Starting phenix.real_space_refine on Wed Feb 21 02:49:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8elj_28228/02_2024/8elj_28228.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8elj_28228/02_2024/8elj_28228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8elj_28228/02_2024/8elj_28228.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8elj_28228/02_2024/8elj_28228.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8elj_28228/02_2024/8elj_28228.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8elj_28228/02_2024/8elj_28228.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 132 5.16 5 C 18732 2.51 5 N 4827 2.21 5 O 5772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 85": "NH1" <-> "NH2" Residue "S ARG 98": "NH1" <-> "NH2" Residue "S TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 28": "OD1" <-> "OD2" Residue "T ASP 52": "OD1" <-> "OD2" Residue "T ASP 84": "OD1" <-> "OD2" Residue "T ASP 87": "OD1" <-> "OD2" Residue "T TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 98": "NH1" <-> "NH2" Residue "U TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 28": "OD1" <-> "OD2" Residue "V ASP 52": "OD1" <-> "OD2" Residue "V ASP 84": "OD1" <-> "OD2" Residue "V ASP 87": "OD1" <-> "OD2" Residue "V TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 85": "NH1" <-> "NH2" Residue "W ARG 98": "NH1" <-> "NH2" Residue "W TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 28": "OD1" <-> "OD2" Residue "X ASP 52": "OD1" <-> "OD2" Residue "X ASP 84": "OD1" <-> "OD2" Residue "X ASP 87": "OD1" <-> "OD2" Residue "X TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29463 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "B" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "C" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "S" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "T" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "U" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "V" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "W" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "X" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 15.35, per 1000 atoms: 0.52 Number of scatterers: 29463 At special positions: 0 Unit cell: (136.8, 139.365, 202.635, 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 132 16.00 O 5772 8.00 N 4827 7.00 C 18732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.08 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.07 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.06 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.06 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.06 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.07 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.08 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.07 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.07 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.07 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.06 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.05 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.08 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.08 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.05 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.07 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.07 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.07 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.05 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.08 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 90 " distance=2.04 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 90 " distance=2.04 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 96 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 90 " distance=2.04 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Time building additional restraints: 11.58 Conformation dependent library (CDL) restraints added in 5.1 seconds 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6852 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 60 sheets defined 22.1% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.09 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 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.812A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.756A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 759 removed outlier: 7.022A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.529A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.586A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.059A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1031 removed outlier: 4.792A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 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 383 through 389 removed outlier: 3.810A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.754A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 759 removed outlier: 7.021A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.529A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.548A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.060A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1031 removed outlier: 4.793A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.811A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.755A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 