Starting phenix.real_space_refine on Fri Aug 9 10:50:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x4z_38056/08_2024/8x4z_38056.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x4z_38056/08_2024/8x4z_38056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x4z_38056/08_2024/8x4z_38056.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x4z_38056/08_2024/8x4z_38056.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x4z_38056/08_2024/8x4z_38056.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x4z_38056/08_2024/8x4z_38056.cif" } resolution = 3.49 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= 0.002 sd= 0.071 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 114 5.16 5 C 16473 2.51 5 N 4200 2.21 5 O 5052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A ASP 627": "OD1" <-> "OD2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A TYR 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1139": "OD1" <-> "OD2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B ASP 627": "OD1" <-> "OD2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B ASP 775": "OD1" <-> "OD2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C ASP 627": "OD1" <-> "OD2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 808": "OD1" <-> "OD2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25839 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1008} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1008} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1008} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "T" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 14.08, per 1000 atoms: 0.54 Number of scatterers: 25839 At special positions: 0 Unit cell: (144.56, 144.56, 170.56, 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 114 16.00 O 5052 8.00 N 4200 7.00 C 16473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.05 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 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 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 BETA1-4 " NAG D 1 " - " BMA D 2 " " NAG E 1 " - " BMA E 2 " " NAG F 1 " - " BMA F 2 " " NAG G 1 " - " BMA G 2 " " NAG H 1 " - " BMA H 2 " " NAG I 1 " - " BMA I 2 " " NAG J 1 " - " BMA J 2 " " NAG K 1 " - " BMA K 2 " " NAG L 1 " - " BMA L 2 " " NAG M 1 " - " BMA M 2 " " NAG N 1 " - " BMA N 2 " " NAG O 1 " - " BMA O 2 " " NAG P 1 " - " BMA P 2 " " NAG Q 1 " - " BMA Q 2 " " NAG R 1 " - " BMA R 2 " " NAG S 1 " - " BMA S 2 " " NAG T 1 " - " BMA T 2 " " NAG U 1 " - " BMA U 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 234 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 234 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG D 1 " - " ASN A 354 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN B 354 " " NAG K 1 " - " ASN B 282 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN C 354 " " NAG Q 1 " - " ASN C 282 " " NAG R 1 " - " ASN C1134 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C1098 " Time building additional restraints: 11.47 Conformation dependent library (CDL) restraints added in 3.9 seconds 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5964 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 53 sheets defined 25.0% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.35 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.534A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 4.112A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 617 through 626 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.645A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.618A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 881 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.357A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.752A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.613A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.001A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1144 removed outlier: 4.444A pdb=" N LEU A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1139 through 1144' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.050A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 618 through 627 removed outlier: 3.785A pdb=" N HIS B 625 " --> pdb=" O SER B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.623A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.702A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 868 through 881 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.333A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.729A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.121A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1144 removed outlier: 4.390A pdb=" N LEU B1143 " --> pdb=" O ASP B1139 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1139 through 1144' Processing helix chain 'C' and resid 212 through 216 removed outlier: 3.792A pdb=" N ASP C 215 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE C 216 " --> pdb=" O GLY C 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 