Starting phenix.real_space_refine on Tue Feb 20 09:38:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jji_22352/02_2024/7jji_22352_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jji_22352/02_2024/7jji_22352.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jji_22352/02_2024/7jji_22352_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jji_22352/02_2024/7jji_22352_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jji_22352/02_2024/7jji_22352_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jji_22352/02_2024/7jji_22352.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jji_22352/02_2024/7jji_22352.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jji_22352/02_2024/7jji_22352_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jji_22352/02_2024/7jji_22352_updated.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= 0.039 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 120 5.16 5 C 17442 2.51 5 N 4437 2.21 5 O 5460 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 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "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 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 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 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 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "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 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 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 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 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "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 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 578": "OD1" <-> "OD2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 906": "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 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" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27459 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 8657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8657 Classifications: {'peptide': 1109} Link IDs: {'PTRANS': 53, 'TRANS': 1055} Chain breaks: 2 Chain: "B" Number of atoms: 8657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8657 Classifications: {'peptide': 1109} Link IDs: {'PTRANS': 53, 'TRANS': 1055} Chain breaks: 2 Chain: "C" Number of atoms: 8657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8657 Classifications: {'peptide': 1109} Link IDs: {'PTRANS': 53, 'TRANS': 1055} Chain breaks: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" 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: "U" 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" 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: "u" 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: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {'EIC': 1, 'NAG': 1, 'VCG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {'EIC': 1, 'NAG': 1, 'VCG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {'EIC': 1, 'NAG': 1, 'VCG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.25, per 1000 atoms: 0.52 Number of scatterers: 27459 At special positions: 0 Unit cell: (156.4, 152.95, 177.1, 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 120 16.00 O 5460 8.00 N 4437 7.00 C 17442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=2.07 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG B1502 " - " ASN B 331 " " NAG C1502 " - " ASN C 331 " " NAG D 1 " - " ASN A 61 " " NAG E 1 " - " ASN A 616 " " NAG F 1 " - " ASN A 343 " " NAG G 1 " - " ASN A 709 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN A 122 " " NAG N 1 " - " ASN A 234 " " NAG O 1 " - " ASN A 282 " " NAG P 1 " - " ASN A 165 " " NAG Q 1 " - " ASN A 17 " " NAG R 1 " - " ASN A 149 " " NAG S 1 " - " ASN B 61 " " NAG T 1 " - " ASN B 616 " " NAG U 1 " - " ASN B 343 " " NAG V 1 " - " ASN B 709 " " NAG W 1 " - " ASN B 717 " " NAG X 1 " - " ASN B 801 " " NAG Y 1 " - " ASN B1074 " " NAG Z 1 " - " ASN B1098 " " NAG a 1 " - " ASN B1134 " " NAG b 1 " - " ASN B 122 " " NAG c 1 " - " ASN B 234 " " NAG d 1 " - " ASN B 282 " " NAG e 1 " - " ASN B 165 " " NAG f 1 " - " ASN B 17 " " NAG g 1 " - " ASN B 149 " " NAG h 1 " - " ASN C 61 " " NAG i 1 " - " ASN C 616 " " NAG j 1 " - " ASN C 343 " " NAG k 1 " - " ASN C 709 " " NAG l 1 " - " ASN C 717 " " NAG m 1 " - " ASN C 801 " " NAG n 1 " - " ASN C1074 " " NAG o 1 " - " ASN C1098 " " NAG p 1 " - " ASN C1134 " " NAG q 1 " - " ASN C 122 " " NAG r 1 " - " ASN C 234 " " NAG s 1 " - " ASN C 282 " " NAG t 1 " - " ASN C 165 " " NAG u 1 " - " ASN C 17 " " NAG v 1 " - " ASN C 149 " Time building additional restraints: 11.81 Conformation dependent library (CDL) restraints added in 5.0 seconds 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6210 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 42 sheets defined 22.0% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.44 Creating