759 removed outlier: 7.023A pdb=" N SER C 758 " --> pdb=" O GLN C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.529A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.523A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.059A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1031 removed outlier: 4.792A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.948A pdb=" N TYR S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 65 Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'T' and resid 81 through 85 Processing helix chain 'U' and resid 28 through 32 removed outlier: 3.949A pdb=" N TYR U 32 " --> pdb=" O PHE U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 62 through 65 Processing helix chain 'U' and resid 87 through 91 Processing helix chain 'V' and resid 81 through 85 Processing helix chain 'W' and resid 28 through 32 removed outlier: 3.948A pdb=" N TYR W 32 " --> pdb=" O PHE W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 62 through 65 Processing helix chain 'W' and resid 87 through 91 Processing helix chain 'X' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.245A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.657A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.380A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.715A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.491A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.290A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.375A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.758A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.237A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.491A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.315A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.315A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.541A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.239A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.380A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.716A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.482A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.292A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.373A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.758A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.238A 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: 6.590A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.477A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.320A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.320A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.538A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.248A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.381A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.715A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.478A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.290A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.757A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.238A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.320A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.320A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.538A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.656A pdb=" N PHE S 34 " --> pdb=" O TRP S 50 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TRP S 50 " --> pdb=" O PHE S 34 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TRP S 36 " --> pdb=" O MET S 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 10 through 11 Processing sheet with id=AF1, first strand: chain 'T' and resid 9 through 12 removed outlier: 6.568A pdb=" N VAL T 10 " --> pdb=" O THR T 108 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP T 37 " --> pdb=" O MET T 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 9 through 12 removed outlier: 6.568A pdb=" N VAL T 10 " --> pdb=" O THR T 108 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 18 through 23 Processing sheet with id=AF4, first strand: chain 'U' and resid 3 through 6 Processing sheet with id=AF5, first strand: chain 'U' and resid 10 through 11 removed outlier: 6.651A pdb=" N PHE U 34 " --> pdb=" O TRP U 50 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TRP U 50 " --> pdb=" O PHE U 34 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TRP U 36 " --> pdb=" O MET U 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 10 through 11 Processing sheet with id=AF7, first strand: chain 'V' and resid 9 through 12 removed outlier: 6.568A pdb=" N VAL V 10 " --> pdb=" O THR V 108 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP V 37 " --> pdb=" O MET V 49 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 9 through 12 removed outlier: 6.568A pdb=" N VAL V 10 " --> pdb=" O THR V 108 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 18 through 23 Processing sheet with id=AG1, first strand: chain 'W' and resid 3 through 6 Processing sheet with id=AG2, first strand: chain 'W' and resid 10 through 11 removed outlier: 6.651A pdb=" N PHE W 34 " --> pdb=" O TRP W 50 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TRP W 50 " --> pdb=" O PHE W 34 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP W 36 " --> pdb=" O MET W 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 10 through 11 Processing sheet with id=AG4, first strand: chain 'X' and resid 9 through 12 removed outlier: 6.569A pdb=" N VAL X 10 " --> pdb=" O THR X 108 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP X 37 " --> pdb=" O MET X 49 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 9 through 12 removed outlier: 6.569A pdb=" N VAL X 10 " --> pdb=" O THR X 108 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 18 through 23 1216 hydrogen bonds defined for protein. 