166 through 172 \ or (resid 188 through 190 and (name N or name CA or name C or name O or name CB \ )) or resid 191 through 204 or (resid 205 and (name N or name CA or name C or n \ ame O or name CB )) or resid 206 through 207 or (resid 208 and (name N or name C \ A or name C or name O or name CB )) or resid 209 or (resid 210 and (name N or na \ me CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 a \ nd (name N or name CA or name C or name O or name CB )) or resid 219 through 220 \ or (resid 221 through 222 and (name N or name CA or name C or name O or name CB \ )) or resid 223 through 227 or (resid 228 through 229 and (name N or name CA or \ name C or name O or name CB )) or resid 230 through 322 or (resid 323 through 3 \ 24 and (name N or name CA or name C or name O or name CB )) or resid 325 through \ 331 or (resid 332 through 335 and (name N or name CA or name C or name O or nam \ e CB )) or resid 336 through 339 or (resid 340 through 342 and (name N or name C \ A or name C or name O or name CB )) or resid 343 through 346 or (resid 347 throu \ gh 352 and (name N or name CA or name C or name O or name CB )) or resid 353 thr \ ough 356 or (resid 357 and (name N or name CA or name C or name O or name CB )) \ or resid 358 or (resid 359 through 360 and (name N or name CA or name C or name \ O or name CB )) or resid 361 through 363 or (resid 364 through 378 and (name N o \ r 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 throu \ gh 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 391 through 397 or (resid 398 through 403 and (name N or name CA or nam \ e 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 name CB )) or resid 412 through 413 or (resid 414 through 41 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 416 or (resi \ d 417 through 425 and (name N or name CA or name C or name O or name CB )) or re \ sid 426 through 428 or (resid 429 through 430 and (name N or name CA or name C o \ r name O or name CB )) or resid 431 through 432 or (resid 433 through 445 and (n \ ame N or name CA or name C or name O or name CB )) or resid 446 through 447 or ( \ resid 448 through 462 and (name N or name CA or name C or name O or name CB )) o \ r resid 463 or (resid 464 through 475 and (name N or name CA or name C or name O \ or name CB )) or resid 476 through 488 or (resid 489 through 490 and (name N or \ name CA or name C or name O or name CB )) or resid 491 or (resid 492 through 49 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 496 or (resi \ d 497 through 498 and (name N or name CA or name C or name O or name CB )) or re \ sid 499 through 500 or (resid 501 and (name N or name CA or name C or name O or \ name CB )) or resid 502 or (resid 503 and (name N or name CA or name C or name O \ or name CB )) or resid 504 or (resid 505 through 506 and (name N or name CA or \ name C or name O or name CB )) or resid 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 (na \ me N or name CA or name C or name O or name CB )) or resid 525 through 527 or (r \ esid 528 through 531 and (name N or name CA or name C or name O or name CB )) or \ resid 532 through 536 or (resid 537 and (name N or name CA or name C or name O \ or name CB )) or resid 538 through 553 or (resid 554 and (name N or name CA or n \ ame C or name O or name CB )) or resid 555 through 580 or (resid 581 and (name N \ or name CA or name C or name O or name CB )) or resid 582 or (resid 583 and (na \ me N or name CA or name C or name O or name CB )) or resid 584 through 653 or (r \ esid 654 and (name N or name CA or name C or name O or name CB )) or resid 655 t \ hrough 675 or (resid 676 and (name N or name CA or name 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 nam \ e O or name CB )) or resid 703 through 744 or (resid 745 through 746 and (name N \ or name CA or name C or name O or name CB )) or resid 747 or (resid 748 and (na \ me N or name CA or name C or name O or name CB )) or resid 749 or (resid 750 and \ (name N or name CA or name C or name O or name CB )) or resid 751 through 757 o \ r (resid 758 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 59 through 785 or (resid 786 and (name N or name CA or name C or name O or name \ CB )) or resid 787 through 793 or (resid 794 and (name N or name CA or name C or \ name O or name CB )) or resid 795 through 810 or (resid 811 and (name N or name \ CA or name C or name O or name CB )) or resid 812 through 813 or (resid 814 and \ (name N or name CA or name C or name O