SS restraints... Processing helix chain 'A' and resid 295 through 302 Processing helix chain 'A' and resid 338 through 341 No H-bonds generated for 'chain 'A' and resid 338 through 341' Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 365 through 368 Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.599A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.616A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 740 through 743 No H-bonds generated for 'chain 'A' and resid 740 through 743' Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.686A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 Processing helix chain 'A' and resid 837 through 840 Processing helix chain 'A' and resid 843 through 846 Processing helix chain 'A' and resid 849 through 856 removed outlier: 3.577A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 883 Processing helix chain 'A' and resid 885 through 888 Processing helix chain 'A' and resid 898 through 909 Processing helix chain 'A' and resid 914 through 918 Processing helix chain 'A' and resid 920 through 940 Processing helix chain 'A' and resid 942 through 967 removed outlier: 4.254A pdb=" N LYS A 947 " --> pdb=" O ALA A 944 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP A 950 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 954 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 965 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 986 through 1032 removed outlier: 4.014A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1145 No H-bonds generated for 'chain 'A' and resid 1142 through 1145' Processing helix chain 'B' and resid 295 through 302 Processing helix chain 'B' and resid 338 through 341 No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 365 through 368 Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.599A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.616A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 740 through 743 No H-bonds generated for 'chain 'B' and resid 740 through 743' Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.686A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 825 Processing helix chain 'B' and resid 837 through 840 Processing helix chain 'B' and resid 843 through 846 Processing helix chain 'B' and resid 849 through 856 removed outlier: 3.576A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 883 Processing helix chain 'B' and resid 885 through 888 Processing helix chain 'B' and resid 898 through 909 Processing helix chain 'B' and resid 914 through 918 Processing helix chain 'B' and resid 920 through 940 Processing helix chain 'B' and resid 942 through 967 removed outlier: 4.254A pdb=" N LYS B 947 " --> pdb=" O ALA B 944 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP B 950 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 954 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 965 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 Processing helix chain 'B' and resid 986 through 1032 removed outlier: 4.015A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1145 No H-bonds generated for 'chain 'B' and resid 1142 through 1145' Processing helix chain 'C' and resid 295 through 302 Processing helix chain 'C' and resid 338 through 341 No H-bonds generated for 'chain 'C' and resid 338 through 341' Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 365 through 368 Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.599A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 4.616A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 740 through 743 No H-bonds generated for 'chain 'C' and resid 740 through 743' Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.686A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 825 Processing helix chain 'C' and resid 837 through 840 Processing helix chain 'C' and resid 843 through 846 Processing helix chain 'C' and resid 849 through 856 removed outlier: 3.577A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 883 Processing helix chain 'C' and resid 885 through 888 Processing helix chain 'C' and resid 898 through 909 Processing helix chain 'C' and resid 914 through 918 Processing helix chain 'C' and resid 920 through 940 Processing helix chain 'C' and resid 942 through 967 removed outlier: 4.254A pdb=" N LYS C 947 " --> pdb=" O ALA C 944 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 950 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 954 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN C 965 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 983 Processing helix chain 'C' and resid 986 through 1032 removed outlier: 4.015A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1145 No H-bonds generated for 'chain 'C' and resid 1142 through 1145' Processing sheet with id= A, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.711A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 47 through 56 removed outlier: 3.675A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 