Starting phenix.real_space_refine on Tue Feb 20 10:55:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d56_27206/02_2024/8d56_27206_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d56_27206/02_2024/8d56_27206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d56_27206/02_2024/8d56_27206.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d56_27206/02_2024/8d56_27206.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d56_27206/02_2024/8d56_27206_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d56_27206/02_2024/8d56_27206_neut.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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 119 5.16 5 C 17602 2.51 5 N 4474 2.21 5 O 5479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 737": "OD1" <-> "OD2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ASP 808": "OD1" <-> "OD2" Residue "A ASP 820": "OD1" <-> "OD2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B ASP 142": "OD1" <-> "OD2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 830": "OD1" <-> "OD2" Residue "B TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 843": "OD1" <-> "OD2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B ASP 1153": "OD1" <-> "OD2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" 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 ARG 357": "NH1" <-> "NH2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 578": "OD1" <-> "OD2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 636": "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 ARG 765": "NH1" <-> "NH2" Residue "C TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C ASP 1118": "OD1" <-> "OD2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1139": "OD1" <-> "OD2" Residue "C ASP 1153": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27674 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8715 Classifications: {'peptide': 1110} Link IDs: {'PTRANS': 51, 'TRANS': 1058} Chain breaks: 4 Chain: "B" Number of atoms: 8820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1124, 8820 Classifications: {'peptide': 1124} Link IDs: {'PTRANS': 51, 'TRANS': 1072} Chain breaks: 3 Chain: "C" Number of atoms: 8777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8777 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 51, 'TRANS': 1067} Chain breaks: 3 Chain: "D" 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: "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: 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: "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: 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: "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: 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: "L" 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: "M" 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: "N" 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'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: "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: 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: "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: 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: "V" 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: "W" 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: "X" 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: "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: 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: "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: 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: "d" 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: "e" 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: "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: "g" 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 14.58, per 1000 atoms: 0.53 Number of scatterers: 27674 At special positions: 0 Unit cell: (147.74, 143.59, 219.12, 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 119 16.00 O 5479 8.00 N 4474 7.00 C 17602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=1.98 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.01 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 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=1.99 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=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 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 Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG G 2 " - " MAN G 3 " " NAG I 2 " - " MAN I 3 " " NAG J 2 " - " MAN J 3 " " NAG L 2 " - " MAN L 3 " " NAG M 2 " - " MAN M 3 " " NAG N 2 " - " MAN N 3 " " NAG Q 2 " - " MAN Q 3 " " NAG S 2 " - " MAN S 3 " " NAG T 2 " - " MAN T 3 " " NAG V 2 " - " MAN V 3 " " NAG W 2 " - " MAN W 3 " " NAG X 2 " - " MAN X 3 " " NAG a 2 " - " MAN a 3 " " NAG c 2 " - " MAN c 3 " " NAG d 2 " - " MAN d 3 " " NAG f 2 " - " MAN f 3 " " NAG g 2 " - " MAN g 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 " " NAG g 1 " - " NAG g 2 " BETA1-6 " NAG K 1 " - " FUC K 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG U 1 " - " FUC U 3 " " NAG e 1 " - " FUC e 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 331 " " NAG A1403 " - " ASN A 343 " " NAG A1404 " - " ASN A 603 " " NAG A1405 " - " ASN A 657 " " NAG A1406 " - " ASN A 709 " " NAG A1407 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 331 " " NAG B1403 " - " ASN B 343 " " NAG B1404 " - " ASN B 603 " " NAG B1405 " - " ASN B 657 " " NAG B1406 " - " ASN B 709 " " NAG B1407 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 331 " " NAG C1403 " - " ASN C 343 " " NAG C1404 " - " ASN C 603 " " NAG C1405 " - " ASN C 657 " " NAG C1406 " - " ASN C 709 " " NAG C1407 " - " ASN C1158 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 165 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 282 " " NAG H 1 " - " ASN A 616 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 122 " " NAG O 1 " - " ASN B 165 " " NAG P 1 " - " ASN B 234 " " NAG Q 1 " - " ASN B 282 " " NAG R 1 " - " ASN B 616 " " NAG S 1 " - " ASN B 717 " " NAG T 1 " - " ASN B 801 " " NAG U 1 " - " ASN B1074 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 122 " " NAG Y 1 " - " ASN C 165 " " NAG Z 1 " - " ASN C 234 " " NAG a 1 " - " ASN C 282 " " NAG b 1 " - " ASN C 616 " " NAG c 1 " - " ASN C 717 " " NAG d 1 " - " ASN C 801 " " NAG e 1 " - " ASN C1074 " " NAG f 1 " - " ASN C1098 " " NAG g 1 " - " ASN C1134 " Time building additional restraints: 12.67 Conformation dependent library (CDL) restraints added in 4.9 seconds 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6284 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 44 sheets defined 27.0% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.67 Creating SS restraints... Processing helix chain 'A' and resid 96 through 99 removed outlier: 3.820A pdb=" N ASN A 99 " --> pdb=" O GLU A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 96 through 99' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.758A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.797A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.534A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 5.360A pdb=" N SER A 408 " --> pdb=" O ASN 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 635 through 639 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.081A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.628A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.734A 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 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.767A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.041A 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 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.590A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.212A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.551A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.564A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.051A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.375A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (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 633 through 639 removed outlier: 3.555A pdb=" N TYR B 636 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.695A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.606A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.663A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.536A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.341A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.673A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.662A pdb=" N GLU B 990 " --> pdb=" O LYS B 986 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1160 removed outlier: 4.335A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 100 removed outlier: 3.736A pdb=" N ASN C 99 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 96 through 100' 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 371 Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 405 through 411 removed outlier: 5.026A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 618 through 623 removed outlier: 3.606A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 638 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.912A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.205A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.629A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 848 Processing helix chain 'C' and resid 848 through 855 removed outlier: 4.086A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.713A 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 912 through 919 removed outlier: 4.114A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.557A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) 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: 