3204 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: 14.83 Time building geometry restraints manager: 12.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4829 1.32 - 1.45: 9913 1.45 - 1.59: 15219 1.59 - 1.73: 0 1.73 - 1.86: 168 Bond restraints: 30129 Sorted by residual: bond pdb=" CE1 HIS C1048 " pdb=" NE2 HIS C1048 " ideal model delta sigma weight residual 1.321 1.368 -0.047 1.00e-02 1.00e+04 2.19e+01 bond pdb=" C THR C1027 " pdb=" O THR C1027 " ideal model delta sigma weight residual 1.237 1.181 0.055 1.19e-02 7.06e+03 2.16e+01 bond pdb=" CE1 HIS A1048 " pdb=" NE2 HIS A1048 " ideal model delta sigma weight residual 1.321 1.367 -0.046 1.00e-02 1.00e+04 2.11e+01 bond pdb=" CE1 HIS B1048 " pdb=" NE2 HIS B1048 " ideal model delta sigma weight residual 1.321 1.367 -0.046 1.00e-02 1.00e+04 2.08e+01 bond pdb=" C THR B1027 " pdb=" O THR B1027 " ideal model delta sigma weight residual 1.237 1.183 0.053 1.19e-02 7.06e+03 2.00e+01 ... (remaining 30124 not shown) Histogram of bond angle deviations from ideal: 93.34 - 101.64: 96 101.64 - 109.94: 5524 109.94 - 118.25: 18289 118.25 - 126.55: 16820 126.55 - 134.85: 269 Bond angle restraints: 40998 Sorted by residual: angle pdb=" CA PHE B 486 " pdb=" CB PHE B 486 " pdb=" CG PHE B 486 " ideal model delta sigma weight residual 113.80 122.25 -8.45 1.00e+00 1.00e+00 7.15e+01 angle pdb=" CA PHE A 486 " pdb=" CB PHE A 486 " pdb=" CG PHE A 486 " ideal model delta sigma weight residual 113.80 122.22 -8.42 1.00e+00 1.00e+00 7.10e+01 angle pdb=" CA PHE C 486 " pdb=" CB PHE C 486 " pdb=" CG PHE C 486 " ideal model delta sigma weight residual 113.80 122.22 -8.42 1.00e+00 1.00e+00 7.09e+01 angle pdb=" N ILE B 909 " pdb=" CA ILE B 909 " pdb=" C ILE B 909 " ideal model delta sigma weight residual 112.43 105.51 6.92 9.20e-01 1.18e+00 5.66e+01 angle pdb=" N ILE C 909 " pdb=" CA ILE C 909 " pdb=" C ILE C 909 " ideal model delta sigma weight residual 112.43 105.52 6.91 9.20e-01 1.18e+00 5.64e+01 ... (remaining 40993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 17025 17.94 - 35.87: 1198 35.87 - 53.81: 198 53.81 - 71.74: 62 71.74 - 89.68: 39 Dihedral angle restraints: 18522 sinusoidal: 7827 harmonic: 10695 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -175.68 89.68 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -175.14 89.14 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -175.12 89.12 1 1.00e+01 1.00e-02 9.45e+01 ... (remaining 18519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 3009 0.105 - 0.209: 1350 0.209 - 0.314: 346 0.314 - 0.419: 65 0.419 - 0.523: 15 Chirality restraints: 4785 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.32e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.18e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.10e+01 ... (remaining 4782 not shown) Planarity restraints: 5247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " 0.231 2.00e-02 2.50e+03 1.94e-01 4.71e+02 pdb=" C7 NAG J 1 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " 0.160 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " -0.325 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.215 2.00e-02 2.50e+03 1.80e-01 4.06e+02 pdb=" C7 NAG E 1 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.300 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " 0.212 2.00e-02 2.50e+03 1.78e-01 3.97e+02 pdb=" C7 NAG O 1 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " 0.150 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " -0.296 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " -0.008 2.00e-02 2.50e+03 ... (remaining 5244 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.85: 14 1.85 - 2.61: 293 2.61 - 3.37: 36381 3.37 - 4.14: 73090 4.14 - 4.90: 124434 Nonbonded interactions: 234212 Sorted by model distance: nonbonded pdb=" O PHE A 486 " pdb=" OH TYR U 102 " model vdw 1.083 2.440 nonbonded pdb=" O PHE B 486 " pdb=" OH TYR S 102 " model vdw 1.104 2.440 nonbonded pdb=" O PHE C 486 " pdb=" OH TYR W 102 " model vdw 1.109 2.440 nonbonded pdb=" NH2 ARG C 328 " pdb=" CD1 LEU C 533 " model vdw 1.659 3.540 nonbonded pdb=" NH2 ARG A 328 " pdb=" CD1 LEU A 533 " model vdw 1.659 3.540 ... (remaining 234207 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'T' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.390 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: 33.670 Check model and map are aligned: 0.460 Set scattering table: 0.290 Process input model: 80.910 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.370 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 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 : 0.010 0.066 30129 Z= 0.667 Angle : 1.783 15.969 40998 Z= 1.154 Chirality : 0.123 0.523 4785 Planarity : 0.012 0.194 5208 Dihedral : 13.283 87.812 11544 Min Nonbonded Distance : 1.083 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.12 % Rotamer: Outliers : 1.03 % Allowed : 4.19 % Favored : 94.77 % Cbeta Deviations : 1.