83 through 85 Processing sheet with id= D, first strand: chain 'A' and resid 243 through 247 removed outlier: 6.742A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.587A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 325 through 328 removed outlier: 8.304A pdb=" N ILE A 326 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN A 540 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ARG A 328 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASN A 542 " --> pdb=" O ARG A 328 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.323A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= I, first strand: chain 'A' and resid 670 through 675 Processing sheet with id= J, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.280A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 717 through 728 removed outlier: 5.900A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.507A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1087 through 1090 removed outlier: 3.560A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 132 through 135 removed outlier: 3.701A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.712A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 47 through 56 removed outlier: 3.675A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 83 through 85 Processing sheet with id= R, first strand: chain 'B' and resid 243 through 247 removed outlier: 6.741A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.587A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 325 through 328 removed outlier: 8.304A pdb=" N ILE B 326 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN B 540 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ARG B 328 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASN B 542 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.322A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= W, first strand: chain 'B' and resid 670 through 675 Processing sheet with id= X, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.280A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 717 through 728 removed outlier: 5.901A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.507A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 1087 through 1090 removed outlier: 3.560A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 132 through 135 removed outlier: 3.701A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.711A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 47 through 56 removed outlier: 3.674A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 83 through 85 Processing sheet with id= AF, first strand: chain 'C' and resid 243 through 247 removed outlier: 6.742A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.587A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 325 through 328 removed outlier: 8.304A pdb=" N ILE C 326 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASN C 540 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ARG C 328 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN C 542 " --> pdb=" O ARG C 328 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.322A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= AK, first strand: chain 'C' and resid 670 through 675 Processing sheet with id= AL, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.279A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 717 through 728 removed outlier: 5.900A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.508A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'C' and resid 1087 through 1090 removed outlier: 3.560A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'C' and resid 132 through 135 removed outlier: 3.701A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) 954 hydrogen bonds defined for protein. 2430 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.27 Time building geometry restraints manager: 12.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 5449 1.32 - 1.46: 10163 1.46 - 1.61: 12291 1.61 - 1.75: 30 1.75 - 1.90: 129 Bond restraints: 28062 Sorted by residual: bond pdb=" C29 VCG C1503 " pdb=" O31 VCG C1503 " ideal model delta sigma weight residual 1.281 1.395 -0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C29 VCG A1302 " pdb=" O31 VCG A1302 " ideal model delta sigma weight residual 1.281 1.395 -0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C29 VCG B1503 " pdb=" O31 VCG B1503 " ideal model delta sigma weight residual 1.281 1.394 -0.113 2.00e-02 2.50e+03 3.21e+01 bond pdb=" CG HIS C1048 " pdb=" ND1 HIS C1048 " ideal model delta sigma weight residual 1.378 1.324 0.054 1.10e-02 8.26e+03 2.42e+01 bond pdb=" CG HIS A1048 " pdb=" ND1 HIS A1048 " ideal model delta sigma weight residual 1.378 1.324 0.054 1.10e-02 8.26e+03 2.41e+01 ... (remaining 28057 not shown) Histogram of bond angle deviations from ideal: 94.90 - 107.79: 1993 107.79 - 120.68: 27255 120.68 - 133.57: 8871 133.57 - 146.47: 20 146.47 - 159.36: 3 Bond angle restraints: 38142 Sorted by residual: angle pdb=" C2 NAG A1301 " pdb=" N2 NAG A1301 " pdb=" C7 NAG A1301 " ideal model delta sigma weight residual 124.56 159.36 -34.80 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C2 NAG C1502 " pdb=" N2 NAG C1502 " pdb=" C7 NAG C1502 " ideal model delta sigma weight residual 124.56 159.34 -34.78 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C2 NAG B1502 " pdb=" N2 NAG B1502 " pdb=" C7 NAG B1502 " ideal model delta sigma weight residual 124.56 159.28 -34.72 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C08 VCG B1503 " pdb=" C09 VCG B1503 " pdb=" C10 VCG B1503 " ideal model delta sigma weight residual 152.67 119.98 32.69 3.00e+00 1.11e-01 1.19e+02 angle pdb=" C08 VCG C1503 " pdb=" C09 VCG C1503 " pdb=" C10 VCG C1503 " ideal model delta sigma weight residual 152.67 119.98 32.69 3.00e+00 1.11e-01 1.19e+02 ... (remaining 38137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.70: 17691 33.70 - 67.40: 189 67.40 - 101.10: 36 101.10 - 134.80: 3 134.80 - 168.50: 3 Dihedral angle restraints: 17922 sinusoidal: 8247 harmonic: 9675 Sorted by residual: dihedral pdb=" CB CYS C 840 " pdb=" SG CYS C 840 " pdb=" SG CYS C 851 " pdb=" CB CYS C 851 " ideal model delta sinusoidal sigma weight residual 93.00 150.80 -57.80 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual 93.00 150.80 -57.80 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual 93.00 150.80 -57.80 1 1.00e+01 1.00e-02 4.48e+01 ... (remaining 17919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 3108 0.106 - 0.212: 979 0.212 - 0.319: 296 0.319 - 0.425: 124 0.425 - 0.531: 56 Chirality restraints: 4563 Sorted by residual: chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.55e+02 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 -2.65 0.25 2.00e-02 2.50e+03 1.52e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.51e+02 ... (remaining 4560 not shown) Planarity restraints: 4863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 122 " -0.056 2.00e-02 2.50e+03 6.07e-02 4.60e+01 pdb=" CG ASN A 122 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 122 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 122 " 0.097 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 122 " -0.056 2.00e-02 2.50e+03 6.05e-02 4.58e+01 pdb=" CG ASN C 122 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN C 122 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C 122 " 0.097 2.00e-02 2.50e+03 pdb=" C1 NAG q 1 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 122 " 0.056 2.00e-02 2.50e+03 6.05e-02 4.57e+01 pdb=" CG ASN B 122 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN B 122 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 122 " -0.097 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " 0.073 2.00e-02 2.50e+03 ... (remaining 4860 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 11214 2.90 - 3.40: 24975 3.40 - 3.90: 45857 3.90 - 4.40: 53695 4.40 - 4.90: 85351 Nonbonded interactions: 221092 Sorted by model distance: nonbonded pdb=" OE2 GLU C 725 " pdb=" NZ LYS C1028 " model vdw 2.399 2.520 nonbonded pdb=" OE2 GLU A 725 " pdb=" NZ LYS A1028 " model vdw 2.399 2.520 nonbonded pdb=" OE2 GLU B 725 " pdb=" NZ LYS B1028 " model vdw 2.399 2.520 nonbonded pdb=" N PRO A 600 " pdb=" O PRO A 600 " model vdw 2.438 2.496 nonbonded pdb=" N PRO C 600 " pdb=" O PRO C 600 " model vdw 2.438 2.496 ... (remaining 221087 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 1146) selection = (chain 'B' and resid 14 through 1146) selection = (chain 'C' and resid 14 through 1146) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } 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: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.080 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 73.880 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.540 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 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 : 0.021 0.114 28062 Z= 1.352 Angle : 1.800 34.799 38142 Z= 1.168 Chirality : 0.134 0.531 4563 Planarity : 0.008 0.058 4815 Dihedral : 10.754 168.499 11577 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.21 % Allowed : 0.41 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.13), residues: 3309 helix: 0.11 (0.17), residues: 702 sheet: 1.16 (0.19), residues: 684 loop : 0.24 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.008 TRP A 353 HIS 0.006 0.002 HIS B 519 PHE 0.031 0.006 PHE A 888 TYR 0.073 0.008 TYR A 707 ARG 0.008 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 540 time to evaluate : 3.