4.182A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.652A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.004A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1160 removed outlier: 4.430A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 31 removed outlier: 8.347A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.025A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.621A 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: 6.902A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 146 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 311 through 314 removed outlier: 3.764A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 327 removed outlier: 4.211A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.654A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.995A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.689A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.689A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.272A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.339A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 31 removed outlier: 8.117A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.654A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.076A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.766A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.524A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.395A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.601A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.253A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.158A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 357 removed outlier: 4.015A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.747A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.765A pdb=" N TYR B 453 " --> pdb=" O ARG B 493 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.585A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.684A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.495A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.495A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.317A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.151A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 20 through 31 removed outlier: 3.613A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS C 69 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY C 261 " --> pdb=" O HIS C 69 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 50 removed outlier: 3.569A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 152 through 153 removed outlier: 6.361A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE2, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.971A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.507A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.507A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.434A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.026A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3102 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: 12.78 Time building geometry restraints manager: 13.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4679 1.31 - 1.44: 7827 1.44 - 1.57: 15637 1.57 - 1.70: 4 1.70 - 1.82: 149 Bond restraints: 28296 Sorted by residual: bond pdb=" N PHE B 133 " pdb=" CA PHE B 133 " ideal model delta sigma weight residual 1.454 1.394 0.061 1.17e-02 7.31e+03 2.67e+01 bond pdb=" CA PHE B 65 " pdb=" C PHE B 65 " ideal model delta sigma weight residual 1.526 1.465 0.061 1.36e-02 5.41e+03 2.00e+01 bond pdb=" CA ARG C 466 " pdb=" C ARG C 466 " ideal model delta sigma weight residual 1.521 1.569 -0.048 1.20e-02 6.94e+03 1.59e+01 bond pdb=" CA HIS B 207 " pdb=" C HIS B 207 " ideal model delta sigma weight residual 1.522 1.569 -0.047 1.18e-02 7.18e+03 1.56e+01 bond pdb=" C GLN C 607 " pdb=" O GLN C 607 " ideal model delta sigma weight residual 1.234 1.190 0.044 1.17e-02 7.31e+03 1.40e+01 ... (remaining 28291 not shown) Histogram of bond angle deviations from ideal: 96.90 - 104.78: 443 104.78 - 112.67: 13476 112.67 - 120.55: 14833 120.55 - 128.44: 9622 128.44 - 136.32: 109 Bond angle restraints: 38483 Sorted by residual: angle pdb=" N SER C 172 " pdb=" CA SER C 172 " pdb=" C SER C 172 " ideal model delta sigma weight residual 108.45 119.22 -10.77 1.26e+00 6.30e-01 7.31e+01 angle pdb=" C LEU B 216 " pdb=" CA LEU B 216 " pdb=" CB LEU B 216 " ideal model delta sigma weight residual 111.20 116.42 -5.22 7.10e-01 1.98e+00 5.41e+01 angle pdb=" N ARG C 246 " pdb=" CA ARG C 246 " pdb=" C ARG C 246 " ideal model delta sigma weight residual 112.25 102.33 9.92 1.36e+00 5.41e-01 5.32e+01 angle pdb=" N ASN A 125 " pdb=" CA ASN A 125 " pdb=" C ASN A 125 " ideal model delta sigma weight residual 108.32 120.22 -11.90 1.64e+00 3.72e-01 5.26e+01 angle pdb=" N ASN C 125 " pdb=" CA ASN C 125 " pdb=" C ASN C 125 " ideal model delta sigma weight residual 108.45 117.51 -9.06 1.26e+00 6.30e-01 5.17e+01 ... (remaining 38478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.76: 