212 through 216' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.844A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.894A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 617 through 627 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: 3.825A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.682A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE C 823 " --> pdb=" O GLU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.676A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 884 removed outlier: 3.629A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.319A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.763A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.041A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1144 removed outlier: 4.322A pdb=" N LEU C1143 " --> pdb=" O ASP C1139 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1139 through 1144' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.310A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASP A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR A 95 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.894A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 170 removed outlier: 4.903A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 7.151A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.561A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.501A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.821A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.905A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 575 through 577 removed outlier: 3.638A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.375A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 713 through 715 removed outlier: 3.519A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.174A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.240A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.313A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.651A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 167 through 169 removed outlier: 3.529A pdb=" N THR B 167 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.116A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.878A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.548A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.820A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.979A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.184A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 713 through 715 removed outlier: 3.774A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.168A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.388A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 787 through 788 removed outlier: 3.538A pdb=" N ILE B 788 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.285A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N THR C 95 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.483A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.672A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.682A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.121A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.986A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.599A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA C 435 " --> pdb=" O PHE C 375 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.912A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.017A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 575 through 577 removed outlier: 3.611A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.195A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 713 through 715 removed outlier: 3.507A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.595A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.348A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 867 hydrogen bonds defined for protein. 2382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.43 Time building geometry restraints manager: 12.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8139 1.35 - 1.47: 6784 1.47 - 1.59: 11374 1.59 - 1.71: 1 1.71 - 1.83: 141 Bond restraints: 26439 Sorted by residual: bond pdb=" CG PRO B 217 " pdb=" CD PRO B 217 " ideal model delta sigma weight residual 1.503 1.269 0.234 3.40e-02 8.65e+02 4.72e+01 bond pdb=" N PRO B 217 " pdb=" CD PRO B 217 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.38e+01 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" CB PRO B 217 " pdb=" CG PRO B 217 " ideal model delta sigma weight residual 1.492 1.656 -0.164 5.00e-02 4.00e+02 1.08e+01 bond pdb=" N PRO B 217 " pdb=" CA PRO B 217 " ideal model delta sigma weight residual 1.466 1.428 0.038 1.21e-02 6.83e+03 9.89e+00 ... (remaining 26434 not shown) Histogram of bond angle deviations from ideal: 90.91 - 99.59: 8 99.59 - 108.27: 1260 108.27 - 116.95: 17934 116.95 - 125.63: 16458 125.63 - 134.31: 325 Bond angle restraints: 35985 Sorted by residual: angle pdb=" CA PRO B 217 " pdb=" N