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.8444 (p) cc_final: 0.7908 (t) REVERT: A 216 LEU cc_start: 0.8299 (mt) cc_final: 0.7658 (tp) REVERT: A 312 ILE cc_start: 0.8858 (mm) cc_final: 0.8340 (tt) REVERT: A 523 THR cc_start: 0.8226 (p) cc_final: 0.7858 (t) REVERT: A 695 TYR cc_start: 0.8897 (p90) cc_final: 0.8661 (p90) REVERT: A 737 ASP cc_start: 0.8026 (t0) cc_final: 0.7817 (t0) REVERT: A 1037 SER cc_start: 0.8749 (t) cc_final: 0.8295 (m) REVERT: B 19 THR cc_start: 0.8305 (p) cc_final: 0.7842 (t) REVERT: B 46 SER cc_start: 0.9147 (m) cc_final: 0.8908 (t) REVERT: B 110 LEU cc_start: 0.8464 (mt) cc_final: 0.8234 (mp) REVERT: B 290 ASP cc_start: 0.7935 (t0) cc_final: 0.7631 (t0) REVERT: B 312 ILE cc_start: 0.8884 (mm) cc_final: 0.8486 (tt) REVERT: B 523 THR cc_start: 0.8228 (p) cc_final: 0.7876 (t) REVERT: B 707 TYR cc_start: 0.8307 (t80) cc_final: 0.7983 (t80) REVERT: B 900 MET cc_start: 0.8700 (mtt) cc_final: 0.8400 (mtp) REVERT: B 1037 SER cc_start: 0.8750 (t) cc_final: 0.8309 (m) REVERT: C 19 THR cc_start: 0.8339 (p) cc_final: 0.7835 (t) REVERT: C 46 SER cc_start: 0.9118 (m) cc_final: 0.8658 (t) REVERT: C 312 ILE cc_start: 0.8912 (mm) cc_final: 0.8503 (tt) REVERT: C 360 ASN cc_start: 0.8602 (m-40) cc_final: 0.8382 (m-40) REVERT: C 523 THR cc_start: 0.8253 (p) cc_final: 0.8049 (t) REVERT: C 737 ASP cc_start: 0.7898 (t0) cc_final: 0.7642 (t0) REVERT: C 740 MET cc_start: 0.8605 (mmm) cc_final: 0.7821 (tpp) REVERT: C 900 MET cc_start: 0.8944 (mtt) cc_final: 0.8712 (mtp) outliers start: 6 outliers final: 0 residues processed: 546 average time/residue: 0.4178 time to fit residues: 352.1502 Evaluate side-chains 197 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 3.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 0.7980 chunk 250 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 133 optimal weight: 6.9990 chunk 258 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 299 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN A 519 HIS A 544 ASN A 755 GLN A 784 GLN B 493 GLN B 519 HIS B 544 ASN B 606 ASN B 913 GLN B 957 GLN C 519 HIS C 544 ASN C 606 ASN C 955 ASN C 957 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28062 Z= 0.254 Angle : 0.680 11.677 38142 Z= 0.359 Chirality : 0.049 0.469 4563 Planarity : 0.004 0.030 4815 Dihedral : 8.183 112.672 5658 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.83 % Allowed : 5.33 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3309 helix: 1.67 (0.20), residues: 675 sheet: 1.05 (0.21), residues: 603 loop : 0.06 (0.12), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 152 HIS 0.004 0.001 HIS B1064 PHE 0.020 0.002 PHE B1095 TYR 0.041 0.002 TYR C 707 ARG 0.004 0.001 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 221 time to evaluate : 3.234 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 19 THR cc_start: 0.8349 (p) cc_final: 0.7876 (t) REVERT: A 312 ILE cc_start: 0.8855 (mm) cc_final: 0.8542 (tt) REVERT: A 974 SER cc_start: 0.9033 (t) cc_final: 0.8797 (m) REVERT: A 1037 SER cc_start: 0.8806 (t) cc_final: 0.8379 (m) REVERT: B 19 THR cc_start: 0.8187 (p) cc_final: 0.7819 (t) REVERT: B 46 SER cc_start: 0.9195 (m) cc_final: 0.8915 (t) REVERT: B 290 ASP cc_start: 0.8063 (t0) cc_final: 0.7711 (t70) REVERT: B 312 ILE cc_start: 0.8954 (mm) cc_final: 0.8652 (tt) REVERT: B 523 THR cc_start: 0.8078 (p) cc_final: 0.7699 (t) REVERT: B 568 ASP cc_start: 0.8194 (p0) cc_final: 0.7741 (p0) REVERT: B 646 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7374 (ttp80) REVERT: B 707 TYR cc_start: 0.8104 (t80) cc_final: 0.7660 (t80) REVERT: B 754 LEU cc_start: 0.8540 (tp) cc_final: 0.8330 (tp) REVERT: B 900 MET cc_start: 0.8166 (mtt) cc_final: 0.7796 (mtp) REVERT: B 974 SER cc_start: 0.9062 (t) cc_final: 0.8826 (m) REVERT: B 1037 SER cc_start: 0.8769 (t) cc_final: 0.8353 (m) REVERT: C 19 THR cc_start: 0.8330 (p) cc_final: 0.7938 (t) REVERT: C 46 SER cc_start: 0.9123 (m) cc_final: 0.8711 (t) REVERT: C 312 ILE cc_start: 0.8974 (mm) cc_final: 0.8749 (tt) REVERT: C 823 PHE cc_start: 0.7938 (t80) cc_final: 0.7600 (t80) REVERT: C 1037 SER cc_start: 0.8670 (OUTLIER) cc_final: 0.8455 (m) outliers start: 53 outliers final: 34 residues processed: 267 average time/residue: 0.4087 time to fit residues: 180.4252 Evaluate side-chains 204 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 168 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1042 PHE Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 204 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 300 optimal weight: 3.9990 chunk 324 optimal weight: 0.9990 chunk 267 optimal weight: 4.9990 chunk 297 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 240 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 207 HIS A 655 HIS A 784 GLN A 913 GLN B 115 GLN B 207 HIS B 498 GLN B 519 HIS B 606 ASN B 655 HIS B 926 GLN B1048 HIS C 115 GLN C 207 HIS C 519 HIS C 606 ASN C 655 HIS C 926 GLN C 955 ASN C1048 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 28062 Z= 0.342 Angle : 0.636 7.317 38142 Z= 0.335 Chirality : 0.048 0.422 4563 Planarity : 0.004 0.032 4815 Dihedral : 7.522 111.977 5658 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.99 % Favored : 97.98 % Rotamer: Outliers : 2.70 % Allowed : 6.22 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3309 