Starting phenix.real_space_refine on Tue Feb 20 05:50:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1v_24124/02_2024/7n1v_24124.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1v_24124/02_2024/7n1v_24124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1v_24124/02_2024/7n1v_24124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1v_24124/02_2024/7n1v_24124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1v_24124/02_2024/7n1v_24124.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1v_24124/02_2024/7n1v_24124.pdb" } resolution = 3.21 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= 0.003 sd= 0.044 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 116 5.16 5 C 17126 2.51 5 N 4360 2.21 5 O 5345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 40": "OD1" <-> "OD2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 570": "OD1" <-> "OD2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 737": "OD1" <-> "OD2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A ASP 1084": "OD1" <-> "OD2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "A TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C ARG 634": "NH1" <-> "NH2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C ASP 737": "OD1" <-> "OD2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 820": "OD1" <-> "OD2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1127": "OD1" <-> "OD2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26947 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 8530 Classifications: {'peptide': 1089} Link IDs: {'PTRANS': 52, 'TRANS': 1036} Chain breaks: 5 Chain: "B" Number of atoms: 8545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1091, 8545 Classifications: {'peptide': 1091} Link IDs: {'PTRANS': 52, 'TRANS': 1038} Chain breaks: 5 Chain: "C" Number of atoms: 8572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1094, 8572 Classifications: {'peptide': 1094} Link IDs: {'PTRANS': 53, 'TRANS': 1040} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: "Y" 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: "Z" 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: 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: "b" 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: "c" 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: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 13.41, per 1000 atoms: 0.50 Number of scatterers: 26947 At special positions: 0 Unit cell: (154.288, 156.763, 216.168, 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 116 16.00 O 5345 8.00 N 4360 7.00 C 17126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 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=2.01 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.01 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 Atom "HETATM26903 O5 NAG C1405 .*. O " rejected from bonding due to valence issues. Atom "HETATM26749 O5 NAG B1403 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG T 2 " - " MAN T 3 " " NAG U 2 " - " MAN U 3 " " NAG e 2 " - " MAN e 3 " " NAG f 2 " - " MAN f 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 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 T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG d 1 " - " FUC d 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1403 " - " ASN A 149 " " NAG A1404 " - " ASN A 165 " " NAG A1405 " - " ASN A 234 " " NAG A1406 " - " ASN A 282 " " NAG A1407 " - " ASN A 343 " " NAG A1408 " - " ASN A 603 " " NAG A1409 " - " ASN A 657 " " NAG A1410 " - " ASN A 709 " " NAG A1411 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1403 " - " ASN B 234 " " NAG B1404 " - " ASN B 331 " " NAG B1405 " - " ASN B 343 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 657 " " NAG B1408 " - " ASN B 709 " " NAG B1409 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 343 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 657 " " NAG C1407 " - " ASN C 709 " " NAG C1408 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 616 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 17 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN B 165 " " NAG O 1 " - " ASN B 282 " " NAG P 1 " - " ASN B 616 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 17 " " NAG W 1 " - " ASN C 122 " " NAG X 1 " - " ASN C 165 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 282 " " NAG a 1 " - " ASN C 616 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN C1134 " Time building additional restraints: 12.05 Conformation dependent library (CDL) restraints added in 5.0 seconds 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6134 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 49 sheets defined 27.6% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.615A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.834A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.993A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.405A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 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 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: 3.969A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.504A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 837 removed outlier: 3.559A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA A 829 " --> pdb=" O LYS A 825 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLY A 832 " --> pdb=" O LEU A 828 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.770A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.273A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.804A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1033 removed outlier: 4.102A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 4.026A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A1152 " --> pdb=" O PHE A1148 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR A1155 " --> pdb=" O GLU A1151 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A1161 " --> pdb=" O LYS A1157 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 344 removed outlier: 4.022A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.651A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.504A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 3.696A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.890A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.585A pdb=" N TYR B 636 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.891A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.438A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.735A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.584A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.537A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.611A pdb=" N GLU B 990 " --> pdb=" O LYS B 986 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 3.801A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (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 364 through 370 removed outlier: 4.016A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.692A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.669A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.522A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 624 Proline residue: C 621 - end of helix Processing helix chain 'C' and resid 635 through 639 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.825A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.419A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.820A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.815A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.656A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.000A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.693A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1161 removed outlier: 3.811A pdb=" N SER C1161 " --> pdb=" O LYS C1157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.631A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.033A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.174A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.444A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.378A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.704A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.852A 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 538 through 543 removed outlier: 