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.13), residues: 3630 helix: -0.55 (0.17), residues: 666 sheet: -0.07 (0.15), residues: 969 loop : -0.89 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.009 TRP S 50 HIS 0.019 0.005 HIS B1064 PHE 0.055 0.010 PHE A 888 TYR 0.067 0.009 TYR W 102 ARG 0.041 0.003 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 411 time to evaluate : 3.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.8160 (mp) cc_final: 0.7854 (mt) REVERT: A 242 LEU cc_start: 0.7676 (mt) cc_final: 0.7227 (mt) REVERT: A 394 ASN cc_start: 0.9154 (m-40) cc_final: 0.8859 (t0) REVERT: A 417 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8805 (mtpt) REVERT: A 979 ASP cc_start: 0.9057 (m-30) cc_final: 0.8640 (t0) REVERT: A 1092 GLU cc_start: 0.9409 (mt-10) cc_final: 0.9012 (pm20) REVERT: B 110 LEU cc_start: 0.8358 (mp) cc_final: 0.8001 (mt) REVERT: B 114 THR cc_start: 0.8889 (t) cc_final: 0.8675 (p) REVERT: B 276 LEU cc_start: 0.9303 (tp) cc_final: 0.9094 (tp) REVERT: B 390 LEU cc_start: 0.8529 (tp) cc_final: 0.8276 (mt) REVERT: B 394 ASN cc_start: 0.9125 (m-40) cc_final: 0.8822 (t0) REVERT: B 979 ASP cc_start: 0.9066 (m-30) cc_final: 0.8629 (t0) REVERT: B 1092 GLU cc_start: 0.9459 (mt-10) cc_final: 0.9168 (pm20) REVERT: C 110 LEU cc_start: 0.8067 (mp) cc_final: 0.7672 (mt) REVERT: C 242 LEU cc_start: 0.7612 (mt) cc_final: 0.7345 (mt) REVERT: C 390 LEU cc_start: 0.8542 (tp) cc_final: 0.8301 (mt) REVERT: C 394 ASN cc_start: 0.9110 (m-40) cc_final: 0.8903 (t0) REVERT: C 417 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8868 (mtpt) REVERT: C 979 ASP cc_start: 0.9114 (m-30) cc_final: 0.8668 (t70) REVERT: C 1092 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9139 (pm20) REVERT: S 89 ASP cc_start: 0.9538 (m-30) cc_final: 0.9254 (p0) REVERT: T 49 MET cc_start: 0.8273 (mmm) cc_final: 0.7858 (mmm) REVERT: U 54 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8910 (mp) REVERT: U 82 GLU cc_start: 0.8545 (tt0) cc_final: 0.8266 (tp30) REVERT: U 89 ASP cc_start: 0.9545 (m-30) cc_final: 0.9302 (p0) REVERT: V 49 MET cc_start: 0.8202 (mmm) cc_final: 0.7782 (mmm) REVERT: V 63 ARG cc_start: 0.7734 (ptt90) cc_final: 0.7478 (ptt180) REVERT: W 89 ASP cc_start: 0.9519 (m-30) cc_final: 0.9281 (p0) REVERT: X 49 MET cc_start: 0.8180 (mmm) cc_final: 0.7711 (mmm) REVERT: X 63 ARG cc_start: 0.7658 (ptt90) cc_final: 0.6732 (ppt170) outliers start: 33 outliers final: 3 residues processed: 434 average time/residue: 0.4974 time to fit residues: 324.4453 Evaluate side-chains 186 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 182 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain U residue 54 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 7.9990 chunk 277 optimal weight: 0.5980 chunk 153 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 286 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 213 optimal weight: 2.9990 chunk 332 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 207 HIS A 360 ASN A 474 GLN A 613 GLN A 804 GLN A 935 GLN B 207 HIS B 321 GLN B 360 ASN B 474 GLN B 613 GLN B 804 GLN B 935 GLN C 66 HIS C 207 HIS C 360 ASN C 474 GLN C 613 GLN C 804 GLN C 935 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 52 ASN T 40 GLN U 3 GLN ** U 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 55 ASN W 3 GLN W 52 ASN X 55 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 30129 Z= 0.217 Angle : 0.673 8.967 40998 Z= 0.356 Chirality : 0.046 0.188 4785 Planarity : 0.004 0.047 5208 Dihedral : 5.538 41.119 5099 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.44 % Allowed : 8.45 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.13), residues: 3630 helix: 1.26 (0.20), residues: 681 sheet: 0.12 (0.14), residues: 1041 loop : -0.67 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP S 104 HIS 0.013 0.001 HIS U 100 PHE 0.025 0.002 PHE C 168 TYR 0.039 0.002 TYR U 102 ARG 0.012 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 205 time to evaluate : 3.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 VAL cc_start: 0.7886 (m) cc_final: 0.7445 (p) REVERT: A 117 LEU cc_start: 0.8368 (tp) cc_final: 0.7919 (mt) REVERT: A 394 ASN cc_start: 0.9113 (m-40) cc_final: 0.8623 (m110) REVERT: A 417 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8790 (mtmt) REVERT: A 505 TYR cc_start: 0.9464 (OUTLIER) cc_final: 0.9238 (t80) REVERT: A 546 LEU cc_start: 0.8316 (tp) cc_final: 0.8001 (tt) REVERT: A 979 ASP cc_start: 0.9225 (m-30) cc_final: 0.8850 (t0) REVERT: B 394 ASN cc_start: 0.9076 (m-40) cc_final: 0.8741 (t160) REVERT: B 546 LEU cc_start: 0.8238 (tp) cc_final: 0.7979 (tt) REVERT: B 955 ASN cc_start: 0.9423 (m-40) cc_final: 0.9211 (t0) REVERT: B 979 ASP cc_start: 0.9189 (m-30) cc_final: 0.8852 (t0) REVERT: C 117 LEU cc_start: 0.8445 (tp) cc_final: 0.7918 (mt) REVERT: C 417 LYS cc_start: 0.9008 (mmtt) cc_final: 0.8807 (mtpt) REVERT: C 505 TYR cc_start: 0.9482 (OUTLIER) cc_final: 0.9240 (t80) REVERT: C 546 LEU cc_start: 0.8167 (tp) cc_final: 0.7917 (tt) REVERT: C 955 ASN cc_start: 0.9446 (m-40) cc_final: 0.9213 (t0) REVERT: C 979 ASP cc_start: 0.9188 (m-30) cc_final: 0.8774 (t0) REVERT: S 70 MET cc_start: 0.7423 (mpp) cc_final: 0.6639 (mmt) REVERT: S 89 ASP cc_start: 0.9479 (m-30) cc_final: 0.9267 (p0) REVERT: S 98 ARG cc_start: 0.6231 (tmm-80) cc_final: 0.5853 (tmm160) REVERT: T 38 TYR cc_start: 