helix: 1.60 (0.20), residues: 675 sheet: 0.57 (0.18), residues: 762 loop : -0.28 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 436 HIS 0.008 0.001 HIS A1064 PHE 0.026 0.002 PHE B 329 TYR 0.022 0.002 TYR A 495 ARG 0.005 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 180 time to evaluate : 3.050 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: A 19 THR cc_start: 0.8269 (p) cc_final: 0.7805 (t) REVERT: A 312 ILE cc_start: 0.8988 (mm) cc_final: 0.8657 (tt) REVERT: A 332 ILE cc_start: 0.9164 (mm) cc_final: 0.8946 (mp) REVERT: A 1037 SER cc_start: 0.9061 (t) cc_final: 0.8616 (m) REVERT: A 1043 CYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7591 (m) REVERT: B 19 THR cc_start: 0.8063 (p) cc_final: 0.7735 (t) REVERT: B 46 SER cc_start: 0.9167 (m) cc_final: 0.8955 (t) REVERT: B 568 ASP cc_start: 0.8277 (p0) cc_final: 0.7879 (p0) REVERT: B 614 ASP cc_start: 0.7629 (p0) cc_final: 0.7415 (p0) REVERT: B 646 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7839 (ttp80) REVERT: B 707 TYR cc_start: 0.8378 (t80) cc_final: 0.7972 (t80) REVERT: B 955 ASN cc_start: 0.8239 (m-40) cc_final: 0.8005 (m-40) REVERT: B 1037 SER cc_start: 0.9022 (t) cc_final: 0.8626 (m) REVERT: C 19 THR cc_start: 0.8293 (p) cc_final: 0.7923 (t) REVERT: C 46 SER cc_start: 0.9130 (m) cc_final: 0.8739 (t) REVERT: C 53 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7919 (m-30) REVERT: C 823 PHE cc_start: 0.7990 (t80) cc_final: 0.7721 (t80) REVERT: C 833 PHE cc_start: 0.7232 (m-80) cc_final: 0.7022 (m-80) REVERT: C 1037 SER cc_start: 0.9010 (t) cc_final: 0.8691 (m) REVERT: C 1043 CYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7850 (m) outliers start: 78 outliers final: 49 residues processed: 250 average time/residue: 0.3791 time to fit residues: 154.5693 Evaluate side-chains 183 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 130 time to evaluate : 3.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1042 PHE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 2.9990 chunk 225 optimal weight: 0.6980 chunk 155 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 301 optimal weight: 2.9990 chunk 318 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 285 optimal weight: 5.9990 chunk 85 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 HIS B 519 HIS B 955 ASN C 519 HIS C 606 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28062 Z= 0.182 Angle : 0.545 10.748 38142 Z= 0.284 Chirality : 0.045 0.420 4563 Planarity : 0.003 0.035 4815 Dihedral : 7.015 95.724 5658 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.35 % Allowed : 7.47 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.14), residues: 3309 helix: 1.67 (0.20), residues: 675 sheet: 0.32 (0.19), residues: 726 loop : -0.24 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.004 0.001 HIS C1048 PHE 0.018 0.001 PHE A 823 TYR 0.029 0.001 TYR C 248 ARG 0.004 0.000 ARG C 847 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 159 time to evaluate : 3.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.8194 (p) cc_final: 0.7755 (t) REVERT: A 312 ILE cc_start: 0.8953 (mm) cc_final: 0.8676 (tt) REVERT: A 697 MET cc_start: 0.8152 (mtp) cc_final: 0.7928 (ttm) REVERT: A 974 SER cc_start: 0.9223 (t) cc_final: 0.9018 (m) REVERT: A 1037 SER cc_start: 0.9019 (t) cc_final: 0.8603 (m) REVERT: A 1043 CYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7315 (m) REVERT: B 19 THR cc_start: 0.8095 (p) cc_final: 0.7697 (t) REVERT: B 46 SER cc_start: 0.9056 (m) cc_final: 0.8855 (t) REVERT: B 312 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8738 (tt) REVERT: B 568 ASP cc_start: 0.8274 (p0) cc_final: 0.7869 (p0) REVERT: B 646 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7874 (ttp80) REVERT: B 1037 SER cc_start: 0.8993 (t) cc_final: 0.8609 (m) REVERT: B 1042 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8201 (t80) REVERT: C 19 THR cc_start: 0.8167 (p) cc_final: 0.7816 (t) REVERT: C 46 SER cc_start: 0.9034 (m) cc_final: 0.8735 (t) REVERT: C 249 LEU cc_start: 0.8919 (mt) cc_final: 0.8692 (tt) REVERT: C 312 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8707 (tt) REVERT: C 823 PHE cc_start: 0.7955 (t80) cc_final: 0.7632 (t80) REVERT: C 1037 SER cc_start: 0.9017 (OUTLIER) cc_final: 0.8731 (m) REVERT: C 1043 CYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7861 (m) outliers start: 68 outliers final: 45 residues processed: 217 average time/residue: 0.3536 time to fit residues: 131.4375 Evaluate side-chains 189 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 137 time to evaluate : 3.