or name CB )) or resid 815 through 936 o \ r (resid 937 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 38 or (resid 939 through 941 and (name N or name CA or name C or name O or name \ CB )) or resid 942 through 973 or (resid 974 and (name N or name CA or name C or \ name O or name CB )) or resid 975 through 987 or (resid 988 through 989 and (na \ me N or name CA or name C or name O or name CB )) or resid 990 through 1044 or ( \ resid 1045 and (name N or name CA or name C or name O or name CB )) or resid 104 \ 6 through 1091 or (resid 1092 and (name N or name CA or name C or name O or name \ CB )) or resid 1093 through 1126 or (resid 1127 and (name N or name CA or name \ C or name O or name CB )) or resid 1128 through 1141 or (resid 1142 and (name N \ or name CA or name C or name O or name CB )) or resid 1143 or (resid 1144 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1145 through 1146 or \ (resid 1147 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 301 through 1311)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 86 or (resid 87 and (nam \ e N or name CA or name C or name O or name CB )) or resid 88 through 93 or (resi \ d 94 through 100 and (name N or name CA or name C or name O or name CB )) or res \ id 101 through 107 or (resid 108 through 110 and (name N or name CA or name C or \ name O or name CB )) or (resid 116 and (name N or name CA or name C or name O o \ r name CB )) or resid 117 through 119 or (resid 120 and (name N or name CA or na \ me C or name O or name CB )) or resid 121 through 125 or (resid 126 through 129 \ and (name N or name CA or name C or name O or name CB )) or resid 130 through 13 \ 1 or (resid 132 and (name N or name CA or name C or name O or name CB )) or resi \ d 133 or (resid 134 and (name N or name CA or name C or name O or name CB )) or \ resid 135 or (resid 138 and (name N or name CA or name C or name O or name CB )) \ or resid 139 or (resid 140 and (name N or name CA or name C or name O or name C \ B )) or resid 166 or (resid 167 through 190 and (name N or name CA or name C or \ name O or name CB )) or resid 191 through 197 or (resid 198 and (name N or name \ CA or name C or name O or name CB )) or resid 199 through 204 or (resid 205 and \ (name N or name CA or name C or name O or name CB )) or resid 206 through 207 or \ (resid 208 and (name N or name CA or name C or name O or name CB )) or resid 20 \ 9 through 217 or (resid 218 and (name N or name CA or name C or name O or name C \ B )) or resid 219 through 228 or (resid 229 and (name N or name CA or name C or \ name O or name CB )) or resid 230 through 280 or (resid 281 and (name N or name \ CA or name C or name O or name CB )) or resid 282 through 323 or (resid 324 and \ (name N or name CA or name C or name O or name CB )) or resid 325 through 331 or \ (resid 332 through 335 and (name N or name CA or name C or name O or name CB )) \ or resid 336 through 339 or (resid 340 through 342 and (name N or name CA or na \ me C or name O or name CB )) or resid 343 through 356 or (resid 357 and (name N \ or name CA or name C or name O or name CB )) or resid 358 through 364 or (resid \ 365 through 378 and (name N or name CA or name C or name O or name CB )) or resi \ d 379 through 389 or (resid 390 and (name N or name CA or name C or name O or na \ me CB )) or resid 391 through 397 or (resid 398 through 403 and (name N or name \ CA or name C or name O or name CB )) or resid 404 through 417 or (resid 418 thro \ ugh 425 and (name N or name CA or name C or name O or name CB )) or resid 426 th \ rough 510 or (resid 511 through 524 and (name N or name CA or name C or name O o \ r name CB )) or resid 525 through 528 or (resid 529 through 531 and (name N or n \ ame CA or name C or name O or name CB )) or resid 532 through 536 or (resid 537 \ and (name N or name CA or name C or name O or name CB )) or resid 538 through 55 \ 5 or (resid 556 and (name N or name CA or name C or name O or name CB )) or resi \ d 557 or (resid 558 and (name N or name CA or name C or name O or name CB )) or \ resid 559 through 580 or (resid 581 and (name N or name CA or name C or name O o \ r name CB )) or resid 582 through 645 or (resid 646 through 647 and (name N or n \ ame CA or name C or name O or name CB )) or resid 648 through 653 or (resid 654 \ and (name N or name CA or name C or name O or name CB )) or resid 655 through 74 \ 4 or (resid 745 through 746 and (name N or name CA or name C or name O or name C \ B )) or resid 