5.503A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.083A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.562A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.811A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.430A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.960A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.361A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.729A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.036A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.926A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.583A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.130A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.077A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.522A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.522A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.642A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.872A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.877A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.386A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.904A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.061A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.310A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.503A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.812A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE3, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AE4, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.206A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.770A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.630A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.638A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.819A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.966A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.253A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.230A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3081 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: 12.50 Time building geometry restraints manager: 12.26 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: 4795 1.32 - 1.45: 7069 1.45 - 1.57: 15533 1.57 - 1.70: 0 1.70 - 1.83: 146 Bond restraints: 27543 Sorted by residual: bond pdb=" N ARG A1000 " pdb=" CA ARG A1000 " ideal model delta sigma weight residual 1.459 1.405 0.054 1.20e-02 6.94e+03 2.06e+01 bond pdb=" CA ARG A1000 " pdb=" C ARG A1000 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.26e-02 6.30e+03 1.78e+01 bond pdb=" C5 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.413 1.495 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C ARG B1014 " pdb=" O ARG B1014 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.16e-02 7.43e+03 1.68e+01 bond pdb=" C1 FUC d 3 " pdb=" O5 FUC d 3 " ideal model delta sigma weight residual 1.400 1.479 -0.079 2.00e-02 2.50e+03 1.57e+01 ... (remaining 27538 not shown) Histogram of bond angle deviations from ideal: 96.90 - 104.64: 409 104.64 - 112.39: 12422 112.39 - 120.13: 13306 120.13 - 127.87: 11214 127.87 - 135.61: 113 Bond angle restraints: 37464 Sorted by residual: angle pdb=" N CYS B 525 " pdb=" CA CYS B 525 " pdb=" C CYS B 525 " ideal model delta sigma weight residual 108.45 122.23 -13.78 1.26e+00 6.30e-01 1.20e+02 angle pdb=" N ARG A1107 " pdb=" CA ARG A1107 " pdb=" C ARG A1107 " ideal model delta sigma weight residual 112.87 122.90 -10.03 1.20e+00 6.94e-01 6.99e+01 angle pdb=" OD1 ASN C1074 " pdb=" CG ASN C1074 " pdb=" ND2 ASN C1074 " ideal model delta sigma weight residual 122.60 114.69 7.91 1.00e+00 1.00e+00 6.26e+01 angle pdb=" OD1 ASN A1074 " pdb=" CG ASN A1074 " pdb=" ND2 ASN A1074 " ideal model delta sigma weight residual 122.60 114.84 7.76 1.00e+00 1.00e+00 6.03e+01 angle pdb=" N ARG A 983 " pdb=" CA ARG A 983 " pdb=" C ARG A 983 " ideal model delta sigma weight residual 111.36 119.63 -8.27 1.09e+00 8.42e-01 5.75e+01 ... (remaining 37459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.25: 16882 25.25 - 50.51: 577 50.51 - 75.76: 100 75.76 - 101.02: 42 101.02 - 126.27: 21 Dihedral angle restraints: 17622 sinusoidal: 8087 harmonic: 9535 Sorted by residual: dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual 93.00 170.98 -77.98 1 1.00e+01 1.00e-02 7.60e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual -86.00 -139.07 53.07 1 1.00e+01 1.00e-02 3.83e+01 dihedral pdb=" CA THR B 95 " pdb=" C THR B 95 " pdb=" N GLU B 96 " pdb=" CA GLU B 96 " ideal model delta harmonic sigma weight residual -180.00 -150.14 -29.86 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 17619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.608: 4498 0.608 - 1.216: 6 1.216 - 1.823: 2 1.823 - 2.431: 0 2.431 - 3.039: 3 Chirality restraints: 4509 Sorted by residual: chirality pdb=" C1 NAG C1401 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1401 " pdb=" O5 NAG C1401 " both_signs ideal model delta sigma weight residual False -2.40 0.64 -3.04 2.00e-01 2.50e+01 2.31e+02 chirality pdb=" C1 NAG C1405 " pdb=" ND2 ASN C 603 " pdb=" C2 NAG C1405 " pdb=" O5 NAG C1405 " both_signs ideal model delta sigma weight residual False -2.40 0.38 -2.78 2.00e-01 2.50e+01 1.94e+02 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 0.13 -2.53 2.00e-01 2.50e+01 1.60e+02 ... (remaining 4506 not shown) Planarity restraints: 4768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 165 " -0.179 2.00e-02 2.50e+03 1.99e-01 4.95e+02 pdb=" CG ASN B 165 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN B 165 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN B 165 " 0.328 2.00e-02 2.50e+03 pdb=" C1 NAG N 1 " -0.232 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 709 " -0.148 2.00e-02 2.50e+03 1.61e-01 3.26e+02 pdb=" CG ASN C 709 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN C 709 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 709 " 0.272 2.00e-02 2.50e+03 pdb=" C1 NAG C1407 " -0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 61 " 0.132 2.00e-02 2.50e+03 1.34e-01 2.23e+02 pdb=" CG ASN B 61 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN B 61 " -0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN B 61 " -0.199 2.00e-02 2.50e+03 pdb=" C1 NAG B1401 " 0.165 2.00e-02 2.50e+03 ... (remaining 4765 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 16 2.40 - 3.03: 14790 3.03 - 3.65: 38432 3.65 - 4.28: 61784 4.28 - 4.90: 99670 Nonbonded interactions: 214692 Sorted by model distance: nonbonded pdb=" O THR A 124 " pdb=" CE1 PHE A 175 " model vdw 1.776 3.340 nonbonded pdb=" O THR A 124 " pdb=" CD1 PHE A 175 " model vdw 1.784 3.340 nonbonded pdb=" ND2 ASN A 122 " pdb=" C1 NAG A1402 " model vdw 1.995 3.550 nonbonded pdb=" NH1 ARG B 21 " pdb=" O PHE B 79 " model vdw 2.059 2.520 nonbonded pdb=" NH1 ARG B1091 " pdb=" O HIS B1118 " model vdw 2.109 2.520 ... (remaining 214687 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 827 or resid 853 through 1162 or resid 1401 thr \ ough 1408)) selection = (chain 'B' and (resid 14 through 621 or resid 641 through 827 or resid 853 throu \ gh 1162 or resid 1401 through 1408)) selection = (chain 'C' and (resid 14 through 621 or resid 641 through 1162 or resid 1401 thr \ ough 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 4.620 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: 22.980 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 72.440 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 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 0.082 27543 Z= 0.897 Angle : 1.773 13.778 37464 Z= 1.167 Chirality : 0.133 3.039 4509 Planarity : 0.012 0.095 4713 Dihedral : 14.538 126.271 11362 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.45 % Favored : 93.21 % Rotamer: Outliers : 0.98 % Allowed : 4.19 % Favored : 94.83 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 3240 helix: -1.36 (0.16), residues: 740 sheet: 0.22 (0.19), residues: 647 loop : -1.45 (0.13), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.170 0.025 TRP C 104 HIS 0.016 0.004 HIS B1159 PHE 0.118 0.013 PHE A 898 TYR 0.119 0.021 TYR B 365 ARG 0.008 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 791 time to evaluate : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7418 (m110) cc_final: 0.7062 (m-40) REVERT: A 129 LYS cc_start: 0.8538 (tttt) cc_final: 0.8040 (tttt) REVERT: A 212 LEU cc_start: 0.7705 (tp) cc_final: 0.7303 (tp) REVERT: A 224 GLU cc_start: 0.8061 (mp0) cc_final: 0.7844 (mp0) REVERT: A 298 GLU cc_start: 0.7989 (tt0) cc_final: 0.7781 (tt0) REVERT: A 319 ARG cc_start: 0.7688 (ptp-170) cc_final: 0.7393 (ptp-170) REVERT: A 422 ASN cc_start: 0.5123 (OUTLIER) cc_final: 0.4761 (p0) REVERT: A 493 GLN cc_start: 0.7277 (tm-30) cc_final: 0.7023 (tm-30) REVERT: A 671 CYS cc_start: 0.5722 (m) cc_final: 0.5473 (m) REVERT: A 819 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7874 (mt-10) REVERT: A 823 PHE cc_start: 0.8319 (t80) cc_final: 0.7929 (t80) REVERT: A 936 ASP cc_start: 0.7867 (m-30) cc_final: 0.7474 (m-30) REVERT: A 941 THR cc_start: 0.7497 (t) cc_final: 0.7147 (t) REVERT: A 950 ASP cc_start: 0.8020 (t0) cc_final: 0.7659 (t70) REVERT: A 957 GLN cc_start: 0.8039 (tt0) cc_final: 0.7735 (tp40) REVERT: A 964 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8471 (mttm) REVERT: A 1038 LYS cc_start: 0.8802 (mtpp) cc_final: 0.8592 (mtpp) REVERT: A 1141 LEU cc_start: 0.8924 (tp) cc_final: 0.8711 (tp) REVERT: B 105 ILE cc_start: 0.8987 (mp) cc_final: 0.8783 (mp) REVERT: B 125 ASN cc_start: 0.7644 (p0) cc_final: 0.7281 (p0) REVERT: B 135 PHE cc_start: 0.6734 (m-80) cc_final: 0.6467 (m-80) REVERT: B 224 GLU cc_start: 0.8063 (mp0) cc_final: 0.7723 (mp0) REVERT: B 237 ARG cc_start: 0.7896 (mtm110) cc_final: 0.7641 (ptp90) REVERT: B 417 LYS cc_start: 0.8109 (mmtp) cc_final: 0.7887 (mmmm) REVERT: B 493 GLN cc_start: 0.7430 (tm-30) cc_final: 0.6872 (tm-30) REVERT: B 524 VAL cc_start: 0.7785 (p) cc_final: 0.7567 (p) REVERT: B 564 GLN cc_start: 0.7473 (tp40) cc_final: 0.6875 (tp-100) REVERT: B 580 GLN cc_start: 0.7406 (mt0) cc_final: 0.7135 (mt0) REVERT: B 596 SER cc_start: 0.8991 (m) cc_final: 0.8435 (p) REVERT: B 619 GLU cc_start: 0.7340 (mt-10) cc_final: 0.7109 (mt-10) REVERT: B 737 ASP cc_start: 0.7501 (t0) cc_final: 0.7198 (t0) REVERT: B 740 MET cc_start: 0.8589 (ttt) cc_final: 0.7333 (ttp) REVERT: B 950 ASP cc_start: 0.8029 (m-30) cc_final: 0.7598 (m-30) REVERT: B 964 LYS cc_start: 0.8725 (ttmm) cc_final: 0.8517 (mttp) REVERT: B 984 LEU cc_start: 0.8680 (mm) cc_final: 0.8459 (mt) REVERT: B 986 LYS cc_start: 0.8445 (tttm) cc_final: 0.8110 (tttm) REVERT: B 1141 LEU cc_start: 0.8757 (tt) cc_final: 0.8540 (tt) REVERT: C 45 SER cc_start: 0.8420 (p) cc_final: 0.8111 (t) REVERT: C 52 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8325 (tm-30) REVERT: C 244 LEU cc_start: 0.4911 (tt) cc_final: 0.4685 (tt) REVERT: C 320 VAL cc_start: 0.8770 (t) cc_final: 0.8524 (m) REVERT: C 321 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8394 (mp10) REVERT: C 365 TYR cc_start: 0.8384 (m-80) cc_final: 0.8174 (m-80) REVERT: C 427 ASP cc_start: 0.7590 (m-30) cc_final: 0.7121 (m-30) REVERT: C 487 ASN cc_start: 0.6401 (p0) cc_final: 0.6125 (p0) REVERT: C 508 TYR cc_start: 0.6622 (m-80) cc_final: 0.6188 (m-80) REVERT: C 534 VAL cc_start: 0.8566 (p) cc_final: 0.8273 (m) REVERT: C 540 ASN cc_start: 0.8553 (m-40) cc_final: 0.8269 (m110) REVERT: C 546 LEU cc_start: 0.8482 (mt) cc_final: 0.8158 (mp) REVERT: C 571 ASP cc_start: 0.8245 (t70) cc_final: 0.7918 (t0) REVERT: C 643 PHE cc_start: 0.8327 (t80) cc_final: 0.7958 (t80) REVERT: C 737 ASP cc_start: 0.7393 (t0) cc_final: 0.7107 (t0) REVERT: C 748 GLU cc_start: 0.8015 (pm20) cc_final: 0.7775 (pm20) REVERT: C 752 LEU cc_start: 0.9116 (mt) cc_final: 0.8554 (mm) REVERT: C 808 ASP cc_start: 0.7946 (t0) cc_final: 0.7737 (t70) REVERT: C 886 TRP cc_start: 0.8844 (p90) cc_final: 0.8559 (p90) REVERT: C 933 LYS cc_start: 0.8772 (mmpt) cc_final: 0.8432 (mmmt) REVERT: C 950 ASP cc_start: 0.8067 (t0) cc_final: 0.7652 (t0) REVERT: C 968 SER cc_start: 0.9173 (m) cc_final: 0.8900 (t) REVERT: C 979 ASP cc_start: 0.8026 (m-30) cc_final: 0.7761 (m-30) REVERT: C 987 VAL cc_start: 0.8988 (t) cc_final: 0.8523 (t) REVERT: C 1045 LYS cc_start: 0.8194 (tmtt) cc_final: 0.7891 (tmtt) REVERT: C 1086 LYS cc_start: 0.8990 (ptpp) cc_final: 0.8653 (ptpp) REVERT: C 1118 HIS cc_start: 0.8312 (m-70) cc_final: 0.8112 (m170) REVERT: C 1119 ASN cc_start: 0.8549 (m110) cc_final: 0.8209 (m110) REVERT: C 1141 LEU cc_start: 0.9003 (tt) cc_final: 0.8741 (tt) REVERT: C 1148 PHE cc_start: 0.7280 (t80) cc_final: 0.6813 (t80) outliers start: 28 outliers final: 5 residues processed: 806 average time/residue: 0.4220 time to fit residues: 515.2963 Evaluate side-chains 648 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 642 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain C residue 122 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 275 optimal weight: 1.9990 chunk 247 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 255 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 chunk 296 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 658 ASN A 872 GLN A1119 ASN B 30 ASN B 149 ASN B 644 GLN B 762 GLN B1119 ASN B1142 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 675 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN C1108 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 27543 Z= 0.255 Angle : 0.739 9.428 37464 Z= 0.376 Chirality : 0.053 1.131 4509 Planarity : 0.004 0.061 4713 Dihedral : 10.594 114.134 5491 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.34 % Allowed : 10.55 % Favored : 87.11 % 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: -0.63 (0.14), residues: 3240 helix: 0.82 (0.19), residues: 750 sheet: 0.00 (0.18), residues: 748 loop : -1.16 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 353 HIS 0.005 0.001 HIS C 66 PHE 0.028 0.002 PHE B1148 TYR 0.035 0.002 TYR B 396 ARG 0.008 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 647 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8555 (tttt) cc_final: 0.7973 (tttt) REVERT: A 153 MET cc_start: 0.6980 (tmm) cc_final: 0.6719 (ppp) REVERT: A 212 LEU cc_start: 0.7629 (tp) cc_final: 0.7139 (tt) REVERT: A 287 ASP cc_start: 0.7871 (t70) cc_final: 0.7585 (t0) REVERT: A 298 GLU cc_start: 0.8089 (tt0) cc_final: 0.7868 (tt0) REVERT: A 319 ARG cc_start: 0.7790 (ptp-170) cc_final: 0.7450 (ptp-170) REVERT: A 516 GLU cc_start: 0.7099 (tt0) cc_final: 0.6672 (tt0) REVERT: A 571 ASP cc_start: 0.7691 (t70) cc_final: 0.7308 (t0) REVERT: A 759 PHE cc_start: 0.8087 (m-80) cc_final: 0.7845 (m-80) REVERT: A 796 ASP cc_start: 0.7778 (t70) cc_final: 0.7567 (t70) REVERT: A 872 GLN cc_start: 0.8189 (tt0) cc_final: 0.7989 (tt0) REVERT: A 901 GLN cc_start: 0.8530 (tt0) cc_final: 0.8219 (tt0) REVERT: A 902 MET cc_start: 0.8687 (tpt) cc_final: 0.8457 (mmt) REVERT: A 936 ASP cc_start: 0.7876 (m-30) cc_final: 0.7486 (m-30) REVERT: A 941 THR cc_start: 0.7548 (t) cc_final: 0.7302 (t) REVERT: A 949 GLN cc_start: 0.8331 (mm-40) cc_final: 0.8043 (mm-40) REVERT: A 950 ASP cc_start: 0.7811 (t0) cc_final: 0.7609 (t70) REVERT: A 957 GLN cc_start: 0.8186 (tt0) cc_final: 0.7891 (tt0) REVERT: A 964 LYS cc_start: 0.8681 (mmtt) cc_final: 0.8424 (mttm) REVERT: A 1055 SER cc_start: 0.8923 (t) cc_final: 0.8626 (m) REVERT: B 125 ASN cc_start: 0.7506 (p0) cc_final: 0.7194 (p0) REVERT: B 224 GLU cc_start: 0.7984 (mp0) cc_final: 0.7781 (mp0) REVERT: B 281 GLU cc_start: 0.8423 (tt0) cc_final: 0.8159 (pt0) REVERT: B 346 ARG cc_start: 0.7130 (mmm160) cc_final: 0.6818 (tpt-90) REVERT: B 436 TRP cc_start: 0.7777 (p90) cc_final: 0.7091 (p90) REVERT: B 564 GLN cc_start: 0.7535 (tp40) cc_final: 0.6920 (tp-100) REVERT: B 577 ARG cc_start: 0.7900 (ttm-80) cc_final: 0.7671 (ttm-80) REVERT: B 580 GLN cc_start: 0.7802 (mt0) cc_final: 0.7589 (mt0) REVERT: B 671 CYS cc_start: 0.5743 (m) cc_final: 0.5535 (m) REVERT: B 740 MET cc_start: 0.8511 (ttt) cc_final: 0.7348 (ttp) REVERT: B 811 LYS cc_start: 0.7367 (ptmm) cc_final: 0.7114 (tmmt) REVERT: B 814 LYS cc_start: 0.7799 (mmtt) cc_final: 0.7549 (mmtt) REVERT: B 950 ASP cc_start: 0.8007 (m-30) cc_final: 0.7639 (m-30) REVERT: B 986 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8163 (tttm) REVERT: B 1148 PHE cc_start: 0.6801 (t80) cc_final: 0.6161 (t80) REVERT: C 52 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8475 (tm-30) REVERT: C 180 GLU cc_start: 0.4049 (OUTLIER) cc_final: 0.3618 (pm20) REVERT: C 190 ARG cc_start: 0.7996 (mmt180) cc_final: 0.7360 (mmt180) REVERT: C 321 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8616 (mm-40) REVERT: C 365 TYR cc_start: 0.8377 (m-80) cc_final: 0.8064 (m-80) REVERT: C 386 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8865 (mmtm) REVERT: C 455 LEU cc_start: 0.8630 (mt) cc_final: 0.8385 (mt) REVERT: C 508 TYR cc_start: 0.6531 (m-80) cc_final: 0.6315 (m-80) REVERT: C 534 VAL cc_start: 0.8583 (p) cc_final: 0.8335 (m) REVERT: C 571 ASP cc_start: 0.8382 (t70) cc_final: 0.8106 (t0) REVERT: C 675 GLN cc_start: 0.7080 (tm130) cc_final: 0.6834 (pp30) REVERT: C 693 ILE cc_start: 0.8917 (mt) cc_final: 0.8590 (mt) REVERT: C 808 ASP cc_start: 0.8062 (t0) cc_final: 0.7806 (t70) REVERT: C 950 ASP cc_start: 0.8066 (t0) cc_final: 0.7730 (t0) REVERT: C 968 SER cc_start: 0.9265 (m) cc_final: 0.8930 (t) REVERT: C 1086 LYS cc_start: 0.8981 (ptpp) cc_final: 0.8752 (ptpp) REVERT: C 1119 ASN cc_start: 0.8512 (m110) cc_final: 0.8167 (m110) REVERT: C 1141 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8660 (tp) outliers start: 67 outliers final: 36 residues processed: 682 average time/residue: 0.4052 time to fit residues: 430.7595 Evaluate side-chains 