0.6604 (m-80) cc_final: 0.6145 (m-80) REVERT: T 63 ARG cc_start: 0.7898 (ptt180) cc_final: 0.7554 (ptt180) REVERT: T 85 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6687 (mt-10) REVERT: U 70 MET cc_start: 0.7598 (mtt) cc_final: 0.6835 (mmt) REVERT: V 38 TYR cc_start: 0.6715 (m-80) cc_final: 0.6454 (m-80) REVERT: V 85 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6760 (mt-10) REVERT: W 70 MET cc_start: 0.7974 (mtt) cc_final: 0.7501 (mmm) REVERT: X 38 TYR cc_start: 0.6675 (m-80) cc_final: 0.6397 (m-80) REVERT: X 85 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6618 (mt-10) outliers start: 46 outliers final: 15 residues processed: 244 average time/residue: 0.5001 time to fit residues: 185.2841 Evaluate side-chains 156 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain X residue 5 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 184 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 226 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 332 optimal weight: 0.9990 chunk 359 optimal weight: 7.9990 chunk 296 optimal weight: 3.9990 chunk 330 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 267 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 388 ASN C 388 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN ** S 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 40 GLN U 39 GLN ** U 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 40 GLN V 55 ASN W 39 GLN ** W 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 40 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 30129 Z= 0.274 Angle : 0.625 10.946 40998 Z= 0.330 Chirality : 0.045 0.231 4785 Planarity : 0.004 0.058 5208 Dihedral : 4.854 31.866 5094 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.50 % Allowed : 8.92 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3630 helix: 1.69 (0.21), residues: 666 sheet: 0.06 (0.14), residues: 1074 loop : -0.64 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP W 104 HIS 0.007 0.001 HIS B1064 PHE 0.030 0.002 PHE C 486 TYR 0.037 0.002 TYR U 102 ARG 0.005 0.001 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 145 time to evaluate : 3.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 VAL cc_start: 0.7985 (m) cc_final: 0.7591 (p) REVERT: A 88 ASP cc_start: 0.9197 (m-30) cc_final: 0.8950 (p0) REVERT: A 117 LEU cc_start: 0.8547 (tp) cc_final: 0.8053 (mp) REVERT: A 394 ASN cc_start: 0.9118 (m-40) cc_final: 0.8594 (m110) REVERT: A 417 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8804 (mtmt) REVERT: A 505 TYR cc_start: 0.9479 (OUTLIER) cc_final: 0.9254 (t80) REVERT: A 546 LEU cc_start: 0.8425 (tp) cc_final: 0.8201 (tt) REVERT: A 979 ASP cc_start: 0.9393 (m-30) cc_final: 0.9059 (t0) REVERT: B 62 VAL cc_start: 0.7973 (m) cc_final: 0.7558 (p) REVERT: B 88 ASP cc_start: 0.9243 (m-30) cc_final: 0.8985 (p0) REVERT: B 394 ASN cc_start: 0.9077 (m-40) cc_final: 0.8574 (m110) REVERT: B 546 LEU cc_start: 0.8304 (tp) cc_final: 0.8024 (tt) REVERT: B 979 ASP cc_start: 0.9366 (m-30) cc_final: 0.9032 (t0) REVERT: C 62 VAL cc_start: 0.8022 (m) cc_final: 0.7770 (p) REVERT: C 88 ASP cc_start: 0.9204 (m-30) cc_final: 0.8978 (p0) REVERT: C 104 TRP cc_start: 0.8586 (m-90) cc_final: 0.8365 (m-90) REVERT: C 117 LEU cc_start: 0.8582 (tp) cc_final: 0.8083 (mp) REVERT: C 505 TYR cc_start: 0.9488 (OUTLIER) cc_final: 0.9258 (t80) REVERT: C 546 LEU cc_start: 0.8314 (tp) cc_final: 0.8040 (tt) REVERT: C 979 ASP cc_start: 0.9409 (m-30) cc_final: 0.9084 (t0) REVERT: S 3 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8248 (tm-30) REVERT: S 70 MET cc_start: 0.7673 (mpp) cc_final: 0.7246 (mmt) REVERT: S 89 ASP cc_start: 0.9486 (m-30) cc_final: 0.9266 (p0) REVERT: T 63 ARG cc_start: 0.7993 (ptt180) cc_final: 0.7577 (ptt180) REVERT: U 70 MET cc_start: 0.7762 (mtt) cc_final: 0.6660 (mtt) REVERT: U 81 MET cc_start: 0.7932 (tmm) cc_final: 0.7466 (tmm) REVERT: W 19 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8128 (tppt) REVERT: W 70 MET cc_start: 0.7793 (mtt) cc_final: 0.7532 (mtt) REVERT: W 81 MET cc_start: 0.8145 (tmm) cc_final: 0.7880 (tpp) REVERT: X 49 MET cc_start: 0.7877 (ptm) cc_final: 0.7614 (ptt) REVERT: X 63 ARG cc_start: 0.8336 (ptt90) cc_final: 0.7807 (ptt180) outliers start: 48 outliers final: 27 residues processed: 189 average time/residue: 0.5100 time to fit residues: 151.4630 Evaluate side-chains 160 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain W residue 19 LYS Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 328 optimal weight: 4.9990 chunk 250 optimal weight: 9.9990 chunk 172 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 334 optimal weight: 30.0000 chunk 353 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 316 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN ** S 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 40 GLN ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 55 ASN W 39 GLN ** W 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 40 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30129 Z= 0.326 Angle : 0.617 9.487 40998 Z= 0.324 Chirality : 0.045 0.226 4785 Planarity : 0.004 0.062 5208 Dihedral : 4.889 38.792 5094 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.07 % Allowed : 10.08 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.13), residues: 3630 helix: 1.83 (0.21), residues: 663 sheet: -0.02 (0.15), residues: 1077 loop : -0.82 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP S 104 HIS 0.007 0.001 HIS B1064 PHE 0.032 0.002 PHE A 898 TYR 0.025 0.001 TYR U 102 ARG 0.005 0.001 ARG T 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 133 time to evaluate : 3.