747 or (resid 748 and (name N or name CA or name C or name O or na \ me CB )) or resid 749 or (resid 750 and (name N or name CA or name C or name O o \ r name CB )) or resid 751 through 757 or (resid 758 and (name N or name CA or na \ me C or name O or name CB )) or resid 759 through 809 or (resid 810 through 811 \ and (name N or name CA or name C or name O or name CB )) or resid 812 through 81 \ 3 or (resid 814 and (name N or name CA or name C or name O or name CB )) or resi \ d 815 through 826 or resid 856 through 936 or (resid 937 and (name N or name CA \ or name C or name O or name CB )) or resid 938 or (resid 939 through 941 and (na \ me N or name CA or name C or name O or name CB )) or resid 942 through 973 or (r \ esid 974 and (name N or name CA or name C or name O or name CB )) or resid 975 t \ hrough 984 or (resid 985 and (name N or name CA or name C or name O or name CB ) \ ) or resid 986 through 987 or (resid 988 through 989 and (name N or name CA or n \ ame C or name O or name CB )) or resid 990 through 1044 or (resid 1045 and (name \ N or name CA or name C or name O or name CB )) or resid 1046 through 1126 or (r \ esid 1127 and (name N or name CA or name C or name O or name CB )) or resid 1128 \ through 1141 or (resid 1142 and (name N or name CA or name C or name O or name \ CB )) or resid 1143 through 1147 or resid 1301 through 1311)) selection = (chain 'C' and (resid 27 through 110 or resid 116 through 126 or (resid 127 thro \ ugh 129 and (name N or name CA or name C or name O or name CB )) or resid 130 th \ rough 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) \ or resid 133 through 135 or resid 138 through 140 or resid 166 through 172 or ( \ resid 188 through 190 and (name N or name CA or name C or name O or name CB )) o \ r resid 191 through 210 or resid 216 through 220 or (resid 221 through 222 and ( \ name N or name CA or name C or name O or name CB )) or resid 223 through 227 or \ (resid 228 through 229 and (name N or name CA or name C or name O or name CB )) \ or resid 230 through 236 or (resid 237 and (name N or name CA or name C or name \ O or name CB )) or resid 238 through 346 or (resid 347 through 352 and (name N o \ r name CA or name C or name O or name CB )) or resid 353 through 373 or (resid 3 \ 74 through 378 and (name N or name CA or name C or name O or name CB )) or resid \ 379 through 393 or (resid 394 and (name N or name CA or name C or name O or nam \ e CB )) or resid 395 through 515 or resid 522 through 553 or (resid 554 and (nam \ e N or name CA or name C or name O or name CB )) or resid 555 or (resid 556 and \ (name N or name CA or name C or name O or name CB )) or resid 557 or (resid 558 \ and (name N or name CA or name C or name O or name CB )) or resid 559 through 56 \ 7 or (resid 568 and (name N or name CA or name C or name O or name CB )) or resi \ d 569 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 675 or (resid 676 and (name N or name \ CA or name 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 793 or \ (resid 794 and (name N or name CA or name C or name O or name CB )) or resid 79 \ 5 through 809 or (resid 810 through 811 and (name N or name CA or name C or name \ O or name CB )) or resid 812 or (resid 813 through 814 and (name N or name CA o \ r name C or name O or name CB )) or resid 815 through 826 or resid 856 through 9 \ 84 or (resid 985 and (name N or name CA or name C or name O or name CB )) or res \ id 986 through 1143 or (resid 1144 and (name N or name CA or name C or name O or \ name CB )) or resid 1145 through 1146 or (resid 1147 and (name N or name CA or \ name C or name O or name CB )) or resid 1301 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.170 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: 0.020 Extract box with map and model: 13.800 Check model and map are aligned: 0.360 Set scattering table: 0.200 Process input model: 64.470 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.260 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:13.