620 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 581 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 986 LYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 164 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 296 optimal weight: 0.7980 chunk 320 optimal weight: 0.4980 chunk 264 optimal weight: 0.7980 chunk 294 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1142 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 644 GLN B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27543 Z= 0.272 Angle : 0.681 9.375 37464 Z= 0.341 Chirality : 0.050 0.874 4509 Planarity : 0.004 0.060 4713 Dihedral : 9.818 111.638 5489 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.00 % Allowed : 13.70 % Favored : 83.30 % 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: -0.43 (0.14), residues: 3240 helix: 1.31 (0.19), residues: 750 sheet: -0.13 (0.17), residues: 770 loop : -1.08 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 353 HIS 0.004 0.001 HIS A 207 PHE 0.024 0.002 PHE C 342 TYR 0.031 0.002 TYR B 396 ARG 0.007 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 599 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.3794 (OUTLIER) cc_final: 0.2925 (ppt-90) REVERT: A 129 LYS cc_start: 0.8511 (tttt) cc_final: 0.7864 (tttt) REVERT: A 287 ASP cc_start: 0.7910 (t70) cc_final: 0.7702 (t0) REVERT: A 298 GLU cc_start: 0.8094 (tt0) cc_final: 0.7816 (tt0) REVERT: A 493 GLN cc_start: 0.7271 (tm-30) cc_final: 0.6145 (tm-30) REVERT: A 571 ASP cc_start: 0.7696 (t70) cc_final: 0.7339 (t0) REVERT: A 796 ASP cc_start: 0.7803 (t70) cc_final: 0.7551 (t70) REVERT: A 872 GLN cc_start: 0.8226 (tt0) cc_final: 0.8024 (tt0) REVERT: A 901 GLN cc_start: 0.8556 (tt0) cc_final: 0.8277 (tt0) REVERT: A 936 ASP cc_start: 0.7924 (m-30) cc_final: 0.7563 (m-30) REVERT: A 941 THR cc_start: 0.7626 (t) cc_final: 0.7363 (t) REVERT: A 949 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8049 (mm-40) REVERT: A 950 ASP cc_start: 0.7847 (t0) cc_final: 0.7605 (t70) REVERT: A 957 GLN cc_start: 0.8158 (tt0) cc_final: 0.7936 (tt0) REVERT: A 964 LYS cc_start: 0.8682 (mmtt) cc_final: 0.8296 (mmmt) REVERT: A 1055 SER cc_start: 0.8955 (t) cc_final: 0.8643 (m) REVERT: A 1148 PHE cc_start: 0.5392 (t80) cc_final: 0.5085 (t80) REVERT: B 125 ASN cc_start: 0.7609 (p0) cc_final: 0.7315 (p0) REVERT: B 224 GLU cc_start: 0.7980 (mp0) cc_final: 0.7751 (mp0) REVERT: B 436 TRP cc_start: 0.7700 (p90) cc_final: 0.7305 (p90) REVERT: B 456 PHE cc_start: 0.7564 (m-80) cc_final: 0.7352 (m-80) REVERT: B 564 GLN cc_start: 0.7634 (tp40) cc_final: 0.7071 (tp-100) REVERT: B 574 ASP cc_start: 0.8134 (p0) cc_final: 0.7880 (p0) REVERT: B 577 ARG cc_start: 0.7913 (ttm-80) cc_final: 0.7672 (ttm-80) REVERT: B 580 GLN cc_start: 0.7793 (mt0) cc_final: 0.7593 (mt0) REVERT: B 740 MET cc_start: 0.8484 (ttt) cc_final: 0.8241 (ttp) REVERT: B 950 ASP cc_start: 0.7973 (m-30) cc_final: 0.7605 (m-30) REVERT: B 986 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8208 (tttm) REVERT: C 52 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8483 (tm-30) REVERT: C 180 GLU cc_start: 0.4023 (OUTLIER) cc_final: 0.3605 (pm20) REVERT: C 190 ARG cc_start: 0.8044 (mmt180) cc_final: 0.7620 (mmt180) REVERT: C 321 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8702 (mm-40) REVERT: C 368 LEU cc_start: 0.8903 (mt) cc_final: 0.8684 (mp) REVERT: C 386 LYS cc_start: 0.9157 (mmtt) cc_final: 0.8851 (mmtm) REVERT: C 508 TYR cc_start: 0.6779 (m-80) cc_final: 0.6452 (m-80) REVERT: C 523 THR cc_start: 0.8526 (p) cc_final: 0.8032 (t) REVERT: C 568 ASP cc_start: 0.8133 (t0) cc_final: 0.7884 (t0) REVERT: C 675 GLN cc_start: 0.7138 (tm130) cc_final: 0.6872 (pp30) REVERT: C 693 ILE cc_start: 0.8916 (mt) cc_final: 0.8599 (mt) REVERT: C 765 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7658 (ttp80) REVERT: C 808 ASP cc_start: 0.8038 (t0) cc_final: 0.7781 (t70) REVERT: C 868 GLU cc_start: 0.7556 (mp0) cc_final: 0.7325 (mp0) REVERT: C 945 LEU cc_start: 0.8804 (mt) cc_final: 0.8576 (mp) REVERT: C 950 ASP cc_start: 0.7997 (t0) cc_final: 0.7630 (t0) REVERT: C 988 GLU cc_start: 0.7996 (tp30) cc_final: 0.7768 (mp0) REVERT: C 1045 LYS cc_start: 0.8296 (tmtt) cc_final: 0.8015 (tmtt) REVERT: C 1086 LYS cc_start: 0.8950 (ptpp) cc_final: 0.8703 (ptpp) REVERT: C 1106 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8353 (pt0) REVERT: C 1119 ASN cc_start: 0.8510 (m110) cc_final: 0.8165 (m-40) outliers start: 86 outliers final: 53 residues processed: 649 average time/residue: 0.4008 time to fit residues: 402.1032 Evaluate side-chains 627 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 569 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 986 LYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 293 optimal weight: 0.9980 chunk 222 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 297 optimal weight: 0.7980 chunk 315 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 282 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27543 Z= 0.239 Angle : 0.661 9.849 37464 Z= 0.327 Chirality : 0.048 0.808 4509 Planarity : 0.004 0.059 4713 Dihedral : 9.133 110.419 5489 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.53 % Allowed : 14.50 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.36 (0.14), residues: 3240 helix: 1.57 (0.19), residues: 751 sheet: -0.21 (0.18), residues: 737 loop : -1.07 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 353 HIS 0.004 0.001 HIS B 207 PHE 0.029 0.002 PHE B1148 TYR 0.041 0.002 TYR C 904 ARG 0.005 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 600 time to evaluate : 3.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.3865 (OUTLIER) cc_final: 0.3099 (ppt-90) REVERT: A 129 LYS cc_start: 0.8480 (tttt) cc_final: 0.7839 (tttt) REVERT: A 287 ASP cc_start: 0.7925 (t70) cc_final: 0.7653 (t0) REVERT: A 493 GLN cc_start: 0.7237 (tm-30) cc_final: 0.6377 (tm-30) REVERT: A 495 TYR cc_start: 0.5488 (OUTLIER) cc_final: 0.5251 (t80) REVERT: A 571 ASP cc_start: 0.7727 (t70) cc_final: 0.7360 (t0) REVERT: A 586 ASP cc_start: 0.7769 (m-30) cc_final: 0.7517 (m-30) REVERT: A 796 ASP cc_start: 0.7774 (t70) cc_final: 0.7537 (t70) REVERT: A 872 GLN cc_start: 0.8287 (tt0) cc_final: 0.8069 (tt0) REVERT: A 901 GLN cc_start: 0.8566 (tt0) cc_final: 0.8280 (tt0) REVERT: A 941 THR cc_start: 0.7562 (t) cc_final: 0.7290 (t) REVERT: A 949 GLN cc_start: 0.8293 (mm-40) cc_final: 0.8031 (mm-40) REVERT: A 950 ASP cc_start: 0.7808 (t0) cc_final: 0.7353 (t0) REVERT: A 957 GLN cc_start: 0.8167 (tt0) cc_final: 0.7926 (tt0) REVERT: A 960 ASN cc_start: 0.8171 (t0) cc_final: 0.7941 (t0) REVERT: A 964 LYS cc_start: 0.8708 (mmtt) cc_final: 0.8281 (mmmt) REVERT: A 1055 SER cc_start: 0.8976 (t) cc_final: 0.8643 (m) REVERT: A 1125 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8713 (p0) REVERT: B 125 ASN cc_start: 0.7511 (p0) cc_final: 0.7259 (p0) REVERT: B 153 MET cc_start: 0.8348 (mtm) cc_final: 0.8124 (pmm) REVERT: B 177 MET cc_start: 0.6162 (ppp) cc_final: 0.4965 (ppp) REVERT: B 223 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8736 (mt) REVERT: B 224 GLU cc_start: 0.7980 (mp0) cc_final: 0.7730 (mp0) REVERT: B 436 TRP cc_start: 0.7766 (p90) cc_final: 0.7406 (p90) REVERT: B 456 PHE cc_start: 0.7577 (m-80) cc_final: 0.7351 (m-80) REVERT: B 564 GLN cc_start: 0.7665 (tp40) cc_final: 0.7101 (tp-100) REVERT: B 574 ASP cc_start: 0.8076 (p0) cc_final: 0.7803 (p0) REVERT: B 577 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7709 (ttm-80) REVERT: B 737 ASP cc_start: 0.7462 (t0) cc_final: 0.7202 (t0) REVERT: B 740 MET cc_start: 0.8417 (ttt) cc_final: 0.7770 (ttp) REVERT: B 750 SER cc_start: 0.8823 (m) cc_final: 0.8566 (p) REVERT: B 762 GLN cc_start: 0.7892 (tt0) cc_final: 0.7690 (tt0) REVERT: B 764 ASN cc_start: 0.8354 (m-40) cc_final: 0.7890 (m110) REVERT: B 814 LYS cc_start: 0.8271 (mmtt) cc_final: 0.7954 (mmmt) REVERT: B 900 MET cc_start: 0.8561 (mtm) cc_final: 0.8223 (mtm) REVERT: B 918 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7851 (mt-10) REVERT: B 950 ASP cc_start: 0.7977 (m-30) cc_final: 0.7560 (m-30) REVERT: B 979 ASP cc_start: 0.8242 (t0) cc_final: 0.8035 (t70) REVERT: C 52 GLN cc_start: 0.8729 (tm-30) cc_final: 0.8456 (tm-30) REVERT: C 190 ARG cc_start: 0.8051 (mmt180) cc_final: 0.7684 (mmt180) REVERT: C 237 ARG cc_start: 0.7850 (mtp-110) cc_final: 0.7602 (mtp-110) REVERT: C 386 LYS cc_start: 0.9174 (mmtt) cc_final: 0.8845 (mmtm) REVERT: C 523 THR cc_start: 0.8567 (p) cc_final: 0.8079 (t) REVERT: C 568 ASP cc_start: 0.8180 (t0) cc_final: 0.7911 (t0) REVERT: C 693 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8585 (mt) REVERT: C 763 LEU cc_start: 0.8548 (mm) cc_final: 0.8268 (mm) REVERT: C 808 ASP cc_start: 0.8054 (t0) cc_final: 0.7806 (t70) REVERT: C 950 ASP cc_start: 0.7988 (t0) cc_final: 0.7586 (t0) REVERT: C 985 ASP cc_start: 0.7638 (p0) cc_final: 0.6618 (p0) REVERT: C 1041 ASP cc_start: 0.8346 (m-30) cc_final: 0.8132 (m-30) REVERT: C 1045 LYS cc_start: 0.8358 (tmtt) cc_final: 0.8003 (tmtt) REVERT: C 1086 LYS cc_start: 0.8924 (ptpp) cc_final: 0.8672 (ptpp) REVERT: C 1119 ASN cc_start: 0.8482 (m110) cc_final: 0.8122 (m-40) REVERT: C 1141 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8628 (tp) outliers start: 101 outliers final: 72 residues processed: 658 average time/residue: 0.4022 time to fit residues: 412.0126 Evaluate side-chains 641 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 563 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 262 optimal weight: 0.0670 chunk 178 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 130 optimal weight: 0.0770 chunk 268 optimal weight: 2.9990 chunk 217 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 160 optimal weight: 0.0030 chunk 282 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 overall best weight: 0.2486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN A 764 ASN A 853 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 658 ASN B1005 GLN B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27543 Z= 0.167 Angle : 0.636 11.398 37464 Z= 0.312 Chirality : 0.047 0.738 4509 Planarity : 0.004 0.059 4713 Dihedral : 8.606 108.735 5489 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.04 % Allowed : 15.76 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3240 helix: 1.83 (0.19), residues: 743 sheet: -0.16 (0.17), residues: 773 loop : -0.98 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 353 HIS 0.006 0.001 HIS C 146 PHE 0.032 0.001 PHE B1148 TYR 0.032 0.001 TYR C 508 ARG 0.006 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 596 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.3938 (OUTLIER) cc_final: 0.3087 (ppt-90) REVERT: A 129 LYS cc_start: 0.8453 (tttt) cc_final: 0.7830 (tttt) REVERT: A 188 ASN cc_start: 0.8036 (m-40) cc_final: 0.7439 (p0) REVERT: A 287 ASP cc_start: 0.7914 (t70) cc_final: 0.7636 (t0) REVERT: A 493 GLN cc_start: 0.7118 (tm-30) cc_final: 0.6357 (tm-30) REVERT: A 571 ASP cc_start: 0.7754 (t70) cc_final: 0.7384 (t0) REVERT: A 586 ASP cc_start: 0.7803 (m-30) cc_final: 0.7563 (m-30) REVERT: A 796 ASP cc_start: 0.7762 (t70) cc_final: 0.7517 (t70) REVERT: A 872 GLN cc_start: 0.8296 (tt0) cc_final: 0.8078 (tt0) REVERT: A 901 GLN cc_start: 0.8530 (tt0) cc_final: 0.8248 (tt0) REVERT: A 941 THR cc_start: 0.7425 (t) cc_final: 0.7132 (t) REVERT: A 949 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7984 (mm-40) REVERT: A 960 ASN cc_start: 0.8189 (t0) cc_final: 0.7930 (t0) REVERT: A 964 LYS cc_start: 0.8693 (mmtt) cc_final: 0.8276 (mmmt) REVERT: A 1055 SER cc_start: 0.8969 (t) cc_final: 0.8630 (m) REVERT: A 1101 HIS cc_start: 0.7949 (m90) cc_final: 0.7712 (m-70) REVERT: A 1123 SER cc_start: 0.8620 (m) cc_final: 0.8400 (m) REVERT: B 125 ASN cc_start: 0.7501 (p0) cc_final: 0.7226 (p0) REVERT: B 177 MET cc_start: 0.6275 (ppp) cc_final: 0.5192 (ppp) REVERT: B 224 GLU cc_start: 0.7970 (mp0) cc_final: 0.7719 (mp0) REVERT: B 237 ARG cc_start: 0.8040 (mtm110) cc_final: 0.7798 (mtm110) REVERT: B 436 TRP cc_start: 0.7778 (p90) cc_final: 0.7416 (p90) REVERT: B 456 PHE cc_start: 0.7583 (m-80) cc_final: 0.7360 (m-80) REVERT: B 564 GLN cc_start: 0.7652 (tp40) cc_final: 0.7098 (tp-100) REVERT: B 574 ASP cc_start: 0.8061 (p0) cc_final: 0.7806 (p0) REVERT: B 577 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7630 (ttm-80) REVERT: B 740 MET cc_start: 0.8296 (ttt) cc_final: 0.8064 (ttp) REVERT: B 750 SER cc_start: 0.8810 (m) cc_final: 0.8569 (p) REVERT: B 764 ASN cc_start: 0.8331 (m-40) cc_final: 0.7904 (m110) REVERT: B 814 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7919 (mmmt) REVERT: B 900 MET cc_start: 0.8482 (mtm) cc_final: 0.8123 (mtm) REVERT: B 918 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7821 (mt-10) REVERT: B 950 ASP cc_start: 0.7942 (m-30) cc_final: 0.7577 (m-30) REVERT: C 40 ASP cc_start: 0.8176 (m-30) cc_final: 0.7975 (p0) REVERT: C 52 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8453 (tm-30) REVERT: C 130 VAL cc_start: 0.7725 (OUTLIER) cc_final: 0.7508 (p) REVERT: C 180 GLU cc_start: 0.4143 (OUTLIER) cc_final: 0.3858 (pm20) REVERT: C 190 ARG cc_start: 0.8061 (mmt180) cc_final: 0.7408 (ttt90) REVERT: C 237 ARG cc_start: 0.7849 (mtp-110) cc_final: 0.7628 (mtp-110) REVERT: C 321 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8750 (mm-40) REVERT: C 386 LYS cc_start: 0.9140 (mmtt) cc_final: 0.8830 (mmtm) REVERT: C 523 THR cc_start: 0.8506 (p) cc_final: 0.8012 (t) REVERT: C 619 GLU cc_start: 0.7260 (mp0) cc_final: 0.6862 (mp0) REVERT: C 693 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8578 (mt) REVERT: C 763 LEU cc_start: 0.8514 (mm) cc_final: 0.8269 (mm) REVERT: C 765 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7659 (ttp80) REVERT: C 950 ASP cc_start: 0.7918 (t0) cc_final: 0.7494 (t0) REVERT: C 1041 ASP cc_start: 0.8310 (m-30) cc_final: 0.8079 (m-30) REVERT: C 1045 LYS cc_start: 0.8369 (tmtt) cc_final: 0.8029 (tmtt) REVERT: C 1086 LYS cc_start: 0.8885 (ptpp) cc_final: 0.8638 (ptpp) REVERT: C 1119 ASN cc_start: 0.8455 (m110) cc_final: 0.8132 (m110) REVERT: C 1141 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8651 (tt) REVERT: C 1148 PHE cc_start: 0.5662 (t80) cc_final: 0.5309 (t80) outliers start: 87 outliers final: 60 residues processed: 647 average time/residue: 0.3940 time to fit residues: 395.7300 Evaluate side-chains 637 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 571 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 106 optimal weight: 2.9990 chunk 283 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 185 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 315 optimal weight: 2.9990 chunk 261 optimal weight: 0.4980 chunk 146 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 104 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 437 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A1119 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 658 ASN B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 271 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27543 Z= 0.207 Angle : 0.627 10.066 37464 Z= 0.308 Chirality : 0.046 0.712 4509 Planarity : 0.004 0.059 4713 Dihedral : 8.143 106.619 5489 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.53 % Allowed : 15.97 % Favored : 80.50 % 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: -0.16 (0.14), residues: 3240 helix: 1.93 (0.19), residues: 748 sheet: -0.13 (0.18), residues: 703 loop : -1.01 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 353 HIS 0.003 0.001 HIS B 66 PHE 0.034 0.001 PHE B 133 TYR 0.031 0.002 TYR B 508 ARG 0.007 0.001 ARG C1091 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 597 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.4027 (OUTLIER) cc_final: 0.3100 (ppt-90) REVERT: A 129 LYS cc_start: 0.8437 (tttt) cc_final: 0.7799 (tttt) REVERT: A 188 ASN cc_start: 0.8029 (OUTLIER) cc_final: 0.7487 (p0) REVERT: A 287 ASP cc_start: 0.7910 (t70) cc_final: 0.7639 (t0) REVERT: A 493 GLN cc_start: 0.7197 (tm-30) cc_final: 0.6095 (tm-30) REVERT: A 571 ASP cc_start: 0.7749 (t70) cc_final: 0.7370 (t0) REVERT: A 586 ASP cc_start: 0.7808 (m-30) cc_final: 0.7534 (m-30) REVERT: A 703 ASN cc_start: 0.8449 (t0) cc_final: 0.8139 (t0) REVERT: A 796 ASP cc_start: 0.7764 (t70) cc_final: 0.7509 (t70) REVERT: A 872 GLN cc_start: 0.8297 (tt0) cc_final: 0.8080 (tt0) REVERT: A 901 GLN cc_start: 0.8521 (tt0) cc_final: 0.8263 (tt0) REVERT: A 936 ASP cc_start: 0.7974 (m-30) cc_final: 0.7637 (m-30) REVERT: A 941 THR cc_start: 0.7386 (t) cc_final: 0.7089 (t) REVERT: A 949 GLN cc_start: 0.8242 (mm-40) cc_final: 0.8016 (mm-40) REVERT: A 960 ASN cc_start: 0.8236 (t0) cc_final: 0.7921 (t0) REVERT: A 964 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8271 (mmmt) REVERT: A 994 ASP cc_start: 0.7899 (t70) cc_final: 0.7667 (t0) REVERT: A 1055 SER cc_start: 0.8997 (t) cc_final: 0.8658 (m) REVERT: A 1101 HIS cc_start: 0.7978 (m90) cc_final: 0.7707 (m-70) REVERT: A 1123 SER cc_start: 0.8592 (m) cc_final: 0.8365 (m) REVERT: A 1125 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8528 (p0) REVERT: B 125 ASN cc_start: 0.7537 (p0) cc_final: 0.7263 (p0) REVERT: B 177 MET cc_start: 0.6323 (ppp) cc_final: 0.5273 (ppp) REVERT: B 202 LYS cc_start: 0.8687 (mttm) cc_final: 0.8474 (mttp) REVERT: B 223 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8731 (mt) REVERT: B 224 GLU cc_start: 