PRO B 217 " pdb=" CD PRO B 217 " ideal model delta sigma weight residual 112.00 94.42 17.58 1.40e+00 5.10e-01 1.58e+02 angle pdb=" N PRO B 217 " pdb=" CD PRO B 217 " pdb=" CG PRO B 217 " ideal model delta sigma weight residual 103.20 90.91 12.29 1.50e+00 4.44e-01 6.71e+01 angle pdb=" C ASN A1074 " pdb=" N PHE A1075 " pdb=" CA PHE A1075 " ideal model delta sigma weight residual 121.90 114.96 6.94 1.26e+00 6.30e-01 3.04e+01 angle pdb=" C ASN C1074 " pdb=" N PHE C1075 " pdb=" CA PHE C1075 " ideal model delta sigma weight residual 121.90 115.10 6.80 1.26e+00 6.30e-01 2.91e+01 angle pdb=" N GLN B 218 " pdb=" CA GLN B 218 " pdb=" C GLN B 218 " ideal model delta sigma weight residual 114.39 107.23 7.16 1.45e+00 4.76e-01 2.44e+01 ... (remaining 35980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.98: 14713 22.98 - 45.96: 1396 45.96 - 68.94: 198 68.94 - 91.92: 143 91.92 - 114.90: 119 Dihedral angle restraints: 16569 sinusoidal: 7284 harmonic: 9285 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 13.03 79.97 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 159.12 -66.12 1 1.00e+01 1.00e-02 5.71e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 29.34 63.66 1 1.00e+01 1.00e-02 5.34e+01 ... (remaining 16566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 4225 0.175 - 0.349: 32 0.349 - 0.524: 0 0.524 - 0.698: 0 0.698 - 0.873: 3 Chirality restraints: 4260 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-01 2.50e+01 1.91e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.54 -0.86 2.00e-01 2.50e+01 1.86e+01 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.74e+01 ... (remaining 4257 not shown) Planarity restraints: 4608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 216 " 0.143 5.00e-02 4.00e+02 1.94e-01 5.99e+01 pdb=" N PRO B 217 " -0.333 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " 0.109 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 208 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO C 209 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 371 " -0.018 2.00e-02 2.50e+03 2.82e-02 1.39e+01 pdb=" CG PHE B 371 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE B 371 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 371 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 371 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 PHE B 371 " 0.028 2.00e-02 2.50e+03 pdb=" CZ PHE B 371 " -0.055 2.00e-02 2.50e+03 ... (remaining 4605 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 495 2.66 - 3.22: 24264 3.22 - 3.78: 38661 3.78 - 4.34: 52485 4.34 - 4.90: 87510 Nonbonded interactions: 203415 Sorted by model distance: nonbonded pdb=" O CYS A 590 " pdb=" OH TYR C 837 " model vdw 2.094 3.040 nonbonded pdb=" OH TYR B 837 " pdb=" O CYS C 590 " model vdw 2.123 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.154 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.162 3.040 nonbonded pdb=" OH TYR A 837 " pdb=" O CYS B 590 " model vdw 2.173 3.040 ... (remaining 203410 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.150 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 72.700 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.005 0.234 26439 Z= 0.318 Angle : 0.824 17.583 35985 Z= 0.419 Chirality : 0.057 0.873 4260 Planarity : 0.006 0.194 4560 Dihedral : 21.367 114.901 10488 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.65 % Favored : 92.25 % Rotamer: Outliers : 0.50 % Allowed : 26.46 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.15), residues: 3162 helix: 0.71 (0.20), residues: 726 sheet: -0.92 (0.21), residues: 588 loop : -1.96 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP B 633 HIS 0.005 0.001 HIS B 505 PHE 0.055 0.002 PHE B 371 TYR 0.037 0.002 TYR B 170 ARG 0.006 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 218 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.8209 (mtp180) cc_final: 0.7947 (mtp85) REVERT: A 904 TYR cc_start: 0.8310 (m-10) cc_final: 0.7640 (m-10) REVERT: B 173 GLN cc_start: 0.7369 (mm-40) cc_final: 0.6432 (tt0) REVERT: B 400 PHE cc_start: 0.8467 (p90) cc_final: 0.8200 (p90) REVERT: B 495 TYR cc_start: 0.4840 (t80) cc_final: 0.4581 (t80) REVERT: B 1130 ILE cc_start: 0.9052 (mm) cc_final: 0.8773 (mt) REVERT: C 127 PHE cc_start: 0.6561 (t80) cc_final: 0.6277 (t80) REVERT: C 495 TYR cc_start: 0.5331 (OUTLIER) cc_final: 0.4463 (t80) REVERT: C 677 GLN cc_start: 0.6318 (OUTLIER) cc_final: 0.5924 (pm20) REVERT: C 1130 ILE cc_start: 0.8981 (mm) cc_final: 0.8754 (mt) outliers start: 14 outliers final: 9 residues processed: 227 average time/residue: 0.3399 time to fit residues: 127.6135 Evaluate side-chains 203 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 192 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 677 GLN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 856 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.8980 chunk 241 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 249 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 151 