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 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 : 0.014 0.125 23575 Z= 0.927 Angle : 1.435 23.131 32220 Z= 0.959 Chirality : 0.100 1.041 3977 Planarity : 0.005 0.024 4144 Dihedral : 9.945 89.979 8856 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.30 % Favored : 97.53 % Rotamer: Outliers : 0.61 % Allowed : 0.93 % Favored : 98.46 % 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: 0.44 (0.14), residues: 3039 helix: 0.31 (0.17), residues: 810 sheet: 0.90 (0.19), residues: 631 loop : 0.16 (0.14), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.006 TRP C1102 HIS 0.005 0.001 HIS A1083 PHE 0.028 0.004 PHE A 898 TYR 0.046 0.005 TYR A 495 ARG 0.006 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 463 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 740 MET cc_start: 0.7654 (ttt) cc_final: 0.7386 (ttm) REVERT: C 756 TYR cc_start: 0.7962 (m-80) cc_final: 0.7733 (m-80) REVERT: C 902 MET cc_start: 0.8493 (mmp) cc_final: 0.8280 (mmp) REVERT: B 725 GLU cc_start: 0.7557 (tt0) cc_final: 0.7326 (tt0) REVERT: B 1029 MET cc_start: 0.9064 (tpp) cc_final: 0.8659 (tpp) outliers start: 13 outliers final: 2 residues processed: 476 average time/residue: 1.2700 time to fit residues: 697.5215 Evaluate side-chains 237 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 235 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain B residue 585 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 0.5980 chunk 233 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 157 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 241 optimal weight: 40.0000 chunk 93 optimal weight: 0.5980 chunk 146 optimal weight: 3.9990 chunk 179 optimal weight: 0.5980 chunk 279 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1002 GLN A1125 ASN C 207 HIS C 613 GLN C 784 GLN C 965 GLN C1005 GLN B 115 GLN B 196 ASN B 544 ASN B 580 GLN B 804 GLN B 856 ASN B 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1005 GLN B1048 HIS B1071 GLN B1135 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23575 Z= 0.226 Angle : 0.607 8.266 32220 Z= 0.324 Chirality : 0.050 0.905 3977 Planarity : 0.004 0.039 4144 Dihedral : 5.483 58.255 4485 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.48 % Favored : 98.49 % Rotamer: Outliers : 2.48 % Allowed : 10.14 % Favored : 87.39 % 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: 0.92 (0.14), residues: 3039 helix: 1.83 (0.18), residues: 804 sheet: 0.60 (0.18), residues: 673 loop : 0.04 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.009 0.001 HIS A 655 PHE 0.025 0.002 PHE B 32 TYR 0.026 0.002 TYR A 495 ARG 0.006 0.001 ARG A1091 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 267 time to evaluate : 2.447 Fit side-chains revert: symmetry clash REVERT: A 332 ILE cc_start: 0.6939 (mp) cc_final: 0.6737 (mp) REVERT: C 760 CYS cc_start: 0.5804 (OUTLIER) cc_final: 0.5574 (t) REVERT: C 902 MET cc_start: 0.8423 (mmp) cc_final: 0.8203 (mmp) REVERT: C 990 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6863 (mt-10) REVERT: B 661 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6854 (tt0) REVERT: B 725 GLU cc_start: 0.7649 (tt0) cc_final: 0.7412 (tt0) REVERT: B 918 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7380 (mt-10) REVERT: B 947 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7841 (mmtm) REVERT: B 1029 MET cc_start: 0.8964 (tpp) cc_final: 0.8664 (tpp) outliers start: 53 outliers final: 21 residues processed: 298 average time/residue: 1.2067 time to fit residues: 419.6685 Evaluate side-chains 238 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 212 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 232 optimal weight: 0.0670 chunk 190 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 302 optimal weight: 0.7980 chunk 249 optimal weight: 0.6980 chunk 277 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 804 GLN A 935 GLN A 955 ASN A1002 GLN A1011 GLN A1071 GLN A1125 ASN C 30 ASN C 207 HIS C 955 ASN B 856 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1101 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23575 Z= 0.217 Angle : 0.546 6.773 32220 Z= 0.289 Chirality : 0.046 0.470 3977 Planarity : 0.004 0.037 4144 Dihedral : 4.729 56.147 4483 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.81 % Favored : 98.09 % Rotamer: Outliers : 3.22 % Allowed : 10.93 % Favored : 85.85 % 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: 0.91 (0.15), residues: 3039 helix: 2.15 (0.18), residues: 797 sheet: 0.46 (0.18), residues: 670 loop : -0.09 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.005 0.001 HIS A 655 PHE 0.024 0.002 PHE B 133 TYR 0.023 0.002 TYR A 495 ARG 0.005 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 241 time to evaluate : 2.728 Fit side-chains REVERT: A 309 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6554 (tm-30) REVERT: A 357 ARG cc_start: 0.6959 (tpt-90) cc_final: 0.6759 (ttm-80) REVERT: C 568 ASP