17108 24.76 - 49.52: 746 49.52 - 74.29: 181 74.29 - 99.05: 57 99.05 - 123.81: 41 Dihedral angle restraints: 18133 sinusoidal: 8354 harmonic: 9779 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -164.88 78.88 1 1.00e+01 1.00e-02 7.75e+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 93.00 166.32 -73.32 1 1.00e+01 1.00e-02 6.85e+01 dihedral pdb=" CA PRO C 491 " pdb=" C PRO C 491 " pdb=" N LEU C 492 " pdb=" CA LEU C 492 " ideal model delta harmonic sigma weight residual 180.00 150.60 29.40 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 18130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.257: 4563 0.257 - 0.514: 65 0.514 - 0.771: 6 0.771 - 1.028: 0 1.028 - 1.284: 3 Chirality restraints: 4637 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.70e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.68e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.44e+01 ... (remaining 4634 not shown) Planarity restraints: 4872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1402 " 0.208 2.00e-02 2.50e+03 1.73e-01 3.74e+02 pdb=" C7 NAG B1402 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG B1402 " 0.149 2.00e-02 2.50e+03 pdb=" N2 NAG B1402 " -0.283 2.00e-02 2.50e+03 pdb=" O7 NAG B1402 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 104 " 0.211 2.00e-02 2.50e+03 1.08e-01 2.92e+02 pdb=" CG TRP B 104 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 104 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP B 104 " -0.099 2.00e-02 2.50e+03 pdb=" NE1 TRP B 104 " -0.071 2.00e-02 2.50e+03 pdb=" CE2 TRP B 104 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 104 " -0.144 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 104 " 0.131 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 104 " -0.047 2.00e-02 2.50e+03 pdb=" CH2 TRP B 104 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1407 " 0.158 2.00e-02 2.50e+03 1.32e-01 2.18e+02 pdb=" C7 NAG B1407 " -0.041 2.00e-02 2.50e+03 pdb=" C8 NAG B1407 " 0.115 2.00e-02 2.50e+03 pdb=" N2 NAG B1407 " -0.218 2.00e-02 2.50e+03 pdb=" O7 NAG B1407 " -0.014 2.00e-02 2.50e+03 ... (remaining 4869 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 3 2.15 - 2.83: 7600 2.83 - 3.52: 37587 3.52 - 4.21: 65331 4.21 - 4.90: 110578 Nonbonded interactions: 221099 Sorted by model distance: nonbonded pdb=" ND2 ASN C 334 " pdb=" O ASN C 360 " model vdw 1.457 2.520 nonbonded pdb=" CD1 LEU B 452 " pdb=" O ARG B 493 " model vdw 1.606 3.460 nonbonded pdb=" O SER B 112 " pdb=" OE2 GLU B 132 " model vdw 2.048 3.040 nonbonded pdb=" O SER C 98 " pdb=" NH2 ARG C 102 " model vdw 2.200 2.520 nonbonded pdb=" OH TYR C 453 " pdb=" NH1 ARG C 493 " model vdw 2.217 2.520 ... (remaining 221094 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 624 or resid 629 through 1160 or resid 1401 thr \ ough 1407)) selection = (chain 'B' and (resid 14 through 71 or resid 80 through 248 or resid 257 through \ 624 or resid 629 through 835 or resid 848 through 1160 or resid 1401 through 14 \ 07)) selection = (chain 'C' and (resid 14 through 248 or resid 257 through 835 or resid 848 throu \ gh 1160 or resid 1401 through 1407)) } ncs_group { reference = (chain 'D' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (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 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'c' 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) selection = (chain 'g' and resid 1 through 2) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' } 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: 5.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 23.770 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 78.250 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.061 28296 Z= 0.781 Angle : 1.733 11.898 38483 Z= 1.149 Chirality : 0.105 1.284 4637 Planarity : 0.013 0.173 4821 Dihedral : 16.187 123.809 11717 Min Nonbonded Distance : 1.457 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.63 % Favored : 92.25 % Rotamer: Outliers : 2.60 % Allowed : 8.32 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.13), residues: 3327 helix: -1.36 (0.16), residues: 752 sheet: -0.00 (0.20), residues: 615 loop : -1.86 (0.12), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.211 0.026 TRP B 104 HIS 0.017 0.002 HIS C 69 PHE 0.076 0.010 PHE B 718 TYR 0.119 0.016 TYR A1138 ARG 0.010 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 238 time to evaluate : 3.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7641 (tt) REVERT: A 365 TYR cc_start: 0.7559 (p90) cc_final: 0.6942 (m-80) REVERT: A 468 ILE cc_start: 0.8327 (pt) cc_final: 0.7705 (mm) REVERT: A 739 THR cc_start: 0.8111 (m) cc_final: 0.7846 (p) REVERT: B 54 LEU cc_start: 0.9269 (mt) cc_final: 0.9051 (mt) REVERT: B 489 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.7095 (m-80) REVERT: C 201 PHE cc_start: 0.6529 (OUTLIER) cc_final: 0.4572 (t80) REVERT: C 366 SER cc_start: 0.8962 (OUTLIER) cc_final: 0.8741 (p) REVERT: C 375 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6528 (p90) outliers start: 76 outliers final: 17 residues processed: 299 average time/residue: 1.3101 time to fit residues: 460.7717 Evaluate side-chains 125 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 3.