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.9102 (m-40) cc_final: 0.8593 (m110) REVERT: A 505 TYR cc_start: 0.9508 (OUTLIER) cc_final: 0.9264 (t80) REVERT: A 546 LEU cc_start: 0.8494 (tp) cc_final: 0.8187 (tt) REVERT: A 979 ASP cc_start: 0.9434 (m-30) cc_final: 0.9185 (t0) REVERT: B 104 TRP cc_start: 0.8794 (m-90) cc_final: 0.8461 (m-90) REVERT: B 138 ASP cc_start: 0.6692 (OUTLIER) cc_final: 0.6466 (p0) REVERT: B 394 ASN cc_start: 0.9051 (m-40) cc_final: 0.8538 (m110) REVERT: B 546 LEU cc_start: 0.8421 (tp) cc_final: 0.8118 (tt) REVERT: B 979 ASP cc_start: 0.9410 (m-30) cc_final: 0.9190 (t0) REVERT: C 104 TRP cc_start: 0.8743 (m-90) cc_final: 0.8513 (m-90) REVERT: C 138 ASP cc_start: 0.6705 (OUTLIER) cc_final: 0.6497 (p0) REVERT: C 505 TYR cc_start: 0.9517 (OUTLIER) cc_final: 0.9298 (t80) REVERT: C 546 LEU cc_start: 0.8399 (tp) cc_final: 0.8122 (tt) REVERT: C 979 ASP cc_start: 0.9445 (m-30) cc_final: 0.9215 (t0) REVERT: S 70 MET cc_start: 0.7401 (mpp) cc_final: 0.7022 (mmm) REVERT: S 89 ASP cc_start: 0.9510 (m-30) cc_final: 0.9287 (p0) REVERT: W 70 MET cc_start: 0.7922 (mtt) cc_final: 0.7704 (mtt) REVERT: W 81 MET cc_start: 0.8150 (tmm) cc_final: 0.7863 (tpp) REVERT: X 63 ARG cc_start: 0.8237 (ptt90) cc_final: 0.7887 (ptt180) outliers start: 66 outliers final: 37 residues processed: 195 average time/residue: 0.4498 time to fit residues: 139.1382 Evaluate side-chains 158 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 117 time to evaluate : 3.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 263 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 301 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 317 optimal weight: 40.0000 chunk 89 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN B 613 GLN C 613 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN ** U 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 55 ASN W 39 GLN W 52 ASN X 40 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 30129 Z= 0.343 Angle : 0.616 12.581 40998 Z= 0.322 Chirality : 0.045 0.218 4785 Planarity : 0.004 0.143 5208 Dihedral : 4.971 42.880 5094 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.41 % Allowed : 11.21 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.13), residues: 3630 helix: 1.88 (0.21), residues: 666 sheet: 0.00 (0.15), residues: 1023 loop : -0.88 (0.13), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP U 104 HIS 0.007 0.001 HIS A1064 PHE 0.016 0.002 PHE C 92 TYR 0.039 0.002 TYR B 904 ARG 0.009 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 117 time to evaluate : 3.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.9104 (m-40) cc_final: 0.8603 (m110) REVERT: A 505 TYR cc_start: 0.9546 (OUTLIER) cc_final: 0.9304 (t80) REVERT: A 979 ASP cc_start: 0.9465 (m-30) cc_final: 0.9259 (t0) REVERT: B 104 TRP cc_start: 0.8821 (m-90) cc_final: 0.8444 (m-90) REVERT: B 394 ASN cc_start: 0.9078 (m-40) cc_final: 0.8536 (m110) REVERT: C 104 TRP cc_start: 0.8799 (m-90) cc_final: 0.8570 (m-90) REVERT: C 979 ASP cc_start: 0.9467 (m-30) cc_final: 0.9263 (t0) REVERT: S 19 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7711 (tptp) REVERT: S 70 MET cc_start: 0.7660 (mpp) cc_final: 0.7131 (mmm) REVERT: S 89 ASP cc_start: 0.9549 (m-30) cc_final: 0.9340 (p0) REVERT: W 48 MET cc_start: 0.6794 (tpt) cc_final: 0.6589 (mmm) REVERT: W 70 MET cc_start: 0.8097 (mtt) cc_final: 0.7773 (mtt) REVERT: W 81 MET cc_start: 0.8170 (tmm) cc_final: 0.7870 (tpp) REVERT: X 63 ARG cc_start: 0.8225 (ptt90) cc_final: 0.7874 (ptt180) outliers start: 77 outliers final: 51 residues processed: 187 average time/residue: 0.4542 time to fit residues: 138.5044 Evaluate side-chains 154 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 101 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 119 optimal weight: 5.9990 chunk 318 optimal weight: 30.0000 chunk 69 optimal weight: 0.0060 chunk 207 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 354 optimal weight: 20.0000 chunk 293 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 185 optimal weight: 0.7980 overall best weight: 1.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A1106 GLN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 100 HIS ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 HIS U 105 ASN V 55 ASN ** W 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30129 Z= 0.211 Angle : 0.553 11.481 40998 Z= 0.288 Chirality : 0.044 0.198 4785 Planarity : 0.004 0.061 5208 Dihedral : 4.682 39.582 5094 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.00 % Allowed : 11.77 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3630 helix: 2.17 (0.21), residues: 666 sheet: 0.04 (0.15), residues: 1050 loop : -0.87 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP U 104 HIS 0.004 0.001 HIS B1064 PHE 0.012 0.001 PHE A 486 TYR 0.026 0.001 TYR B 904 ARG 0.004 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 112 time to evaluate : 3.