cc_start: 0.6330 (m-30) cc_final: 0.6007 (p0) REVERT: C 760 CYS cc_start: 0.5894 (OUTLIER) cc_final: 0.5672 (t) REVERT: C 990 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6944 (mt-10) REVERT: B 725 GLU cc_start: 0.7687 (tt0) cc_final: 0.7442 (tt0) REVERT: B 787 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7434 (mt0) REVERT: B 918 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7303 (mt-10) outliers start: 69 outliers final: 28 residues processed: 287 average time/residue: 1.1805 time to fit residues: 396.6364 Evaluate side-chains 235 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 202 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 297 optimal weight: 0.5980 chunk 146 optimal weight: 0.7980 chunk 266 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN C 207 HIS C 613 GLN C 690 GLN B 66 HIS B 613 GLN B 658 ASN B 856 ASN B 926 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1101 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 23575 Z= 0.394 Angle : 0.633 9.173 32220 Z= 0.331 Chirality : 0.049 0.419 3977 Planarity : 0.004 0.039 4144 Dihedral : 5.118 58.055 4483 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.44 % Favored : 97.47 % Rotamer: Outliers : 3.92 % Allowed : 11.02 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.54 (0.15), residues: 3039 helix: 1.96 (0.19), residues: 798 sheet: 0.25 (0.18), residues: 673 loop : -0.39 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 886 HIS 0.006 0.002 HIS A 655 PHE 0.029 0.002 PHE B 133 TYR 0.026 0.002 TYR C1067 ARG 0.006 0.001 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 232 time to evaluate : 2.447 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7473 (tt0) REVERT: A 309 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6551 (tm-30) REVERT: A 786 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6879 (mttp) REVERT: A 787 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7415 (mt0) REVERT: A 1113 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7577 (mt0) REVERT: C 237 ARG cc_start: 0.7274 (mtp-110) cc_final: 0.6892 (ptm-80) REVERT: C 990 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7094 (mt-10) REVERT: B 200 TYR cc_start: 0.6500 (m-80) cc_final: 0.6271 (m-80) REVERT: B 661 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.6953 (tt0) REVERT: B 725 GLU cc_start: 0.7729 (tt0) cc_final: 0.7508 (tt0) REVERT: B 787 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7601 (mt0) REVERT: B 918 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: B 1029 MET cc_start: 0.9052 (tpp) cc_final: 0.8763 (tpp) outliers start: 84 outliers final: 38 residues processed: 287 average time/residue: 1.1134 time to fit residues: 378.1634 Evaluate side-chains 257 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 210 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 20.0000 chunk 168 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 254 optimal weight: 2.9990 chunk 205 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN B 66 HIS B 544 ASN B 856 ASN B 926 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23575 Z= 0.280 Angle : 0.564 8.964 32220 Z= 0.292 Chirality : 0.046 0.401 3977 Planarity : 0.004 0.037 4144 Dihedral : 4.816 52.141 4482 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.14 % Favored : 97.76 % Rotamer: Outliers : 3.78 % Allowed : 12.66 % Favored : 83.56 % 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: 0.61 (0.15), residues: 3039 helix: 2.12 (0.19), residues: 798 sheet: 0.27 (0.19), residues: 652 loop : -0.40 (0.14), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1102 HIS 0.004 0.001 HIS A1048 PHE 0.023 0.002 PHE B 133 TYR 0.020 0.002 TYR C1067 ARG 0.007 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 221 time to evaluate : 2.485 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: A 309 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6491 (tm-30) REVERT: A 553 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8379 (m) REVERT: A 786 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6871 (mttp) REVERT: A 1113 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7582 (mt0) REVERT: C 237 ARG cc_start: 0.7239 (mtp-110) cc_final: 0.6888 (ptm-80) REVERT: C 574 ASP cc_start: 0.6761 (p0) cc_final: 0.6559 (p0) REVERT: C 731 MET cc_start: 0.8540 (mtp) cc_final: 0.8338 (mtp) REVERT: C 990 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7062 (mt-10) REVERT: B 654 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: B 661 