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 491 PRO Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 957 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 282 optimal weight: 0.7980 chunk 253 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 170 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 261 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 159 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 303 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 487 ASN A 913 GLN A 955 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN A1106 GLN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 188 ASN B 245 HIS ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 450 ASN B 506 GLN B 613 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 774 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 955 ASN B 957 GLN B1010 GLN B1071 GLN B1159 HIS C 14 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 196 ASN C 245 HIS C 580 GLN C 607 GLN C 914 ASN C 919 ASN C1002 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28296 Z= 0.213 Angle : 0.733 15.209 38483 Z= 0.365 Chirality : 0.047 0.317 4637 Planarity : 0.004 0.063 4821 Dihedral : 12.776 111.127 5745 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.88 % Allowed : 11.47 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3327 helix: 1.00 (0.19), residues: 743 sheet: 0.13 (0.18), residues: 707 loop : -1.44 (0.13), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 152 HIS 0.008 0.001 HIS C1048 PHE 0.017 0.002 PHE A 338 TYR 0.021 0.002 TYR C1067 ARG 0.007 0.001 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 117 time to evaluate : 3.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7778 (tp) REVERT: A 341 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8401 (p) REVERT: A 365 TYR cc_start: 0.7655 (p90) cc_final: 0.7042 (m-80) REVERT: A 468 ILE cc_start: 0.8319 (pt) cc_final: 0.8046 (mt) REVERT: B 429 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.6321 (p90) REVERT: B 489 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.7191 (m-80) REVERT: C 369 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.6895 (p90) REVERT: C 375 PHE cc_start: 0.7210 (OUTLIER) cc_final: 0.6921 (p90) REVERT: C 515 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.8187 (p90) REVERT: C 658 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8164 (p0) REVERT: C 957 GLN cc_start: 0.8151 (tt0) cc_final: 0.7941 (tm-30) outliers start: 84 outliers final: 22 residues processed: 187 average time/residue: 1.0219 time to fit residues: 237.7136 Evaluate side-chains 120 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 90 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 168 optimal weight: 0.0000 chunk 94 optimal weight: 2.9990 chunk 252 optimal weight: 0.8980 chunk 206 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 303 optimal weight: 5.9990 chunk 328 optimal weight: 0.9990 chunk 270 optimal weight: 20.0000 chunk 301 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 243 optimal weight: 7.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 409 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28296 Z= 0.196 Angle : 0.660 17.237 38483 Z= 0.318 Chirality : 0.044 0.277 4637 Planarity : 0.004 0.046 4821 Dihedral : 10.989 106.422 5722 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.60 % Allowed : 12.88 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3327 helix: 1.59 (0.19), residues: 749 sheet: 0.21 (0.18), residues: 753 loop : -1.30 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 104 HIS 0.004 0.001 HIS B1064 PHE 0.023 0.001 PHE B 456 TYR 0.026 0.001 TYR A 369 ARG 0.009 0.000 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 99 time to evaluate : 3.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7712 (tp) REVERT: A 351 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.8267 (p90) REVERT: A 461 LEU cc_start: 0.5423 (OUTLIER) cc_final: 0.5219 (pp) REVERT: A 468 ILE cc_start: 0.8281 (pt) cc_final: 0.7991 (mt) REVERT: B 96 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7115 (tm-30) REVERT: B 429 PHE cc_start: 0.7021 (OUTLIER) cc_final: 0.6383 (p90) REVERT: B 489 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.7267 (m-80) REVERT: B 646 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8183 (mpp80) REVERT: C 69 HIS cc_start: 0.4852 (OUTLIER) cc_final: 0.4650 (p-80) REVERT: C 353 TRP cc_start: 0.7334 (p-90) cc_final: 0.6907 (p-90) REVERT: C 375 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.7025 (p90) REVERT: C 515 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8142 (p90) REVERT: C 658 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8252 (p0) outliers start: 76 outliers final: 21 residues processed: 166 average time/residue: 0.9535 time to fit residues: 201.0643 Evaluate side-chains 120 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 88 time to evaluate : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 300 optimal weight: 2.9990 chunk 228 optimal weight: 20.0000 chunk 157 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 204 optimal weight: 0.0040 chunk 304 optimal weight: 3.9990 chunk 322 optimal weight: 4.9990 chunk 159 optimal weight: 0.0060 chunk 289 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.0014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 87 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28296 Z= 0.217 Angle : 0.635 17.030 38483 Z= 0.303 Chirality : 0.044 0.245 4637 Planarity : 0.003 0.037 4821 Dihedral : 9.941 103.832 5720 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.60 % Allowed : 13.80 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3327 helix: 1.94 (0.20), residues: 734 sheet: 0.21 (0.18), residues: 761 loop : -1.23 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 152 HIS 0.011 0.001 HIS C 69 PHE 0.019 0.001 PHE B 456 TYR 0.021 0.001 TYR C1067 ARG 0.006 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 95 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7733 (tp) REVERT: A 468 ILE cc_start: 0.8319 (pt) cc_final: 0.8015 (mt) REVERT: B 429 PHE cc_start: 0.6928 (OUTLIER) cc_final: 0.6226 (p90) REVERT: B 489 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.7273 (m-80) REVERT: B 646 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8168 (mpp80) REVERT: C 371 PHE cc_start: 0.6009 (OUTLIER) cc_final: 0.5198 (p90) REVERT: C 375 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6691 (p90) REVERT: C 658 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8408 (p0) outliers start: 76 outliers final: 27 residues processed: 161 average time/residue: 0.8890 time to fit residues: 183.0812 Evaluate side-chains 120 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 86 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 268 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 275 optimal weight: 0.9990 chunk 223 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 289 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 69 HIS C 907 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 28296 Z= 0.437 Angle : 0.703 16.989 38483 Z= 0.337 Chirality : 0.046 0.236 4637 Planarity : 0.004 0.035 4821 Dihedral : 9.311 103.271 5720 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.15 % Allowed : 14.25 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.14), residues: 3327 helix: 1.66 (0.19), residues: 746 sheet: 0.01 (0.18), residues: 765 loop : -1.20 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 104 HIS 0.010 0.001 HIS B1064 PHE 0.019 0.002 PHE A 338 TYR 0.025 0.002 TYR A 369 ARG 0.006 0.001 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 91 time to evaluate : 3.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7702 (tp) REVERT: B 96 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7004 (tm-30) REVERT: B 428 ASP cc_start: 0.7875 (p0) cc_final: 0.7641 (p0) REVERT: B 429 PHE cc_start: 0.7472 (OUTLIER) cc_final: 0.6437 (p90) REVERT: B 489 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7384 (m-80) REVERT: B 646 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8163 (mpp80) REVERT: B 990 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8298 (tm-30) REVERT: B 1050 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.8581 (ppp) REVERT: C 371 PHE cc_start: 0.6077 (OUTLIER) cc_final: 0.5250 (p90) REVERT: C 375 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.6727 (p90) REVERT: C 957 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8082 (tm-30) outliers start: 92 outliers final: 39 residues processed: 170 average time/residue: 0.9488 time to fit residues: 203.1798 Evaluate side-chains 134 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 86 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1149 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 108 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 189 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 323 optimal weight: 0.9990 chunk 268 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 913 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28296 Z= 0.246 Angle : 0.635 17.859 38483 Z= 0.301 Chirality : 0.044 0.234 4637 Planarity : 0.003 0.033 4821 Dihedral : 8.791 102.208 5717 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.64 % Allowed : 15.27 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3327 helix: 1.87 (0.19), residues: 744 sheet: 0.19 (0.18), residues: 731 loop : -1.13 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 104 HIS 0.005 0.001 HIS C 69 PHE 0.025 0.001 PHE A 855 TYR 0.021 0.001 TYR C1067 ARG 0.005 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 91 time to evaluate : 3.