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 288 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 207 HIS C 360 ASN C 370 ASN C 394 ASN C 439 ASN C 613 GLN C 677 GLN C 957 GLN C1002 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26439 Z= 0.226 Angle : 0.710 13.125 35985 Z= 0.344 Chirality : 0.052 0.613 4260 Planarity : 0.005 0.112 4560 Dihedral : 13.465 107.569 4791 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.05 % Favored : 92.85 % Rotamer: Outliers : 4.39 % Allowed : 23.15 % Favored : 72.46 % 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: -1.42 (0.15), residues: 3162 helix: 1.10 (0.21), residues: 708 sheet: -0.70 (0.20), residues: 627 loop : -1.96 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 353 HIS 0.003 0.001 HIS C 207 PHE 0.023 0.001 PHE B 456 TYR 0.021 0.001 TYR B1067 ARG 0.007 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 201 time to evaluate : 2.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5068 (OUTLIER) cc_final: 0.4369 (pttp) REVERT: A 237 ARG cc_start: 0.7970 (mtp180) cc_final: 0.7718 (mtp180) REVERT: A 636 TYR cc_start: 0.7360 (t80) cc_final: 0.7058 (t80) REVERT: A 904 TYR cc_start: 0.8361 (m-10) cc_final: 0.7659 (m-10) REVERT: A 998 THR cc_start: 0.9549 (OUTLIER) cc_final: 0.9309 (m) REVERT: B 173 GLN cc_start: 0.7357 (mm-40) cc_final: 0.6444 (tt0) REVERT: B 495 TYR cc_start: 0.4973 (t80) cc_final: 0.4721 (t80) REVERT: B 558 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8459 (mmmt) REVERT: B 788 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9089 (mt) REVERT: B 979 ASP cc_start: 0.8458 (t0) cc_final: 0.8219 (t0) REVERT: B 1130 ILE cc_start: 0.9132 (mm) cc_final: 0.8880 (mt) REVERT: C 127 PHE cc_start: 0.6783 (t80) cc_final: 0.6293 (t80) REVERT: C 495 TYR cc_start: 0.5784 (OUTLIER) cc_final: 0.4571 (t80) REVERT: C 523 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7783 (p) REVERT: C 1130 ILE cc_start: 0.9051 (mm) cc_final: 0.8846 (mt) outliers start: 122 outliers final: 56 residues processed: 309 average time/residue: 0.3385 time to fit residues: 174.7187 Evaluate side-chains 240 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 179 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 240 optimal weight: 9.9990 chunk 196 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 289 optimal weight: 9.9990 chunk 312 optimal weight: 0.0670 chunk 257 optimal weight: 4.9990 chunk 286 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 232 optimal weight: 0.4980 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 394 ASN B 804 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 677 GLN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26439 Z= 0.191 Angle : 0.658 13.898 35985 Z= 0.322 Chirality : 0.050 0.614 4260 Planarity : 0.004 0.075 4560 Dihedral : 10.337 102.063 4780 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.86 % Favored : 93.01 % Rotamer: Outliers : 4.07 % Allowed : 23.25 % Favored : 72.68 % 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: -1.31 (0.15), residues: 3162 helix: 1.15 (0.20), residues: 714 sheet: -0.61 (0.20), residues: 663 loop : -1.91 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 633 HIS 0.004 0.001 HIS C 339 PHE 0.016 0.001 PHE C1095 TYR 0.016 0.001 TYR B1067 ARG 0.005 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 201 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5045 (OUTLIER) cc_final: 0.4347 (pttp) REVERT: A 374 PHE cc_start: 0.6281 (m-10) cc_final: 0.5378 (m-10) REVERT: A 533 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7987 (tt) REVERT: A 759 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7639 (t80) REVERT: A 904 TYR cc_start: 0.8406 (m-10) cc_final: 0.7726 (m-10) REVERT: A 998 THR cc_start: 0.9537 (OUTLIER) cc_final: 0.9298 (m) REVERT: B 173 GLN cc_start: 0.7383 (mm-40) cc_final: 0.7100 (tp40) REVERT: B 465 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6683 (pt0) REVERT: B 495 TYR cc_start: 0.4910 (t80) cc_final: 0.4607 (t80) REVERT: B 759 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7862 (t80) REVERT: B 788 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9099 (mt) REVERT: B 979 ASP cc_start: 0.8547 (t0) cc_final: 0.8225 (t0) REVERT: B 1130 ILE cc_start: 0.9193 (mm) cc_final: 0.8946 (mt) REVERT: C 127 PHE cc_start: 0.6646 (t80) cc_final: 0.6125 (t80) REVERT: C 358 ILE cc_start: 0.8121 (mm) cc_final: 0.7886 (mm) REVERT: C 393 THR cc_start: 0.7256 (OUTLIER) cc_final: 0.6834 (t) REVERT: C 495 TYR cc_start: 0.5624 (OUTLIER) cc_final: 0.4543 (t80) REVERT: C 508 TYR cc_start: 0.7754 (m-10) cc_final: 0.7268 (m-10) REVERT: C 523 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7646 (p) REVERT: C 759 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7587 (t80) REVERT: C 957 GLN cc_start: 0.8527 (tt0) cc_final: 0.8168 (tm-30) REVERT: C 1029 MET cc_start: 0.9332 (tpp) cc_final: 0.8996 (tpp) REVERT: C 1130 ILE cc_start: 0.9160 (mm) cc_final: 0.8932 (mt) outliers start: 113 outliers final: 56 residues processed: 298 average