0.7982 (mp0) cc_final: 0.7727 (mp0) REVERT: B 237 ARG cc_start: 0.8017 (mtm110) cc_final: 0.7724 (ptp-110) REVERT: B 436 TRP cc_start: 0.7827 (p90) cc_final: 0.7624 (p90) REVERT: B 456 PHE cc_start: 0.7589 (m-80) cc_final: 0.7361 (m-80) REVERT: B 493 GLN cc_start: 0.7521 (tm-30) cc_final: 0.7124 (tm-30) REVERT: B 564 GLN cc_start: 0.7700 (tp40) cc_final: 0.7171 (tp-100) REVERT: B 574 ASP cc_start: 0.8074 (p0) cc_final: 0.7813 (p0) REVERT: B 577 ARG cc_start: 0.7843 (ttm-80) cc_final: 0.7628 (ttm-80) REVERT: B 587 ILE cc_start: 0.9006 (mt) cc_final: 0.8704 (mp) REVERT: B 750 SER cc_start: 0.8806 (m) cc_final: 0.8572 (p) REVERT: B 762 GLN cc_start: 0.7611 (tt0) cc_final: 0.7287 (tm-30) REVERT: B 764 ASN cc_start: 0.8329 (m-40) cc_final: 0.7771 (m-40) REVERT: B 814 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7954 (mmmt) REVERT: B 900 MET cc_start: 0.8515 (mtm) cc_final: 0.8120 (mtt) REVERT: B 918 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7821 (mt-10) REVERT: B 950 ASP cc_start: 0.7945 (m-30) cc_final: 0.7539 (m-30) REVERT: B 1107 ARG cc_start: 0.7124 (ttm-80) cc_final: 0.6125 (ttm-80) REVERT: C 52 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8453 (tm-30) REVERT: C 100 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7344 (mp) REVERT: C 180 GLU cc_start: 0.4207 (OUTLIER) cc_final: 0.3916 (pm20) REVERT: C 190 ARG cc_start: 0.8061 (mmt180) cc_final: 0.7425 (ttt90) REVERT: C 237 ARG cc_start: 0.7866 (mtp-110) cc_final: 0.7656 (mtp-110) REVERT: C 321 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8783 (mm-40) REVERT: C 386 LYS cc_start: 0.9089 (mmtt) cc_final: 0.8838 (mmtm) REVERT: C 437 ASN cc_start: 0.6567 (t0) cc_final: 0.6326 (t0) REVERT: C 523 THR cc_start: 0.8511 (p) cc_final: 0.8040 (t) REVERT: C 546 LEU cc_start: 0.8474 (mp) cc_final: 0.8154 (mp) REVERT: C 574 ASP cc_start: 0.8524 (p0) cc_final: 0.8290 (p0) REVERT: C 619 GLU cc_start: 0.7283 (mp0) cc_final: 0.6943 (mp0) REVERT: C 693 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8563 (mt) REVERT: C 763 LEU cc_start: 0.8500 (mm) cc_final: 0.8237 (mm) REVERT: C 765 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7699 (ttp80) REVERT: C 950 ASP cc_start: 0.7915 (t0) cc_final: 0.7494 (t0) REVERT: C 1041 ASP cc_start: 0.8318 (m-30) cc_final: 0.8085 (m-30) REVERT: C 1045 LYS cc_start: 0.8381 (tmtt) cc_final: 0.8115 (tmtt) REVERT: C 1086 LYS cc_start: 0.8853 (ptpp) cc_final: 0.8606 (ptpp) REVERT: C 1119 ASN cc_start: 0.8459 (m110) cc_final: 0.8118 (m110) REVERT: C 1141 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8645 (tt) REVERT: C 1148 PHE cc_start: 0.5869 (t80) cc_final: 0.5527 (t80) outliers start: 101 outliers final: 78 residues processed: 651 average time/residue: 0.4153 time to fit residues: 422.7363 Evaluate side-chains 659 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 572 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 304 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 179 optimal weight: 0.6980 chunk 230 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 265 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 314 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 239 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 764 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 658 ASN B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27543 Z= 0.214 Angle : 0.630 10.250 37464 Z= 0.311 Chirality : 0.046 0.691 4509 Planarity : 0.004 0.059 4713 Dihedral : 7.912 105.354 5489 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.95 % Allowed : 16.28 % Favored : 79.77 % 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: -0.14 (0.14), residues: 3240 helix: 2.00 (0.19), residues: 742 sheet: -0.15 (0.18), residues: 729 loop : -1.00 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 353 HIS 0.004 0.001 HIS A 519 PHE 0.037 0.001 PHE B1148 TYR 0.041 0.002 TYR C 904 ARG 0.009 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 582 time to evaluate : 3.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.4040 (OUTLIER) cc_final: 0.3104 (ppt-90) REVERT: A 129 LYS cc_start: 0.8408 (tttt) cc_final: 0.7695 (tptt) REVERT: A 188 ASN cc_start: 0.8009 (OUTLIER) cc_final: 0.7475 (p0) REVERT: A 287 ASP cc_start: 0.7920 (t70) cc_final: 0.7644 (t0) REVERT: A 493 GLN cc_start: 0.7335 (tm-30) cc_final: 0.6526 (tm-30) REVERT: A 571 ASP cc_start: 0.7751 (t70) cc_final: 0.7345 (t0) REVERT: A 586 ASP cc_start: 0.7808 (m-30) cc_final: 0.7524 (m-30) REVERT: A 703 ASN cc_start: 0.8444 (t0) cc_final: 0.8147 (t0) REVERT: A 796 ASP cc_start: 0.7769 (t70) cc_final: 0.7516 (t70) REVERT: A 821 LEU cc_start: 0.8534 (mm) cc_final: 0.8212 (mp) REVERT: A 872 GLN cc_start: 0.8295 (tt0) cc_final: 0.8081 (tt0) REVERT: A 901 GLN cc_start: 0.8512 (tt0) cc_final: 0.8262 (tt0) REVERT: A 936 ASP cc_start: 0.7980 (m-30) cc_final: 0.7651 (m-30) REVERT: A 941 THR cc_start: 0.7357 (t) cc_final: 0.7051 (t) REVERT: A 949 GLN cc_start: 0.8241 (mm-40) cc_final: 0.8009 (mm-40) REVERT: A 960 ASN cc_start: 0.8240 (t0) cc_final: 0.7896 (t0) REVERT: A 964 LYS cc_start: 0.8699 (mmtt) cc_final: 0.8262 (mmmt) REVERT: A 1101 HIS cc_start: 0.7982 (m90) cc_final: 0.7478 (m-70) REVERT: A 1123 SER cc_start: 0.8570 (m) cc_final: 0.8343 (m) REVERT: A 1125 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8416 (p0) REVERT: B 125 ASN cc_start: 0.7585 (p0) cc_final: 0.7284 (p0) REVERT: B 177 MET cc_start: 0.6337 (ppp) cc_final: 0.5317 (ppp) REVERT: B 202 LYS cc_start: 0.8681 (mttm) cc_final: 0.8453 (mttp) REVERT: B 223 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8738 (mt) REVERT: B 224 GLU cc_start: 0.7964 (mp0) cc_final: 0.7677 (mp0) REVERT: B 237 ARG cc_start: 0.8005 (mtm110) cc_final: 0.7725 (ptp-110) REVERT: B 346 ARG cc_start: 0.7028 (mmm160) cc_final: 0.6699 (tpt90) REVERT: B 452 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7106 (mp) REVERT: B 493 GLN cc_start: 0.7494 (tm-30) cc_final: 0.7113 (tm-30) REVERT: B 564 GLN cc_start: 0.7742 (tp40) cc_final: 0.7215 (tp-100) REVERT: B 587 ILE cc_start: 0.8989 (mt) cc_final: 0.8678 (mp) REVERT: B 633 TRP cc_start: 0.7098 (OUTLIER) cc_final: 0.6749 (p-90) REVERT: B 737 ASP cc_start: 0.7864 (t0) cc_final: 0.7522 (t0) REVERT: B 750 SER cc_start: 0.8813 (m) cc_final: 0.8574 (p) REVERT: B 762 GLN cc_start: 0.7624 (tt0) cc_final: 0.7309 (tm-30) REVERT: B 764 ASN cc_start: 0.8318 (m-40) cc_final: 0.7781 (m-40) REVERT: B 814 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7942 (mmmt) REVERT: B 900 MET cc_start: 0.8499 (mtm) cc_final: 0.8106 (mtt) REVERT: B 950 ASP cc_start: 0.7948 (m-30) cc_final: 0.7587 (m-30) REVERT: C 52 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8460 (tm-30) REVERT: C 100 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8223 (mp) REVERT: C 152 TRP cc_start: 0.4578 (m-90) cc_final: 0.4215 (m-90) REVERT: C 190 ARG cc_start: 0.8049 (mmt180) cc_final: 0.7500 (ttt90) REVERT: C 237 ARG cc_start: 0.7866 (mtp-110) cc_final: 0.7430 (mtp-110) REVERT: C 321 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8784 (mm-40) REVERT: C 568 ASP cc_start: 0.8319 (t0) cc_final: 0.7969 (t0) REVERT: C 574 ASP cc_start: 0.8493 (p0) cc_final: 0.8240 (p0) REVERT: C 619 GLU cc_start: 0.7253 (mp0) cc_final: 0.6944 (mp0) REVERT: C 693 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8563 (mt) REVERT: C 750 SER cc_start: 0.8854 (m) cc_final: 0.8573 (p) REVERT: C 763 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8230 (mm) REVERT: C 765 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7675 (ttp80) REVERT: C 808 ASP cc_start: 0.7898 (t0) cc_final: 0.7616 (t70) REVERT: C 945 LEU cc_start: 0.8774 (mt) cc_final: 0.8559 (mp) REVERT: C 950 ASP cc_start: 0.7897 (t0) cc_final: 0.7468 (t0) REVERT: C 1041 ASP cc_start: 0.8302 (m-30) cc_final: 0.8080 (m-30) REVERT: C 1045 LYS cc_start: 0.8389 (tmtt) cc_final: 0.8101 (tmtt) REVERT: C 1086 LYS cc_start: 0.8809 (ptpp) cc_final: 0.8557 (ptpp) REVERT: C 1119 ASN cc_start: 0.8453 (m110) cc_final: 0.8123 (m110) REVERT: C 1141 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8546 (tt) REVERT: C 1148 PHE cc_start: 0.5863 (t80) cc_final: 0.5639 (t80) outliers start: 113 outliers final: 88 residues processed: 646 average time/residue: 0.3921 time to fit residues: 396.2089 Evaluate side-chains 665 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 566 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 194 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 187 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 199 optimal weight: 0.2980 chunk 214 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 246 optimal weight: 0.1980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 