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7662 (tp) REVERT: B 96 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7026 (tm-30) REVERT: B 105 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8433 (pt) REVERT: B 428 ASP cc_start: 0.7845 (p0) cc_final: 0.7639 (p0) REVERT: B 519 HIS cc_start: 0.7988 (m-70) cc_final: 0.7628 (m-70) REVERT: B 646 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8162 (mpp80) REVERT: B 1050 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.8464 (ppp) REVERT: C 269 TYR cc_start: 0.6918 (m-80) cc_final: 0.6682 (m-80) REVERT: C 368 LEU cc_start: 0.8966 (tt) cc_final: 0.8676 (tt) REVERT: C 371 PHE cc_start: 0.6080 (OUTLIER) cc_final: 0.5226 (p90) REVERT: C 375 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.6790 (p90) outliers start: 77 outliers final: 36 residues processed: 155 average time/residue: 0.9500 time to fit residues: 186.1534 Evaluate side-chains 127 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 84 time to evaluate : 2.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 311 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 272 optimal weight: 0.7980 chunk 180 optimal weight: 0.6980 chunk 321 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28296 Z= 0.192 Angle : 0.612 18.209 38483 Z= 0.290 Chirality : 0.043 0.231 4637 Planarity : 0.003 0.037 4821 Dihedral : 8.229 100.216 5716 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.60 % Allowed : 15.24 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3327 helix: 2.04 (0.20), residues: 743 sheet: 0.28 (0.18), residues: 737 loop : -1.07 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 104 HIS 0.003 0.001 HIS B1064 PHE 0.030 0.001 PHE A 855 TYR 0.028 0.001 TYR A 369 ARG 0.004 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 90 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7598 (tp) REVERT: B 96 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6827 (pp20) REVERT: B 105 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8488 (pt) REVERT: B 135 PHE cc_start: 0.8012 (m-80) cc_final: 0.7756 (m-80) REVERT: B 429 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6144 (p90) REVERT: B 646 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8132 (mpp80) REVERT: B 1050 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8386 (ppp) REVERT: C 368 LEU cc_start: 0.8970 (tt) cc_final: 0.8697 (tt) REVERT: C 371 PHE cc_start: 0.6057 (OUTLIER) cc_final: 0.5196 (p90) REVERT: C 375 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.6768 (p90) REVERT: C 830 ASP cc_start: 0.7394 (t0) cc_final: 0.7179 (t0) outliers start: 76 outliers final: 35 residues processed: 158 average time/residue: 0.9028 time to fit residues: 181.8536 Evaluate side-chains 129 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 86 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 199 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 219 optimal weight: 0.0770 chunk 159 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 253 optimal weight: 0.1980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 188 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28296 Z= 0.166 Angle : 0.600 18.166 38483 Z= 0.285 Chirality : 0.043 0.233 4637 Planarity : 0.003 0.042 4821 Dihedral : 7.795 98.016 5716 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.26 % Allowed : 15.86 % Favored : 81.88 % 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: 0.04 (0.14), residues: 3327 helix: 2.12 (0.20), residues: 742 sheet: 0.34 (0.19), residues: 719 loop : -1.01 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 104 HIS 0.002 0.001 HIS B1064 PHE 0.030 0.001 PHE B 168 TYR 0.022 0.001 TYR B 449 ARG 0.005 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 96 time to evaluate : 3.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7659 (tp) REVERT: A 990 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8220 (tm-30) REVERT: B 96 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6968 (pp20) REVERT: B 105 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8497 (pt) REVERT: B 429 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.6130 (p90) REVERT: B 646 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8113 (mpp80) REVERT: B 1050 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.8296 (ppp) REVERT: C 269 TYR cc_start: 0.6929 (m-80) cc_final: 0.6542 (m-80) REVERT: C 371 PHE cc_start: 0.6113 (OUTLIER) cc_final: 0.5310 (p90) REVERT: C 375 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.6764 (p90) outliers start: 66 outliers final: 40 residues processed: 154 average time/residue: 0.8827 time to fit residues: 173.8910 Evaluate side-chains 134 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 86 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 292 optimal weight: 2.9990 chunk 308 optimal weight: 0.5980 chunk 281 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 235 