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.6956 (tt0) REVERT: B 725 GLU cc_start: 0.7750 (tt0) cc_final: 0.7525 (tt0) REVERT: B 787 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7508 (mt0) REVERT: B 918 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7205 (mt-10) REVERT: B 1029 MET cc_start: 0.9021 (tpp) cc_final: 0.8652 (tpp) outliers start: 81 outliers final: 45 residues processed: 278 average time/residue: 1.1600 time to fit residues: 379.4487 Evaluate side-chains 261 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 206 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 20.0000 chunk 268 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 298 optimal weight: 0.8980 chunk 247 optimal weight: 20.0000 chunk 137 optimal weight: 50.0000 chunk 24 optimal weight: 3.9990 chunk 98 optimal weight: 30.0000 chunk 156 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 703 ASN B 30 ASN B 544 ASN B 856 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 23575 Z= 0.296 Angle : 0.565 7.327 32220 Z= 0.294 Chirality : 0.046 0.376 3977 Planarity : 0.004 0.037 4144 Dihedral : 4.680 30.745 4482 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.50 % Favored : 97.40 % Rotamer: Outliers : 3.92 % Allowed : 13.26 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.15), residues: 3039 helix: 2.12 (0.19), residues: 799 sheet: 0.23 (0.19), residues: 652 loop : -0.48 (0.14), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 64 HIS 0.004 0.001 HIS B1058 PHE 0.022 0.002 PHE B 898 TYR 0.022 0.002 TYR C1067 ARG 0.006 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 223 time to evaluate : 2.519 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7477 (tt0) REVERT: A 309 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6438 (tm-30) REVERT: A 697 MET cc_start: 0.8375 (ptm) cc_final: 0.8084 (ptm) REVERT: A 786 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6935 (mttp) REVERT: A 1113 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7575 (mt0) REVERT: C 237 ARG cc_start: 0.7222 (mtp-110) cc_final: 0.6881 (ptm-80) REVERT: C 990 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7121 (mt-10) REVERT: B 310 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8039 (ttmm) REVERT: B 654 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: B 661 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6977 (tt0) REVERT: B 725 GLU cc_start: 0.7757 (tt0) cc_final: 0.7520 (tt0) REVERT: B 787 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7487 (mt0) REVERT: B 918 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7261 (mt-10) REVERT: B 1029 MET cc_start: 0.9022 (tpp) cc_final: 0.8670 (tpp) outliers start: 84 outliers final: 50 residues processed: 280 average time/residue: 1.1232 time to fit residues: 371.4465 Evaluate side-chains 278 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 218 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 0.4980 chunk 33 optimal weight: 10.0000 chunk 169 optimal weight: 0.8980 chunk 217 optimal weight: 4.9990 chunk 168 optimal weight: 0.3980 chunk 250 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 296 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 137 optimal weight: 50.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B 926 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23575 Z= 0.216 Angle : 0.524 7.536 32220 Z= 0.271 Chirality : 0.045 0.361 3977 Planarity : 0.004 0.039 4144 Dihedral : 4.436 28.898 4482 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.84 % Favored : 98.06 % Rotamer: Outliers : 3.41 % Allowed : 13.78 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 3039 helix: 2.22 (0.19), residues: 808 sheet: 0.30 (0.19), residues: 660 loop : -0.47 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1102 HIS 0.003 0.001 HIS B 49 PHE 0.023 0.002 PHE B 541 TYR 0.018 0.001 TYR A1138 ARG 0.008 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 225 time to evaluate : 2.478 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7887 (tt0) cc_final: 0.7495 (tt0) REVERT: A 309 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6408 (tm-30) REVERT: A 356 LYS cc_start: 0.7337 (ttpt) cc_final: 0.7113 (ttpt) REVERT: A 786 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6792 (mttp) REVERT: A 1113 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7557 (mt0) REVERT: C 237 ARG cc_start: 0.7190 (mtp-110) cc_final: 0.6883 (ptm-80) REVERT: C 532 ASN cc_start: 0.5882 (t0) cc_final: 0.5654 (m-40) REVERT: C 