658 ASN A 764 ASN B 271 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 271 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27543 Z= 0.204 Angle : 0.631 10.317 37464 Z= 0.312 Chirality : 0.046 0.666 4509 Planarity : 0.004 0.058 4713 Dihedral : 7.733 104.768 5489 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.91 % Allowed : 17.02 % Favored : 79.07 % 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: -0.08 (0.14), residues: 3240 helix: 2.16 (0.20), residues: 730 sheet: -0.14 (0.18), residues: 707 loop : -0.97 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 353 HIS 0.004 0.001 HIS A 519 PHE 0.035 0.001 PHE B1148 TYR 0.034 0.001 TYR C 904 ARG 0.007 0.001 ARG C1091 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 578 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.4016 (OUTLIER) cc_final: 0.3117 (ppt-90) REVERT: A 129 LYS cc_start: 0.8394 (tttt) cc_final: 0.7736 (tttt) REVERT: A 188 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7391 (p0) REVERT: A 190 ARG cc_start: 0.7934 (tpt170) cc_final: 0.7399 (tpp80) REVERT: A 191 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7542 (mt-10) REVERT: A 287 ASP cc_start: 0.7909 (t70) cc_final: 0.7662 (t0) REVERT: A 306 PHE cc_start: 0.8621 (m-80) cc_final: 0.8384 (m-80) REVERT: A 493 GLN cc_start: 0.7283 (tm-30) cc_final: 0.6109 (tm-30) REVERT: A 586 ASP cc_start: 0.7807 (m-30) cc_final: 0.7515 (m-30) REVERT: A 703 ASN cc_start: 0.8441 (t0) cc_final: 0.8157 (t0) REVERT: A 794 ILE cc_start: 0.8660 (mt) cc_final: 0.8456 (mm) REVERT: A 796 ASP cc_start: 0.7775 (t70) cc_final: 0.7506 (t70) REVERT: A 821 LEU cc_start: 0.8523 (mm) cc_final: 0.8227 (mp) REVERT: A 872 GLN cc_start: 0.8294 (tt0) cc_final: 0.8084 (tt0) REVERT: A 901 GLN cc_start: 0.8490 (tt0) cc_final: 0.8239 (tt0) REVERT: A 936 ASP cc_start: 0.7973 (m-30) cc_final: 0.7645 (m-30) REVERT: A 941 THR cc_start: 0.7367 (t) cc_final: 0.7050 (t) REVERT: A 949 GLN cc_start: 0.8233 (mm-40) cc_final: 0.8005 (mm-40) REVERT: A 960 ASN cc_start: 0.8249 (t0) cc_final: 0.7890 (t0) REVERT: A 964 LYS cc_start: 0.8699 (mmtt) cc_final: 0.8271 (mmmt) REVERT: A 1101 HIS cc_start: 0.7986 (m90) cc_final: 0.7499 (m-70) REVERT: A 1123 SER cc_start: 0.8564 (m) cc_final: 0.8335 (m) REVERT: B 125 ASN cc_start: 0.7564 (p0) cc_final: 0.7271 (p0) REVERT: B 177 MET cc_start: 0.6389 (ppp) cc_final: 0.5411 (ppp) REVERT: B 202 LYS cc_start: 0.8688 (mttm) cc_final: 0.8479 (mttp) REVERT: B 223 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8738 (mt) REVERT: B 224 GLU cc_start: 0.7957 (mp0) cc_final: 0.7664 (mp0) REVERT: B 237 ARG cc_start: 0.7992 (mtm110) cc_final: 0.7716 (ptp-110) REVERT: B 346 ARG cc_start: 0.7065 (mmm160) cc_final: 0.6727 (tpt90) REVERT: B 493 GLN cc_start: 0.7581 (tm-30) cc_final: 0.7330 (tm-30) REVERT: B 587 ILE cc_start: 0.8962 (mt) cc_final: 0.8657 (mp) REVERT: B 633 TRP cc_start: 0.7087 (OUTLIER) cc_final: 0.6799 (p-90) REVERT: B 750 SER cc_start: 0.8814 (m) cc_final: 0.8575 (p) REVERT: B 762 GLN cc_start: 0.7605 (tt0) cc_final: 0.7287 (tm-30) REVERT: B 764 ASN cc_start: 0.8253 (m-40) cc_final: 0.7710 (m-40) REVERT: B 814 LYS cc_start: 0.8269 (mmtt) cc_final: 0.7931 (mmmt) REVERT: B 900 MET cc_start: 0.8492 (mtm) cc_final: 0.8146 (mtm) REVERT: B 918 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7778 (mt-10) REVERT: B 950 ASP cc_start: 0.7947 (m-30) cc_final: 0.7538 (m-30) REVERT: C 40 ASP cc_start: 0.8180 (m-30) cc_final: 0.7971 (p0) REVERT: C 52 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8435 (tm-30) REVERT: C 104 TRP cc_start: 0.6914 (m-90) cc_final: 0.6539 (m-90) REVERT: C 152 TRP cc_start: 0.4567 (m-90) cc_final: 0.4336 (m-90) REVERT: C 190 ARG cc_start: 0.8045 (mmt180) cc_final: 0.7506 (ttt90) REVERT: C 237 ARG cc_start: 0.7845 (mtp-110) cc_final: 0.7459 (mtp-110) REVERT: C 386 LYS cc_start: 0.9105 (mmtt) cc_final: 0.8849 (mmtm) REVERT: C 568 ASP cc_start: 0.8368 (t0) cc_final: 0.8057 (t0) REVERT: C 574 ASP cc_start: 0.8495 (p0) cc_final: 0.8231 (p0) REVERT: C 619 GLU cc_start: 0.7320 (mp0) cc_final: 0.7069 (mp0) REVERT: C 693 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8563 (mt) REVERT: C 750 SER cc_start: 0.8831 (m) cc_final: 0.8575 (p) REVERT: C 752 LEU cc_start: 0.9089 (mt) cc_final: 0.8871 (mt) REVERT: C 763 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8205 (mm) REVERT: C 765 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7812 (ttp80) REVERT: C 808 ASP cc_start: 0.7868 (t0) cc_final: 0.7573 (t70) REVERT: C 945 LEU cc_start: 0.8764 (mt) cc_final: 0.8555 (mp) REVERT: C 950 ASP cc_start: 0.7883 (t0) cc_final: 0.7462 (t0) REVERT: C 1017 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7612 (tt0) REVERT: C 1041 ASP cc_start: 0.8306 (m-30) cc_final: 0.8075 (m-30) REVERT: C 1045 LYS cc_start: 0.8398 (tmtt) cc_final: 0.8140 (tmtt) REVERT: C 1086 LYS cc_start: 0.8809 (ptpp) cc_final: 0.8561 (ptpp) REVERT: C 1119 ASN cc_start: 0.8439 (m110) cc_final: 0.8118 (m110) REVERT: C 1141 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8545 (tt) outliers start: 112 outliers final: 90 residues processed: 639 average time/residue: 0.3899 time to fit residues: 389.4336 Evaluate side-chains 666 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 568 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 285 optimal weight: 0.9980 chunk 301 optimal weight: 0.6980 chunk 274 optimal weight: 3.9990 chunk 292 optimal weight: 2.9990 chunk 300 optimal weight: 0.5980 chunk 176 optimal weight: 1.9990 chunk 127 optimal weight: 0.0060 chunk 229 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 264 optimal weight: 0.8980 chunk 276 optimal weight: 4.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 764 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 271 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27543 Z= 0.207 Angle : 0.633 10.403 37464 Z= 0.313 Chirality : 0.046 0.652 4509 Planarity : 0.004 0.072 4713 Dihedral : 7.594 105.415 5489 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.60 % Allowed : 17.68 % Favored : 78.72 % 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: -0.06 (0.14), residues: 3240 helix: 2.14 (0.20), residues: 737 sheet: -0.05 (0.18), residues: 724 loop : -1.00 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 353 HIS 0.004 0.001 HIS A 519 PHE 0.040 0.001 PHE B 456 TYR 0.028 0.001 TYR C 904 ARG 0.007 0.001 ARG C1091 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 584 time to evaluate : 3.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.3988 (OUTLIER) cc_final: 0.3094 (ppt-90) REVERT: A 129 LYS cc_start: 0.8382 (tttt) cc_final: 0.7721 (tttt) REVERT: A 144 TYR cc_start: 0.6540 (m-10) cc_final: 0.6288 (m-80) REVERT: A 188 ASN cc_start: 0.7957 (OUTLIER) cc_final: 0.7480 (t0) REVERT: A 190 ARG cc_start: 0.7933 (tpt170) cc_final: 0.7351 (tpp80) REVERT: A 287 ASP cc_start: 0.7908 (t70) cc_final: 0.7672 (t0) REVERT: A 306 PHE cc_start: 0.8624 (m-80) cc_final: 0.8399 (m-80) REVERT: A 390 LEU cc_start: 0.8156 (mt) cc_final: 0.7837 (mm) REVERT: A 493 GLN cc_start: 0.7292 (tm-30) cc_final: 0.6086 (tm-30) REVERT: A 586 ASP cc_start: 0.7806 (m-30) cc_final: 0.7499 (m-30) REVERT: A 703 ASN cc_start: 0.8441 (t0) cc_final: 0.8159 (t0) REVERT: A 794 ILE cc_start: 0.8672 (mt) cc_final: 0.8464 (mm) REVERT: A 796 ASP cc_start: 0.7775 (t70) cc_final: 0.7511 (t70) REVERT: A 821 LEU cc_start: 0.8518 (mm) cc_final: 0.8250 (mp) REVERT: A 872 GLN cc_start: 0.8304 (tt0) cc_final: 0.8086 (tt0) REVERT: A 901 GLN cc_start: 0.8474 (tt0) cc_final: 0.8237 (tt0) REVERT: A 936 ASP cc_start: 0.7973 (m-30) cc_final: 0.7650 (m-30) REVERT: A 941 THR cc_start: 0.7420 (t) cc_final: 0.7095 (t) REVERT: A 949 GLN cc_start: 0.8228 (mm-40) cc_final: 0.8002 (mm-40) REVERT: A 960 ASN cc_start: 0.8261 (t0) cc_final: 0.7892 (t0) REVERT: A 964 LYS cc_start: 0.8700 (mmtt) cc_final: 0.8273 (mmmt) REVERT: A 1101 HIS cc_start: 0.7980 (m90) cc_final: 0.7505 (m-70) REVERT: A 1123 SER cc_start: 0.8545 (m) cc_final: 0.8313 (m) REVERT: B 125 ASN cc_start: 0.7568 (p0) cc_final: 0.7283 (p0) REVERT: B 177 MET cc_start: 0.6382 (ppp) cc_final: 0.5355 (ppp) REVERT: B 202 LYS cc_start: 0.8680 (mttm) cc_final: 0.8471 (mttp) REVERT: B 223 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8732 (mt) REVERT: B 224 GLU cc_start: 0.7953 (mp0) cc_final: 0.7653 (mp0) REVERT: B 237 ARG cc_start: 0.7997 (mtm110) cc_final: 0.7724 (ptp-110) REVERT: B 271 GLN cc_start: 0.8478 (mt0) cc_final: 0.8107 (mt0) REVERT: B 587 ILE cc_start: 0.8987 (mt) cc_final: 0.8692 (mp) REVERT: B 633 TRP cc_start: 0.7077 (OUTLIER) cc_final: 0.6819 (p-90) REVERT: B 750 SER cc_start: 0.8815 (m) cc_final: 0.8575 (p) REVERT: B 762 GLN cc_start: 0.7581 (tt0) cc_final: 0.7267 (tm-30) REVERT: B 764 ASN cc_start: 0.8231 (m-40) cc_final: 0.7699 (m-40) REVERT: B 814 LYS cc_start: 0.8257 (mmtt) cc_final: 0.7927 (mmmt) REVERT: B 918 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7772 (mt-10) REVERT: B 950 ASP cc_start: 0.7954 (m-30) cc_final: 0.7581 (m-30) REVERT: C 52 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8431 (tm-30) REVERT: C 190 ARG cc_start: 0.8038 (mmt180) cc_final: 0.7517 (ttt90) REVERT: C 329 PHE cc_start: 0.8185 (m-80) cc_final: 0.7976 (m-80) REVERT: C 386 LYS cc_start: 0.9103 (mmtt) cc_final: 0.8839 (mmtm) REVERT: C 398 ASP cc_start: 0.7063 (m-30) cc_final: 0.6713 (t0) REVERT: C 568 ASP cc_start: 0.8362 (t0) cc_final: 0.8040 (t0) REVERT: C 574 ASP cc_start: 0.8486 (p0) cc_final: 0.8245 (p0) REVERT: C 619 GLU cc_start: 0.7300 (mp0) cc_final: 0.7057 (mp0) REVERT: C 693 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8560 (mt) REVERT: C 750 SER cc_start: 0.8832 (m) cc_final: 0.8573 (p) REVERT: C 752 LEU cc_start: 0.9076 (mt) cc_final: 0.8846 (mt) REVERT: C 763 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8205 (mm) REVERT: C 765 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7822 (ttp80) REVERT: C 945 LEU cc_start: 0.8767 (mt) cc_final: 0.8563 (mp) REVERT: C 950 ASP cc_start: 0.7881 (t0) cc_final: 0.7466 (t0) REVERT: C 1017 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7611 (tt0) REVERT: C 1041 ASP cc_start: 0.8306 (m-30) cc_final: 0.8077 (m-30) REVERT: C 1045 LYS cc_start: 0.8398 (tmtt) cc_final: 0.8144 (tmtt) REVERT: C 1086 LYS cc_start: 0.8779 (ptpp) cc_final: 0.8532 (ptpp) REVERT: C 1119 ASN cc_start: 0.8441 (m110) cc_final: 0.8119 (m110) REVERT: C 1141 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8533 (tt) outliers start: 103 outliers final: 87 residues processed: 640 average time/residue: 0.4084 time to fit residues: 411.5789 Evaluate side-chains 665 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 570 time to evaluate : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 291 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 309 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 324 optimal weight: 0.1980 chunk 298 optimal weight: 3.9990 chunk 258 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 764 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 580 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 115 GLN C 271 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27543 Z= 0.220 Angle : 0.645 10.400 37464 Z= 0.319 Chirality : 0.046 0.642 4509 Planarity : 0.004 0.060 4713 Dihedral : 7.426 106.030 5489 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.49 % Allowed : 18.06 % Favored : 78.44 % 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: -0.05 (0.14), residues: 3240 helix: 2.15 (0.20), residues: 737 sheet: -0.04 (0.18), residues: 716 loop : -1.00 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 152 HIS 0.004 0.001 HIS A 519 PHE 0.042 0.002 PHE B 456 TYR 0.030 0.001 TYR C 904 ARG 0.008 0.001 ARG C1091 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 581 time to evaluate : 3.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.3992 (OUTLIER) cc_final: 0.3049 (ppt-90) REVERT: A 129 LYS cc_start: 0.8382 (tttt) cc_final: 0.7726 (tttt) REVERT: A 188 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7492 (t0) REVERT: A 190 ARG cc_start: 0.7952 (tpt170) cc_final: 0.7349 (tpp80) REVERT: A 287 ASP cc_start: 0.7902 (t70) cc_final: 0.7657 (t0) REVERT: A 306 PHE cc_start: 0.8630 (m-80) cc_final: 0.8398 (m-80) REVERT: A 390 LEU cc_start: 0.8174 (mt) cc_final: 0.7841 (mm) REVERT: A 493 GLN cc_start: 0.7324 (tm-30) cc_final: 0.6129 (tm-30) REVERT: A 586 ASP cc_start: 0.7807 (m-30) cc_final: 0.7506 (m-30) REVERT: A 703 ASN cc_start: 0.8442 (t0) cc_final: 0.8177 (t0) REVERT: A 794 ILE cc_start: 0.8669 (mt) cc_final: 0.8464 (mm) REVERT: A 796 ASP cc_start: 0.7791 (t70) cc_final: 0.7532 (t70) REVERT: A 821 LEU cc_start: 0.8521 (mm) cc_final: 0.8317 (mp) REVERT: A 872 GLN cc_start: 0.8313 (tt0) cc_final: 0.8094 (tt0) REVERT: A 901 GLN cc_start: 0.8460 (tt0) cc_final: 0.8229 (tt0) REVERT: A 936 ASP cc_start: 0.7980 (m-30) cc_final: 0.7657 (m-30) REVERT: A 941 THR cc_start: 0.7405 (t) cc_final: 0.7077 (t) REVERT: A 949 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7985 (mm-40) REVERT: A 950 ASP cc_start: 0.7771 (t0) cc_final: 0.7540 (t70) REVERT: A 960 ASN cc_start: 0.8276 (t0) cc_final: 0.7896 (t0) REVERT: A 964 LYS cc_start: 0.8699 (mmtt) cc_final: 0.8269 (mmmt) REVERT: A 1101 HIS cc_start: 0.7983 (m90) cc_final: 0.7510 (m-70) REVERT: B 125 ASN cc_start: 0.7617 (p0) cc_final: 0.7286 (p0) REVERT: B 177 MET cc_start: 0.6272 (ppp) cc_final: 0.5230 (ppp) REVERT: B 216 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7414 (mp) REVERT: B 223 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8719 (mt) REVERT: B 224 GLU cc_start: 0.7946 (mp0) cc_final: 0.7645 (mp0) REVERT: B 237 ARG cc_start: 0.8005 (mtm110) cc_final: 0.7469 (ptp90) REVERT: B 271 GLN cc_start: 0.8505 (mt0) cc_final: 0.8090 (mt0) REVERT: B 587 ILE cc_start: 0.8989 (mt) cc_final: 0.8694 (mp) REVERT: B 633 TRP cc_start: 0.7082 (OUTLIER) cc_final: 0.6867 (p-90) REVERT: B 750 SER cc_start: 0.8821 (m) cc_final: 0.8575 (p) REVERT: B 764 ASN cc_start: 0.8243 (m-40) cc_final: 0.7708 (m-40) REVERT: B 814 LYS cc_start: 0.8253 (mmtt) cc_final: 0.7918 (mmmt) REVERT: B 918 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7774 (mt-10) REVERT: B 950 ASP cc_start: 0.7960 (m-30) cc_final: 0.7536 (m-30) REVERT: B 988 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7787 (mm-30) REVERT: C 52 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8424 (tm-30) REVERT: C 190 ARG cc_start: 0.8053 (mmt180) cc_final: 0.7781 (mmt180) REVERT: C 195 LYS cc_start: 0.8311 (mtmt) cc_final: 0.7726 (mtmm) REVERT: C 329 PHE cc_start: 0.8180 (m-80) cc_final: 0.7964 (m-80) REVERT: C 398 ASP cc_start: 0.7116 (m-30) cc_final: 0.6746 (t0) REVERT: C 568 ASP cc_start: 0.8363 (t0) cc_final: 0.8049 (t0) REVERT: C 574 ASP cc_start: 0.8490 (p0) cc_final: 0.8219 (p0) REVERT: C 619 GLU cc_start: 0.7285 (mp0) cc_final: 0.7013 (mp0) REVERT: C 693 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8561 (mt) REVERT: C 750 SER cc_start: 0.8824 (m) cc_final: 0.8573 (p) REVERT: C 763 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8220 (mm) REVERT: C 765 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7816 (ttp80) REVERT: C 945 LEU cc_start: 0.8767 (mt) cc_final: 0.8561 (mp) REVERT: C 950 ASP cc_start: 0.7884 (t0) cc_final: 0.7465 (t0) REVERT: C 1017 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7611 (tt0) REVERT: C 1041 ASP cc_start: 0.8309 (m-30) cc_final: 0.8093 (m-30) REVERT: C 1045 LYS cc_start: 0.8399 (tmtt) cc_final: 0.8057 (tmtt) REVERT: C 1086 LYS cc_start: 0.8764 (ptpp) cc_final: 0.8492 (ptpp) REVERT: C 1119 ASN cc_start: 0.8438 (m110) cc_final: 0.8114 (m110) REVERT: C 1141 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8524 (tt) outliers start: 100 outliers final: 83 residues processed: 634 average time/residue: 0.4071 time to fit residues: 403.2196 Evaluate side-chains 661 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 569 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 158 optimal weight: 0.3980 chunk 205 optimal weight: 1.9990 chunk 275 optimal weight: 0.9990 chunk 79 optimal weight: 0.0980 chunk 238 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 259 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 265 optimal weight: 0.0030 chunk 32 optimal weight: 4.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 762 GLN B 978 ASN B1119 ASN C 271 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.102090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.084015 restraints weight = 66792.715| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.33 r_work: 0.3174 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27543 Z= 0.176 Angle : 0.633 10.609 37464 Z= 0.312 Chirality : 0.045 0.617 4509 Planarity : 0.004 0.057 4713 Dihedral : 7.157 104.936 5489 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.35 % Allowed : 18.59 % Favored : 78.06 % 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: 0.00 (0.14), residues: 3240 helix: 2.21 (0.20), residues: 737 sheet: -0.02 (0.18), residues: 709 loop : -0.96 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 353 HIS 0.004 0.001 HIS A 519 PHE 0.041 0.001 PHE B 456 TYR 0.026 0.001 TYR C 904 ARG 0.008 0.001 ARG C1091 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8010.10 seconds wall clock time: 145 minutes 30.79 seconds (8730.79 seconds total)