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 271 optimal weight: 6.9990 chunk 283 optimal weight: 5.9990 chunk 298 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 188 ASN C 405 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28296 Z= 0.267 Angle : 0.628 17.649 38483 Z= 0.298 Chirality : 0.043 0.276 4637 Planarity : 0.003 0.034 4821 Dihedral : 7.578 96.964 5714 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.09 % Allowed : 16.20 % Favored : 81.71 % 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: -0.01 (0.14), residues: 3327 helix: 2.09 (0.20), residues: 743 sheet: 0.30 (0.19), residues: 707 loop : -1.04 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 104 HIS 0.005 0.001 HIS B1064 PHE 0.037 0.001 PHE A 855 TYR 0.041 0.001 TYR A 144 ARG 0.004 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 85 time to evaluate : 2.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7674 (tp) REVERT: A 572 THR cc_start: 0.9583 (OUTLIER) cc_final: 0.9218 (p) REVERT: B 96 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6910 (pp20) REVERT: B 105 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8578 (mt) REVERT: B 429 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6168 (p90) REVERT: B 646 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8126 (mpp80) REVERT: B 1050 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8342 (ppp) REVERT: C 371 PHE cc_start: 0.6032 (OUTLIER) cc_final: 0.5214 (p90) REVERT: C 375 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.6795 (p90) outliers start: 61 outliers final: 39 residues processed: 139 average time/residue: 0.9653 time to fit residues: 172.2510 Evaluate side-chains 134 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 86 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 196 optimal weight: 3.9990 chunk 317 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 332 optimal weight: 3.9990 chunk 306 optimal weight: 0.7980 chunk 264 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 913 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1159 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 28296 Z= 0.477 Angle : 0.713 16.857 38483 Z= 0.344 Chirality : 0.046 0.272 4637 Planarity : 0.004 0.034 4821 Dihedral : 7.613 96.126 5714 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.96 % Favored : 95.01 % Rotamer: Outliers : 1.92 % Allowed : 16.51 % Favored : 81.58 % 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: -0.25 (0.14), residues: 3327 helix: 1.78 (0.19), residues: 745 sheet: 0.15 (0.18), residues: 725 loop : -1.16 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 104 HIS 0.009 0.001 HIS B1064 PHE 0.022 0.002 PHE C1148 TYR 0.033 0.002 TYR A 144 ARG 0.005 0.001 ARG A 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 89 time to evaluate : 3.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7756 (tp) REVERT: A 572 THR cc_start: 0.9594 (OUTLIER) cc_final: 0.9237 (p) REVERT: B 96 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6988 (pp20) REVERT: B 429 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.6540 (p90) REVERT: B 646 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8152 (mpp80) REVERT: B 1050 MET cc_start: 0.9311 (OUTLIER) cc_final: 0.8625 (ppp) REVERT: C 371 PHE cc_start: 0.6133 (OUTLIER) cc_final: 0.5329 (p90) REVERT: C 375 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6854 (p90) REVERT: C 830 ASP cc_start: 0.7519 (t0) cc_final: 0.7287 (t0) outliers start: 56 outliers final: 42 residues processed: 138 average time/residue: 0.9475 time to fit residues: 166.2073 Evaluate side-chains 133 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 83 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 210 optimal weight: 0.9990 chunk 282 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 265 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 272 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 188 ASN C 913 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.098328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.060659 restraints weight = 76095.460| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.52 r_work: 0.2837 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28296 Z= 0.200 Angle : 0.626 18.477 38483 Z= 0.298 Chirality : 0.043 0.255 4637 Planarity : 0.003 0.035 4821 Dihedral : 7.287 96.725 5714 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.21 % Favored : 95.76 % Rotamer: Outliers : 1.85 % Allowed : 16.64 % Favored : 81.51 % 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: -0.07 (0.14), residues: 3327 helix: 2.02 (0.20), residues: 737 sheet: 0.20 (0.19), residues: 723 loop : -1.03 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 104 HIS 0.003 0.001 HIS B1064 PHE 0.029 0.001 PHE B 823 TYR 0.025 0.001 TYR A 369 ARG 0.004 0.000 ARG A 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6552.81 seconds wall clock time: 120 minutes 14.89 seconds (7214.89 seconds total)