time/residue: 0.3352 time to fit residues: 166.7838 Evaluate side-chains 241 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 174 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 290 optimal weight: 0.6980 chunk 307 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN B 121 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 677 GLN C1054 GLN C1071 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 26439 Z= 0.331 Angle : 0.699 13.002 35985 Z= 0.351 Chirality : 0.050 0.586 4260 Planarity : 0.005 0.052 4560 Dihedral : 8.122 96.239 4778 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.72 % Favored : 92.16 % Rotamer: Outliers : 5.69 % Allowed : 23.18 % Favored : 71.13 % 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: -1.41 (0.15), residues: 3162 helix: 1.06 (0.20), residues: 708 sheet: -0.71 (0.20), residues: 657 loop : -1.94 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 353 HIS 0.005 0.001 HIS A1064 PHE 0.021 0.002 PHE C 456 TYR 0.020 0.002 TYR A 265 ARG 0.006 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 189 time to evaluate : 2.911 Fit side-chains revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5505 (OUTLIER) cc_final: 0.4512 (pttp) REVERT: A 237 ARG cc_start: 0.7753 (mtp180) cc_final: 0.7439 (mtp180) REVERT: A 495 TYR cc_start: 0.6026 (OUTLIER) cc_final: 0.5132 (t80) REVERT: A 759 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7987 (t80) REVERT: A 904 TYR cc_start: 0.8474 (m-10) cc_final: 0.7860 (m-10) REVERT: A 957 GLN cc_start: 0.8721 (tt0) cc_final: 0.8425 (tm-30) REVERT: A 998 THR cc_start: 0.9560 (OUTLIER) cc_final: 0.9328 (m) REVERT: A 1029 MET cc_start: 0.9303 (tpp) cc_final: 0.8897 (ttm) REVERT: B 173 GLN cc_start: 0.7449 (mm-40) cc_final: 0.6625 (tt0) REVERT: B 358 ILE cc_start: 0.8372 (mm) cc_final: 0.8118 (mm) REVERT: B 430 THR cc_start: 0.8533 (m) cc_final: 0.8318 (p) REVERT: B 465 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6660 (pt0) REVERT: B 759 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.8181 (t80) REVERT: B 957 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7770 (tm-30) REVERT: B 979 ASP cc_start: 0.8540 (t0) cc_final: 0.8250 (t0) REVERT: B 981 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8694 (mp) REVERT: B 1130 ILE cc_start: 0.9386 (mm) cc_final: 0.9167 (mt) REVERT: C 127 PHE cc_start: 0.7133 (t80) cc_final: 0.6652 (t80) REVERT: C 358 ILE cc_start: 0.8326 (mm) cc_final: 0.8006 (mm) REVERT: C 430 THR cc_start: 0.8412 (m) cc_final: 0.7912 (p) REVERT: C 495 TYR cc_start: 0.5787 (OUTLIER) cc_final: 0.4627 (t80) REVERT: C 523 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7969 (p) REVERT: C 759 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7885 (t80) REVERT: C 957 GLN cc_start: 0.8569 (tt0) cc_final: 0.8073 (tm-30) REVERT: C 1029 MET cc_start: 0.9372 (tpp) cc_final: 0.9095 (tpp) outliers start: 158 outliers final: 79 residues processed: 328 average time/residue: 0.3136 time to fit residues: 173.1104 Evaluate side-chains 253 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 164 time to evaluate : 2.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 228 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 212 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 156 optimal weight: 9.9990 chunk 275 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26439 Z= 0.212 Angle : 0.637 14.750 35985 Z= 0.317 Chirality : 0.049 0.583 4260 Planarity : 0.004 0.051 4560 Dihedral : 7.923 92.456 4776 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.64 % Favored : 93.26 % Rotamer: Outliers : 3.92 % Allowed : 25.20 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.15), residues: 3162 helix: 1.22 (0.20), residues: 711 sheet: -0.69 (0.20), residues: 660 loop : -1.86 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 633 HIS 0.003 0.001 HIS C 954 PHE 0.027 0.001 PHE A 127 TYR 0.015 0.001 TYR B1067 ARG 0.006 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 189 time to evaluate : 2.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5352 (OUTLIER) cc_final: 0.4261 (pttp) REVERT: A 127 PHE cc_start: 0.6735 (t80) cc_final: 0.6297 (t80) REVERT: A 237 ARG cc_start: 0.7694 (mtp180) cc_final: 0.7451 (mtp180) REVERT: A 357 ARG cc_start: 0.7962 (ptm160) cc_final: 0.7401 (ptm160) REVERT: A 495 TYR cc_start: 0.6207 (OUTLIER) cc_final: 0.5204 (t80) REVERT: A 904 TYR cc_start: 0.8386 (m-10) cc_final: 0.7850 (m-10) REVERT: A 957 GLN cc_start: 0.8688 (tt0) cc_final: 0.8270 (tm-30) REVERT: A 998 THR cc_start: 0.9535 (OUTLIER) cc_final: 0.9295 (m) REVERT: A 1029 MET cc_start: 0.9311 (tpp) cc_final: 0.8916 (ttm) REVERT: B 188 ASN cc_start: 0.7131 (OUTLIER) cc_final: 0.5575 (p0) REVERT: B 358 ILE cc_start: 0.8407 (mm) cc_final: 0.8162 (mm) REVERT: B 430 THR cc_start: 0.8421 (m) cc_final: 0.8178 (p) REVERT: B 788 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9115 (mt) REVERT: B 957 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7729 (tm-30) REVERT: B 979 ASP cc_start: 0.8435 (t0) cc_final: 