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1042 PHE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 chunk 220 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 162 optimal weight: 5.9990 chunk 286 optimal weight: 3.9990 chunk 80 optimal weight: 0.0870 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 784 GLN A 804 GLN B 146 HIS B 519 HIS ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN C 146 HIS C 519 HIS C 606 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 28062 Z= 0.480 Angle : 0.684 11.281 38142 Z= 0.354 Chirality : 0.049 0.431 4563 Planarity : 0.004 0.037 4815 Dihedral : 7.270 95.517 5658 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.01 % Allowed : 7.92 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3309 helix: 1.36 (0.20), residues: 678 sheet: 0.20 (0.19), residues: 735 loop : -0.64 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 436 HIS 0.006 0.001 HIS B1064 PHE 0.027 0.002 PHE A 429 TYR 0.026 0.002 TYR B 495 ARG 0.005 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 152 time to evaluate : 3.453 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: A 19 THR cc_start: 0.8351 (p) cc_final: 0.7901 (t) REVERT: A 312 ILE cc_start: 0.8984 (mm) cc_final: 0.8679 (tt) REVERT: A 697 MET cc_start: 0.8433 (mtp) cc_final: 0.8161 (ttm) REVERT: A 1037 SER cc_start: 0.9192 (t) cc_final: 0.8789 (m) REVERT: A 1043 CYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7714 (m) REVERT: B 19 THR cc_start: 0.7985 (p) cc_final: 0.7649 (t) REVERT: B 312 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.8766 (tt) REVERT: B 646 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7983 (ttp80) REVERT: B 1037 SER cc_start: 0.9089 (t) cc_final: 0.8837 (m) REVERT: C 19 THR cc_start: 0.8297 (p) cc_final: 0.7937 (t) REVERT: C 46 SER cc_start: 0.9109 (m) cc_final: 0.8797 (t) REVERT: C 53 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: C 176 LEU cc_start: 0.8402 (tp) cc_final: 0.8132 (tp) REVERT: C 823 PHE cc_start: 0.8127 (t80) cc_final: 0.7902 (t80) REVERT: C 1043 CYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8045 (m) outliers start: 87 outliers final: 53 residues processed: 225 average time/residue: 0.3628 time to fit residues: 136.4585 Evaluate side-chains 178 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 120 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 0.6980 chunk 287 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 187 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 319 optimal weight: 0.9980 chunk 265 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 167 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN A 907 ASN A 913 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN C 519 HIS C 606 ASN C 804 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28062 Z= 0.186 Angle : 0.545 9.441 38142 Z= 0.282 Chirality : 0.045 0.408 4563 Planarity : 0.003 0.037 4815 Dihedral : 6.824 96.244 5658 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.39 % Allowed : 8.96 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.14), residues: 3309 helix: 1.61 (0.20), residues: 672 sheet: 0.06 (0.18), residues: 774 loop : -0.50 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.002 0.001 HIS A1048 PHE 0.020 0.001 PHE A 823 TYR 0.023 0.001 TYR C 248 ARG 0.011 0.000 ARG B 847 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 144 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.8258 (p) cc_final: 0.7834 (t) REVERT: A 312 ILE cc_start: 0.8959 (mm) cc_final: 0.8741 (tt) REVERT: A 697 MET cc_start: 0.8220 (mtp) cc_final: 0.7964 (ttm) REVERT: A 1037 SER cc_start: 0.9159 (t) cc_final: 0.8808 (m) REVERT: A 1043 CYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7800 (m) REVERT: B 19 THR cc_start: 0.8110 (p) cc_final: 0.7771 (t) REVERT: B 111 ASP cc_start: 0.7838 (t0) cc_final: 0.7616 (t0) REVERT: B 312 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8757 (tt) REVERT: B 646 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7992 (ttp80) REVERT: B 1037 SER cc_start: 0.8941 (t) cc_final: 0.8678 (m) REVERT: C 19 THR cc_start: 0.8171 (p) cc_final: 0.7831 (t) REVERT: C 312 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.8763 (tt) REVERT: C 779 GLN cc_start: 0.8314 (tt0) cc_final: 0.7985 (tt0) REVERT: C 823 PHE cc_start: 0.8030 (t80) cc_final: 0.7789 (t80) REVERT: C 1037 SER cc_start: 0.9118 (OUTLIER) cc_final: 0.8811 (m) REVERT: C 1043 CYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7560 (m) outliers start: 69 outliers final: 40 residues processed: 201 average time/residue: 0.3603 time to fit residues: 121.1841 Evaluate side-chains 170 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 124 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1042 PHE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 181 optimal weight: 0.5980 chunk 233 optimal weight: 7.9990 chunk 180 optimal weight: 0.7980 chunk 268 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 318 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28062 Z= 0.273 Angle : 0.559 8.823 38142 Z= 0.289 Chirality : 0.046 0.418 4563 Planarity : 0.004 0.038 4815 Dihedral : 6.749 96.552 5658 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.46 % Allowed : 9.16 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3309 helix: 1.59 (0.20), residues: 675 sheet: 0.14 (0.18), residues: 795 loop : -0.57 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS A1064 PHE 0.021 0.002 PHE A 823 TYR 0.027 0.001 TYR B 707 ARG 0.003 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 129 time to evaluate : 3.