544 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7216 (m110) REVERT: B 310 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.7996 (ttmm) REVERT: B 591 SER cc_start: 0.7672 (OUTLIER) cc_final: 0.7348 (t) REVERT: B 654 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: B 725 GLU cc_start: 0.7754 (tt0) cc_final: 0.7519 (tt0) REVERT: B 918 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7183 (mt-10) outliers start: 73 outliers final: 39 residues processed: 272 average time/residue: 1.2201 time to fit residues: 387.2500 Evaluate side-chains 259 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 212 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 188 optimal weight: 0.9990 chunk 202 optimal weight: 50.0000 chunk 146 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 856 ASN B 926 GLN B 935 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23575 Z= 0.236 Angle : 0.535 9.589 32220 Z= 0.275 Chirality : 0.045 0.344 3977 Planarity : 0.004 0.053 4144 Dihedral : 4.394 27.658 4482 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.37 % Favored : 97.53 % Rotamer: Outliers : 3.32 % Allowed : 14.53 % Favored : 82.16 % 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: 0.61 (0.15), residues: 3039 helix: 2.28 (0.19), residues: 800 sheet: 0.24 (0.19), residues: 682 loop : -0.50 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C1102 HIS 0.003 0.001 HIS B 49 PHE 0.026 0.002 PHE C 592 TYR 0.020 0.002 TYR C1067 ARG 0.006 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 219 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7884 (tt0) cc_final: 0.7470 (tt0) REVERT: A 309 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6370 (tm-30) REVERT: A 501 ASN cc_start: 0.6617 (m110) cc_final: 0.6353 (m110) REVERT: A 505 TYR cc_start: 0.6575 (m-10) cc_final: 0.6194 (m-80) REVERT: A 697 MET cc_start: 0.8393 (ptm) cc_final: 0.8010 (ptm) REVERT: A 786 LYS cc_start: 0.7202 (OUTLIER) cc_final: 0.6809 (mttp) REVERT: A 1113 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: C 237 ARG cc_start: 0.7180 (mtp-110) cc_final: 0.6824 (ptm-80) REVERT: C 532 ASN cc_start: 0.5944 (t0) cc_final: 0.5720 (m-40) REVERT: C 544 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7225 (m110) REVERT: B 310 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.7995 (ttmm) REVERT: B 591 SER cc_start: 0.7669 (OUTLIER) cc_final: 0.7351 (t) REVERT: B 654 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7717 (tt0) REVERT: B 725 GLU cc_start: 0.7740 (tt0) cc_final: 0.7508 (tt0) REVERT: B 787 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7335 (mt0) REVERT: B 918 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7245 (mt-10) outliers start: 71 outliers final: 47 residues processed: 261 average time/residue: 1.1721 time to fit residues: 362.4454 Evaluate side-chains 267 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 211 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 0.9980 chunk 284 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 276 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 249 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 chunk 275 optimal weight: 0.4980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 935 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN B 544 ASN B 926 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23575 Z= 0.251 Angle : 0.540 8.523 32220 Z= 0.277 Chirality : 0.045 0.340 3977 Planarity : 0.004 0.058 4144 Dihedral : 4.399 26.597 4482 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.17 % Favored : 97.73 % Rotamer: Outliers : 3.04 % Allowed : 14.95 % Favored : 82.02 % 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: 0.61 (0.15), residues: 3039 helix: 2.28 (0.19), residues: 800 sheet: 0.26 (0.19), residues: 682 loop : -0.50 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C1102 HIS 0.004 0.001 HIS B 49 PHE 0.029 0.002 PHE C 592 TYR 0.020 0.002 TYR C1067 ARG 0.009 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 216 time to evaluate : 2.528 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7884 (tt0) cc_final: 0.7477 (tt0) REVERT: A 309 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6381 (tm-30) REVERT: A 501 ASN cc_start: 0.6560 (m110) cc_final: 0.6322 (m110) REVERT: A 505 TYR cc_start: 0.6671 (m-10) cc_final: 0.6278 (m-80) REVERT: A 697 MET cc_start: 0.8388 (ptm) cc_final: 0.7998 (ptm) REVERT: A 786 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6823 (mttp) REVERT: A 1113 