0.8158 (t0) REVERT: B 1130 ILE cc_start: 0.9374 (mm) cc_final: 0.9169 (mt) REVERT: C 127 PHE cc_start: 0.7060 (t80) cc_final: 0.6536 (t80) REVERT: C 298 GLU cc_start: 0.8675 (tp30) cc_final: 0.8468 (tp30) REVERT: C 358 ILE cc_start: 0.8376 (mm) cc_final: 0.8081 (mm) REVERT: C 393 THR cc_start: 0.7143 (OUTLIER) cc_final: 0.6658 (t) REVERT: C 430 THR cc_start: 0.8279 (m) cc_final: 0.7796 (p) REVERT: C 495 TYR cc_start: 0.5637 (OUTLIER) cc_final: 0.4498 (t80) REVERT: C 523 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7930 (p) REVERT: C 677 GLN cc_start: 0.5957 (pm20) cc_final: 0.5473 (pm20) REVERT: C 759 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7879 (t80) REVERT: C 957 GLN cc_start: 0.8559 (tt0) cc_final: 0.8166 (tm-30) outliers start: 109 outliers final: 65 residues processed: 283 average time/residue: 0.3311 time to fit residues: 155.5644 Evaluate side-chains 243 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 169 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 0.8980 chunk 276 optimal weight: 2.9990 chunk 60 optimal weight: 0.0980 chunk 180 optimal weight: 5.9990 chunk 75 optimal weight: 30.0000 chunk 307 optimal weight: 3.9990 chunk 255 optimal weight: 0.1980 chunk 142 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26439 Z= 0.238 Angle : 0.632 13.870 35985 Z= 0.315 Chirality : 0.048 0.582 4260 Planarity : 0.004 0.050 4560 Dihedral : 7.726 91.112 4776 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.18 % Favored : 92.73 % Rotamer: Outliers : 4.39 % Allowed : 24.84 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.15), residues: 3162 helix: 1.25 (0.20), residues: 711 sheet: -0.69 (0.20), residues: 657 loop : -1.83 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 353 HIS 0.002 0.001 HIS C1064 PHE 0.022 0.001 PHE A 127 TYR 0.016 0.001 TYR A 265 ARG 0.004 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 171 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5289 (OUTLIER) cc_final: 0.4166 (pttp) REVERT: A 127 PHE cc_start: 0.6741 (t80) cc_final: 0.6292 (t80) REVERT: A 237 ARG cc_start: 0.7697 (mtp180) cc_final: 0.7447 (mtp180) REVERT: A 298 GLU cc_start: 0.8857 (tp30) cc_final: 0.8647 (tp30) REVERT: A 338 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7767 (m-80) REVERT: A 495 TYR cc_start: 0.6196 (OUTLIER) cc_final: 0.5184 (t80) REVERT: A 904 TYR cc_start: 0.8446 (m-10) cc_final: 0.7922 (m-10) REVERT: A 957 GLN cc_start: 0.8682 (tt0) cc_final: 0.8292 (tm-30) REVERT: A 998 THR cc_start: 0.9533 (OUTLIER) cc_final: 0.9292 (m) REVERT: A 1029 MET cc_start: 0.9353 (tpp) cc_final: 0.8940 (ttm) REVERT: B 188 ASN cc_start: 0.7167 (OUTLIER) cc_final: 0.5655 (p0) REVERT: B 358 ILE cc_start: 0.8488 (mm) cc_final: 0.8211 (mm) REVERT: B 430 THR cc_start: 0.8425 (m) cc_final: 0.8163 (p) REVERT: B 788 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9107 (mt) REVERT: B 957 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7738 (tm-30) REVERT: B 979 ASP cc_start: 0.8509 (t0) cc_final: 0.8226 (t0) REVERT: B 981 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8813 (mp) REVERT: C 127 PHE cc_start: 0.7079 (t80) cc_final: 0.6716 (t80) REVERT: C 246 ARG cc_start: 0.1733 (OUTLIER) cc_final: -0.0997 (mtt90) REVERT: C 393 THR cc_start: 0.7159 (OUTLIER) cc_final: 0.6600 (t) REVERT: C 495 TYR cc_start: 0.5785 (OUTLIER) cc_final: 0.4595 (t80) REVERT: C 523 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7899 (p) REVERT: C 677 GLN cc_start: 0.6002 (pm20) cc_final: 0.5577 (pm20) REVERT: C 759 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7899 (t80) REVERT: C 957 GLN cc_start: 0.8531 (tt0) cc_final: 0.8140 (tm-30) outliers start: 122 outliers final: 74 residues processed: 277 average time/residue: 0.3202 time to fit residues: 148.5240 Evaluate side-chains 246 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 160 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 0.7980 chunk 34 optimal weight: 0.0570 chunk 175 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 259 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 306 optimal weight: 3.9990 chunk 191 optimal weight: 0.4980 chunk 186 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 26439 Z= 0.161 Angle : 0.612 16.385 35985 Z= 0.303 Chirality : 0.048 0.580 4260 Planarity : 0.004 0.052 4560 Dihedral : 7.446 88.681 4776 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.36 % Favored : 93.52 % Rotamer: Outliers : 3.89 % Allowed : 25.63 % Favored : 70.48 % 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: -1.13 (0.15), residues: 3162 helix: 1.37 (0.20), residues: 714 sheet: -0.64 (0.20), residues: 660 loop : -1.76 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 353 HIS 0.002 0.000 HIS C 207 PHE 0.016 0.001 PHE C 456 TYR 0.014 0.001 TYR B1067 ARG 0.005 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 181 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5284 (OUTLIER) cc_final: 0.4278 (pttp) REVERT: A 127 PHE cc_start: 0.6550 (t80) cc_final: 0.6144 (t80) REVERT: A 237 ARG cc_start: 0.7670 (mtp180) cc_final: 0.7382 (mtp85) REVERT: A 389 ASP cc_start: 0.8222 (m-30) cc_final: 0.7810 (t0) REVERT: A 495 TYR cc_start: 0.6206 (OUTLIER) cc_final: 0.5164 (t80) REVERT: A 636 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.7094 (t80) REVERT: A 904 TYR cc_start: 0.8343 (m-10) cc_final: 0.7831 (m-10) REVERT: A 957 GLN cc_start: 0.8629 (tt0) cc_final: 0.8226 (tm-30) REVERT: A 998 THR cc_start: 0.9518 (OUTLIER) cc_final: 0.9265 (m) REVERT: A 1029 MET cc_start: 0.9313 (tpp) cc_final: 0.8923 (ttm) REVERT: B 127 PHE cc_start: 0.6875 (t80) cc_final: 0.6623 (t80) REVERT: B 188 ASN cc_start: 0.7291 (OUTLIER) cc_final: 0.5584 (p0) REVERT: B 358 ILE cc_start: 0.8519 (mm) cc_final: 0.8266 (mm) REVERT: B 430 THR cc_start: 0.8333 (m) cc_final: 0.8058 (p) REVERT: B 449 TYR cc_start: 0.7746 (p90) cc_final: 0.7121 (m-80) REVERT: B 957 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7695 (tm-30) REVERT: B 979 ASP cc_start: 0.8406 (t0) cc_final: 0.8110 (t0) REVERT: C 127 PHE cc_start: 0.6790 (t80) cc_final: 0.6457 (t80) REVERT: C 200 TYR cc_start: 0.6983 (OUTLIER) cc_final: 0.6687 (m-80) REVERT: C 246 ARG cc_start: 0.1719 (OUTLIER) cc_final: -0.1056 (mtt90) REVERT: C 495 TYR cc_start: 0.5760 (OUTLIER) cc_final: 0.4547 (t80) REVERT: C 523 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7895 (p) REVERT: C 557 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8249 (mttp) REVERT: C 759 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7897 (t80) REVERT: C 850 ILE cc_start: 0.4227 (OUTLIER) cc_final: 0.3462 (mm) REVERT: C 957 GLN cc_start: 0.8496 (tt0) cc_final: 0.8179 (tm-30) REVERT: C 1029 MET cc_start: 0.9345 (tpp) cc_final: 0.9045 (tpp) outliers start: 108 outliers final: 65 residues processed: 277 average time/residue: 0.3242 time to fit residues: 149.9128 Evaluate side-chains 251 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 174 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 3.9990 chunk 122 optimal weight: 0.4980 chunk 183 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 59 optimal weight: 0.0770 chunk 194 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 240 optimal weight: 6.9990 overall best weight: 2.1144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 26439 Z= 0.277 Angle : 0.649 14.937 35985 Z= 0.322 Chirality : 0.048 0.568 4260 Planarity : 0.004 0.057 4560 Dihedral : 7.545 87.856 4776 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.40 % Favored : 92.50 % Rotamer: Outliers : 4.00 % Allowed : 25.49 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.15), residues: 3162 helix: 1.33 (0.21), residues: 711 sheet: -0.70 (0.20), residues: 657 loop : -1.79 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 353 HIS 0.003 0.001 HIS A1064 PHE 0.034 0.001 PHE B 371 TYR 0.018 0.001 TYR A 265 ARG 0.004 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 179 time to evaluate : 2.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5203 (OUTLIER) cc_final: 0.4059 (pttp) REVERT: A 338 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7840 (m-80) REVERT: A 389 ASP cc_start: 0.8307 (m-30) cc_final: 0.7862 (t0) REVERT: A 495 TYR cc_start: 0.6263 (OUTLIER) cc_final: 0.5128 (t80) REVERT: A 904 TYR cc_start: 0.8486 (m-10) cc_final: 0.8001 (m-10) REVERT: A 957 GLN cc_start: 0.8670 (tt0) cc_final: 0.8288 (tm-30) REVERT: A 998 THR cc_start: 0.9531 (OUTLIER) cc_final: 0.9288 (m) REVERT: A 1029 MET cc_start: 0.9406 (tpp) cc_final: 0.8967 (ttm) REVERT: B 87 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8620 (p0) REVERT: B 358 ILE cc_start: 0.8614 (mm) cc_final: 0.8393 (mm) REVERT: B 430 THR cc_start: 0.8503 (m) cc_final: 0.8040 (p) REVERT: B 449 TYR cc_start: 0.7857 (p90) cc_final: 0.7158 (m-80) REVERT: B 523 THR cc_start: 0.8303 (m) cc_final: 0.7923 (p) REVERT: B 957 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7721 (tm-30) REVERT: B 981 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8859 (mp) REVERT: C 127 PHE cc_start: 0.7033 (t80) cc_final: 0.6731 (t80) REVERT: C 200 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.6925 (m-10) REVERT: C 246 ARG cc_start: 0.1905 (OUTLIER) cc_final: -0.1047 (mtt90) REVERT: C 298 GLU cc_start: 0.8763 (tp30) cc_final: 0.8466 (tp30) REVERT: C 495 TYR cc_start: 0.5865 (OUTLIER) cc_final: 0.4691 (t80) REVERT: C 523 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7954 (p) REVERT: C 759 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7918 (t80) REVERT: C 957 GLN cc_start: 0.8512 (tt0) cc_final: 0.8109 (tm-30) REVERT: C 1029 MET cc_start: 0.9374 (tpp) cc_final: 0.9087 (ttm) outliers start: 111 outliers final: 77 residues processed: 274 average time/residue: 0.3140 time to fit residues: 144.1802 Evaluate side-chains 259 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 171 time to evaluate : 3.