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8579 (tp) cc_final: 0.8109 (mp) REVERT: A 394 ASN cc_start: 0.9079 (m-40) cc_final: 0.8597 (m110) REVERT: A 505 TYR cc_start: 0.9552 (OUTLIER) cc_final: 0.9270 (t80) REVERT: A 979 ASP cc_start: 0.9455 (m-30) cc_final: 0.9237 (t0) REVERT: B 394 ASN cc_start: 0.9051 (m-40) cc_final: 0.8525 (m110) REVERT: B 490 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7533 (m-80) REVERT: C 104 TRP cc_start: 0.8811 (m-90) cc_final: 0.8565 (m-90) REVERT: S 70 MET cc_start: 0.7493 (mpp) cc_final: 0.6696 (mmt) REVERT: W 81 MET cc_start: 0.8148 (tmm) cc_final: 0.7904 (tpp) REVERT: X 63 ARG cc_start: 0.8201 (ptt90) cc_final: 0.7874 (ptt180) outliers start: 64 outliers final: 35 residues processed: 171 average time/residue: 0.4175 time to fit residues: 116.4513 Evaluate side-chains 142 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 105 time to evaluate : 3.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 258 optimal weight: 6.9990 chunk 200 optimal weight: 8.9990 chunk 298 optimal weight: 0.0020 chunk 197 optimal weight: 4.9990 chunk 352 optimal weight: 10.0000 chunk 220 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 162 optimal weight: 0.9980 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 317 ASN B 804 GLN C 317 ASN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 901 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 100 HIS ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 HIS ** W 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 30129 Z= 0.349 Angle : 0.617 10.300 40998 Z= 0.322 Chirality : 0.045 0.211 4785 Planarity : 0.004 0.056 5208 Dihedral : 4.980 44.768 5094 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.22 % Allowed : 11.71 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 3630 helix: 1.97 (0.21), residues: 666 sheet: -0.04 (0.15), residues: 1026 loop : -0.96 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP W 104 HIS 0.007 0.001 HIS B1064 PHE 0.030 0.002 PHE B 486 TYR 0.029 0.002 TYR B 904 ARG 0.007 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 109 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.9079 (m-40) cc_final: 0.8535 (m110) REVERT: A 505 TYR cc_start: 0.9530 (OUTLIER) cc_final: 0.9168 (t80) REVERT: A 979 ASP cc_start: 0.9507 (m-30) cc_final: 0.9298 (t0) REVERT: B 394 ASN cc_start: 0.9065 (m-40) cc_final: 0.8506 (m110) REVERT: B 490 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: C 104 TRP cc_start: 0.8857 (m-90) cc_final: 0.8588 (m-90) REVERT: C 461 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7611 (mt) REVERT: C 505 TYR cc_start: 0.9421 (OUTLIER) cc_final: 0.8833 (t80) REVERT: S 70 MET cc_start: 0.7567 (mpp) cc_final: 0.6811 (mmt) REVERT: S 98 ARG cc_start: 0.6336 (tmm-80) cc_final: 0.5896 (tmm-80) REVERT: X 63 ARG cc_start: 0.8177 (ptt90) cc_final: 0.7855 (ptt180) outliers start: 71 outliers final: 47 residues processed: 175 average time/residue: 0.3838 time to fit residues: 110.7570 Evaluate side-chains 154 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 103 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 218 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 210 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 69 optimal weight: 0.2980 chunk 68 optimal weight: 0.7980 chunk 224 optimal weight: 3.9990 chunk 240 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 277 optimal weight: 0.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 644 GLN B 935 GLN C 901 GLN C 935 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 105 ASN ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30129 Z= 0.234 Angle : 0.555 9.823 40998 Z= 0.290 Chirality : 0.044 0.188 4785 Planarity : 0.004 0.058 5208 Dihedral : 4.862 57.172 5094 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.63 % Allowed : 12.64 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3630 helix: 2.19 (0.21), residues: 666 sheet: 0.02 (0.15), residues: 1020 loop : -0.92 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP W 104 HIS 0.005 0.001 HIS B1064 PHE 0.028 0.001 PHE C 486 TYR 0.020 0.001 TYR B 904 ARG 0.013 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 112 time to evaluate : 3.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.9067 (m-40) cc_final: 0.8528 (m110) REVERT: A 486 PHE cc_start: 0.6897 (OUTLIER) cc_final: 0.6485 (t80) REVERT: A 505 TYR cc_start: 0.9482 (OUTLIER) cc_final: 0.9178 (t80) REVERT: B 117 LEU cc_start: 0.8699 (tp) cc_final: 0.8062 (mp) REVERT: B 394 ASN cc_start: 0.9072 (m-40) cc_final: 0.8511 (m110) REVERT: B 490 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7685 (m-80) REVERT: C 461 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7667 (mt) REVERT: C 486 PHE cc_start: 0.6696 (OUTLIER) cc_final: 0.6205 (t80) REVERT: S 70 MET cc_start: 0.7507 (mpp) cc_final: 0.6760 (mmt) REVERT: S 98 ARG cc_start: 0.6280 (tmm-80) cc_final: 0.5792 (tmm-80) REVERT: W 48 MET cc_start: 0.6854 (mmm) cc_final: 0.6345 (mmm) REVERT: X 63 ARG cc_start: 0.8116 (ptt90) cc_final: 0.7810 (ptt180) outliers start: 52 outliers final: 37 residues processed: 158 average time/residue: 0.4102 time to fit residues: 107.0169 Evaluate side-chains 146 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 104 time to evaluate : 3.