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7549 (mt0) REVERT: C 237 ARG cc_start: 0.7184 (mtp-110) cc_final: 0.6864 (ptm-80) REVERT: C 532 ASN cc_start: 0.5925 (t0) cc_final: 0.5706 (m-40) REVERT: C 544 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7285 (m110) REVERT: B 310 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8002 (ttmm) REVERT: B 591 SER cc_start: 0.7669 (OUTLIER) cc_final: 0.7348 (t) REVERT: B 654 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: B 661 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6858 (tt0) REVERT: B 725 GLU cc_start: 0.7741 (tt0) cc_final: 0.7508 (tt0) REVERT: B 787 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7337 (mt0) REVERT: B 918 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7264 (mt-10) outliers start: 65 outliers final: 47 residues processed: 253 average time/residue: 1.0904 time to fit residues: 327.2364 Evaluate side-chains 268 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 211 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 2.9990 chunk 292 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 138 optimal weight: 30.0000 chunk 203 optimal weight: 2.9990 chunk 306 optimal weight: 9.9990 chunk 282 optimal weight: 0.6980 chunk 244 optimal weight: 0.8980 chunk 25 optimal weight: 0.1980 chunk 188 optimal weight: 0.5980 chunk 149 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B 935 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23575 Z= 0.204 Angle : 0.520 8.471 32220 Z= 0.267 Chirality : 0.044 0.334 3977 Planarity : 0.004 0.053 4144 Dihedral : 4.297 26.232 4482 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.17 % Favored : 97.73 % Rotamer: Outliers : 2.80 % Allowed : 15.09 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 3039 helix: 2.30 (0.19), residues: 806 sheet: 0.26 (0.19), residues: 684 loop : -0.51 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.003 0.001 HIS B 49 PHE 0.027 0.001 PHE C 592 TYR 0.019 0.001 TYR A1138 ARG 0.009 0.000 ARG B 995 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 216 time to evaluate : 2.450 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7877 (tt0) cc_final: 0.7460 (tt0) REVERT: A 309 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6324 (tm-30) REVERT: A 505 TYR cc_start: 0.6630 (m-10) cc_final: 0.6206 (m-80) REVERT: A 786 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6800 (mttp) REVERT: C 237 ARG cc_start: 0.7166 (mtp-110) cc_final: 0.6866 (ptm-80) REVERT: C 532 ASN cc_start: 0.5840 (t0) cc_final: 0.5614 (m-40) REVERT: C 544 ASN cc_start: 0.7929 (OUTLIER) cc_final: 0.7309 (m110) REVERT: B 310 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.7990 (ttmm) REVERT: B 591 SER cc_start: 0.7623 (OUTLIER) cc_final: 0.7331 (t) REVERT: B 654 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: B 661 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6858 (tt0) REVERT: B 725 GLU cc_start: 0.7738 (tt0) cc_final: 0.7509 (tt0) REVERT: B 918 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7237 (mt-10) outliers start: 60 outliers final: 45 residues processed: 249 average time/residue: 1.1239 time to fit residues: 332.6956 Evaluate side-chains 263 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 210 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 0.6980 chunk 260 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 225 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 244 optimal weight: 0.0270 chunk 102 optimal weight: 20.0000 chunk 251 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.197316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.156111 restraints weight = 28854.208| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.59 r_work: 0.3637 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23575 Z= 0.192 Angle : 0.518 9.704 32220 Z= 0.265 Chirality : 0.044 0.332 3977 Planarity : 0.004 0.054 4144 Dihedral : 4.254 25.756 4482 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.01 % Favored : 97.89 % Rotamer: Outliers : 2.62 % Allowed : 15.41 % Favored : 81.97 % 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: 0.66 (0.15), residues: 3039 helix: 2.33 (0.19), residues: 807 sheet: 0.29 (0.19), residues: 682 loop : -0.49 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.003 0.001 HIS B 49 PHE 0.031 0.001 PHE C 592 TYR 0.019 0.001 TYR A1138 ARG 0.009 0.000 ARG B 995 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7851.07 seconds wall clock time: 141 minutes 43.55 seconds (8503.55 seconds total)