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 4.9990 chunk 293 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 chunk 285 optimal weight: 8.9990 chunk 171 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 224 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 258 optimal weight: 3.9990 chunk 270 optimal weight: 0.7980 chunk 284 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 26439 Z= 0.260 Angle : 0.649 14.651 35985 Z= 0.323 Chirality : 0.048 0.565 4260 Planarity : 0.004 0.058 4560 Dihedral : 7.533 88.237 4776 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.93 % Favored : 92.95 % Rotamer: Outliers : 4.07 % Allowed : 25.52 % Favored : 70.41 % 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: -1.21 (0.15), residues: 3162 helix: 1.29 (0.20), residues: 711 sheet: -0.70 (0.20), residues: 657 loop : -1.79 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 353 HIS 0.003 0.001 HIS C1064 PHE 0.027 0.001 PHE B 371 TYR 0.017 0.001 TYR A 265 ARG 0.004 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 171 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5460 (OUTLIER) cc_final: 0.4295 (pttp) REVERT: A 127 PHE cc_start: 0.6692 (t80) cc_final: 0.6374 (t80) REVERT: A 338 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7879 (m-80) REVERT: A 389 ASP cc_start: 0.8344 (m-30) cc_final: 0.7731 (t0) REVERT: A 495 TYR cc_start: 0.6299 (OUTLIER) cc_final: 0.5128 (t80) REVERT: A 759 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7982 (t80) REVERT: A 904 TYR cc_start: 0.8424 (m-10) cc_final: 0.7926 (m-10) REVERT: A 957 GLN cc_start: 0.8668 (tt0) cc_final: 0.8287 (tm-30) REVERT: A 998 THR cc_start: 0.9530 (OUTLIER) cc_final: 0.9295 (m) REVERT: A 1029 MET cc_start: 0.9377 (tpp) cc_final: 0.8938 (ttm) REVERT: B 87 ASN cc_start: 0.8883 (OUTLIER) cc_final: 0.8624 (p0) REVERT: B 127 PHE cc_start: 0.6969 (t80) cc_final: 0.6683 (t80) REVERT: B 383 SER cc_start: 0.9000 (t) cc_final: 0.8739 (p) REVERT: B 430 THR cc_start: 0.8509 (m) cc_final: 0.8055 (p) REVERT: B 523 THR cc_start: 0.8307 (m) cc_final: 0.7920 (p) REVERT: B 759 PHE cc_start: 0.8428 (t80) cc_final: 0.8159 (t80) REVERT: B 957 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7707 (tm-30) REVERT: B 981 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8882 (mp) REVERT: C 102 ARG cc_start: 0.8314 (mmt90) cc_final: 0.7897 (mpt180) REVERT: C 127 PHE cc_start: 0.6995 (t80) cc_final: 0.6727 (t80) REVERT: C 246 ARG cc_start: 0.1975 (OUTLIER) cc_final: -0.0734 (mtt-85) REVERT: C 298 GLU cc_start: 0.8860 (tp30) cc_final: 0.8520 (tp30) REVERT: C 495 TYR cc_start: 0.5850 (OUTLIER) cc_final: 0.4636 (t80) REVERT: C 523 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7954 (p) REVERT: C 759 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7953 (t80) REVERT: C 850 ILE cc_start: 0.4228 (OUTLIER) cc_final: 0.3452 (mm) REVERT: C 957 GLN cc_start: 0.8517 (tt0) cc_final: 0.8083 (tm-30) outliers start: 113 outliers final: 85 residues processed: 269 average time/residue: 0.3157 time to fit residues: 142.9816 Evaluate side-chains 263 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 166 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.1062 > 50: distance: 31 - 36: 7.074 distance: 36 - 37: 14.339 distance: 37 - 38: 10.663 distance: 37 - 40: 11.631 distance: 38 - 39: 10.443 distance: 38 - 42: 6.714 distance: 40 - 41: 4.065 distance: 43 - 44: 8.452 distance: 43 - 46: 10.672 distance: 44 - 45: 7.463 distance: 44 - 49: 6.412 distance: 46 - 47: 5.645 distance: 46 - 48: 14.262 distance: 49 - 50: 18.150 distance: 50 - 51: 15.666 distance: 50 - 53: 6.128 distance: 51 - 52: 11.009 distance: 51 - 58: 20.511 distance: 53 - 54: 29.696 distance: 54 - 55: 9.673 distance: 55 - 56: 27.923 distance: 55 - 57: 21.876 distance: 58 - 59: 19.420 distance: 59 - 60: 9.756 distance: 59 - 62: 16.566 distance: 60 - 61: 12.272 distance: 60 - 66: 13.285 distance: 62 - 63: 30.863 distance: 62 - 64: 15.952 distance: 63 - 65: 35.264 distance: 66 - 67: 3.507 distance: 66 - 145: 21.624 distance: 67 - 68: 16.226 distance: 67 - 70: 16.438 distance: 68 - 69: 23.285 distance: 68 - 78: 13.030 distance: 70 - 71: 8.412 distance: 71 - 72: 13.871 distance: 71 - 73: 6.261 distance: 72 - 74: 10.683 distance: 73 - 75: 5.466 distance: 74 - 76: 10.945 distance: 75 - 76: 8.637 distance: 76 - 77: 5.848 distance: 78 - 79: 5.899 distance: 79 - 80: 11.460 distance: 79 - 82: 10.941 distance: 80 - 81: 5.384 distance: 82 - 83: 11.714 distance: 83 - 84: 14.158 distance: 84 - 85: 14.401 distance: 84 - 86: 8.677 distance: 87 - 88: 11.600 distance: 88 - 89: 14.795 distance: 88 - 91: 11.469 distance: 89 - 90: 36.706 distance: 89 - 92: 14.463 distance: 92 - 93: 8.891 distance: 93 - 94: 12.645 distance: 94 - 95: 6.256 distance: 94 - 96: 12.015 distance: 96 - 97: 9.385 distance: 97 - 98: 7.395 distance: 97 - 100: 7.289 distance: 98 - 99: 9.833 distance: 98 - 104: 5.600 distance: 100 - 101: 6.818 distance: 101 - 102: 7.248 distance: 101 - 103: 3.808 distance: 104 - 105: 16.789 distance: 105 - 106: 8.125 distance: 105 - 108: 9.328 distance: 106 - 107: 9.607 distance: 106 - 113: 11.641 distance: 108 - 109: 22.122 distance: 109 - 110: 12.276 distance: 110 - 111: 7.385