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 7.9990 chunk 337 optimal weight: 7.9990 chunk 308 optimal weight: 10.0000 chunk 328 optimal weight: 10.0000 chunk 197 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 258 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 297 optimal weight: 6.9990 chunk 310 optimal weight: 7.9990 chunk 327 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1135 ASN B 388 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1135 ASN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 901 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.114 30129 Z= 0.752 Angle : 0.900 10.272 40998 Z= 0.466 Chirality : 0.052 0.262 4785 Planarity : 0.005 0.092 5208 Dihedral : 6.349 49.488 5094 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.07 % Allowed : 12.71 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.13), residues: 3630 helix: 1.06 (0.19), residues: 657 sheet: -0.27 (0.15), residues: 996 loop : -1.41 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.004 TRP W 104 HIS 0.011 0.002 HIS A1064 PHE 0.030 0.003 PHE C 486 TYR 0.045 0.003 TYR C 904 ARG 0.013 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 97 time to evaluate : 3.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.9037 (m-40) cc_final: 0.8429 (m110) REVERT: A 486 PHE cc_start: 0.6876 (OUTLIER) cc_final: 0.6454 (t80) REVERT: A 505 TYR cc_start: 0.9548 (OUTLIER) cc_final: 0.9218 (t80) REVERT: B 394 ASN cc_start: 0.9019 (m-40) cc_final: 0.8463 (m-40) REVERT: C 486 PHE cc_start: 0.6828 (OUTLIER) cc_final: 0.6354 (t80) REVERT: S 70 MET cc_start: 0.7908 (mpp) cc_final: 0.7572 (mmm) REVERT: W 70 MET cc_start: 0.7787 (mmt) cc_final: 0.7575 (mmt) REVERT: X 63 ARG cc_start: 0.8063 (ptt90) cc_final: 0.7539 (ppt170) outliers start: 66 outliers final: 53 residues processed: 156 average time/residue: 0.3741 time to fit residues: 100.6987 Evaluate side-chains 143 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 87 time to evaluate : 3.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 29 VAL Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 215 optimal weight: 5.9990 chunk 347 optimal weight: 8.9990 chunk 212 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 241 optimal weight: 0.0870 chunk 364 optimal weight: 30.0000 chunk 335 optimal weight: 50.0000 chunk 290 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 644 GLN B 901 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 901 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 55 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.6141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30129 Z= 0.215 Angle : 0.583 8.908 40998 Z= 0.304 Chirality : 0.044 0.175 4785 Planarity : 0.004 0.047 5208 Dihedral : 5.357 46.698 5094 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.22 % Allowed : 13.49 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 3630 helix: 1.97 (0.20), residues: 666 sheet: -0.12 (0.15), residues: 1005 loop : -1.14 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP W 104 HIS 0.007 0.001 HIS S 35 PHE 0.027 0.001 PHE C 486 TYR 0.029 0.001 TYR C 904 ARG 0.006 0.000 ARG X 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 105 time to evaluate : 3.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.9002 (m-40) cc_final: 0.8428 (m-40) REVERT: A 486 PHE cc_start: 0.6754 (OUTLIER) cc_final: 0.6260 (t80) REVERT: A 505 TYR cc_start: 0.9505 (OUTLIER) cc_final: 0.9172 (t80) REVERT: B 191 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.9009 (mt-10) REVERT: B 394 ASN cc_start: 0.9022 (m-40) cc_final: 0.8680 (m-40) REVERT: B 900 MET cc_start: 0.9144 (ptp) cc_final: 0.8912 (mtp) REVERT: C 191 GLU cc_start: 0.9259 (OUTLIER) cc_final: 0.8990 (mt-10) REVERT: C 486 PHE cc_start: 0.6735 (OUTLIER) cc_final: 0.6260 (t80) REVERT: S 70 MET cc_start: 0.7694 (mpp) cc_final: 0.7349 (mmm) REVERT: V 29 VAL cc_start: 0.4722 (p) cc_final: 0.4403 (m) outliers start: 39 outliers final: 30 residues processed: 140 average time/residue: 0.3972 time to fit residues: 94.3457 Evaluate side-chains 132 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 97 time to evaluate : 4.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 4.9990 chunk 309 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 267 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 290 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 298 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 53 optimal weight: 0.0370 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 100 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.076148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.047035 restraints weight = 126204.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.048730 restraints weight = 60827.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.049814 restraints weight = 39185.061| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 30129 Z= 0.157 Angle : 0.533 9.245 40998 Z= 0.278 Chirality : 0.044 0.174 4785 Planarity : 0.004 0.048 5208 Dihedral : 4.876 55.410 5094 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.22 % Allowed : 13.87 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3630 helix: 2.40 (0.21), residues: 666 sheet: -0.02 (0.16), residues: 1011 loop : -0.93 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP S 104 HIS 0.005 0.001 HIS S 35 PHE 0.028 0.001 PHE C 486 TYR 0.023 0.001 TYR C 904 ARG 0.007 0.000 ARG C 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5475.74 seconds wall clock time: 102 minutes 5.94 seconds (6125.94 seconds total)