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.8259 (p) cc_final: 0.7851 (t) REVERT: A 312 ILE cc_start: 0.8987 (mm) cc_final: 0.8727 (tt) REVERT: A 697 MET cc_start: 0.8170 (mtp) cc_final: 0.7926 (ttm) REVERT: A 1037 SER cc_start: 0.9192 (t) cc_final: 0.8828 (m) REVERT: A 1043 CYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7847 (m) REVERT: B 19 THR cc_start: 0.8073 (p) cc_final: 0.7707 (t) REVERT: B 312 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.8784 (tt) REVERT: B 646 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8027 (ttp80) REVERT: B 1037 SER cc_start: 0.9002 (t) cc_final: 0.8706 (m) REVERT: B 1043 CYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7943 (m) REVERT: C 19 THR cc_start: 0.8154 (p) cc_final: 0.7843 (t) REVERT: C 312 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8784 (tt) REVERT: C 779 GLN cc_start: 0.8338 (tt0) cc_final: 0.8009 (tt0) REVERT: C 823 PHE cc_start: 0.8076 (t80) cc_final: 0.7795 (t80) REVERT: C 1037 SER cc_start: 0.9153 (t) cc_final: 0.8859 (m) REVERT: C 1043 CYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7729 (m) outliers start: 71 outliers final: 49 residues processed: 192 average time/residue: 0.3542 time to fit residues: 115.8627 Evaluate side-chains 177 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 122 time to evaluate : 3.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1042 PHE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 chunk 157 optimal weight: 0.0470 chunk 29 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28062 Z= 0.300 Angle : 0.567 8.141 38142 Z= 0.293 Chirality : 0.046 0.417 4563 Planarity : 0.004 0.038 4815 Dihedral : 6.700 96.896 5658 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.39 % Allowed : 9.44 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.14), residues: 3309 helix: 1.56 (0.20), residues: 672 sheet: 0.07 (0.18), residues: 771 loop : -0.59 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS A1064 PHE 0.022 0.002 PHE A 823 TYR 0.022 0.002 TYR C1138 ARG 0.003 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 127 time to evaluate : 3.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.8254 (p) cc_final: 0.7849 (t) REVERT: A 312 ILE cc_start: 0.9003 (mm) cc_final: 0.8712 (tt) REVERT: A 697 MET cc_start: 0.8216 (mtp) cc_final: 0.7945 (ttm) REVERT: A 1037 SER cc_start: 0.9199 (t) cc_final: 0.8826 (m) REVERT: A 1043 CYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7647 (m) REVERT: B 19 THR cc_start: 0.8013 (p) cc_final: 0.7656 (t) REVERT: B 312 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8781 (tt) REVERT: B 646 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8075 (ttp80) REVERT: B 1037 SER cc_start: 0.9012 (t) cc_final: 0.8726 (m) REVERT: B 1043 CYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7968 (m) REVERT: C 19 THR cc_start: 0.8152 (p) cc_final: 0.7849 (t) REVERT: C 312 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.8787 (tt) REVERT: C 571 ASP cc_start: 0.8837 (t0) cc_final: 0.8605 (t0) REVERT: C 779 GLN cc_start: 0.8362 (tt0) cc_final: 0.8029 (tt0) REVERT: C 823 PHE cc_start: 0.8090 (t80) cc_final: 0.7846 (t80) REVERT: C 1037 SER cc_start: 0.9171 (t) cc_final: 0.8904 (m) REVERT: C 1043 CYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7749 (m) outliers start: 69 outliers final: 52 residues processed: 192 average time/residue: 0.3417 time to fit residues: 110.3921 Evaluate side-chains 179 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 121 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1042 PHE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 0.8980 chunk 304 optimal weight: 0.8980 chunk 278 optimal weight: 0.0980 chunk 296 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 267 optimal weight: 0.1980 chunk 280 optimal weight: 3.9990 chunk 295 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 28062 Z= 0.153 Angle : 0.509 7.656 38142 Z= 0.263 Chirality : 0.044 0.383 4563 Planarity : 0.003 0.054 4815 Dihedral : 6.294 97.190 5658 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.94 % Allowed : 10.06 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3309 helix: 1.88 (0.21), residues: 660 sheet: 0.21 (0.18), residues: 795 loop : -0.48 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.002 0.000 HIS C1048 PHE 0.022 0.001 PHE A 823 TYR 0.029 0.001 TYR A 904 ARG 0.010 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 141 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.8080 (p) cc_final: 0.7728 (t) REVERT: A 312 ILE cc_start: 0.8964 (mm) cc_final: 0.8743 (tt) REVERT: A 572 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8478 (p) REVERT: A 1037 SER cc_start: 0.9134 (t) cc_final: 0.8845 (m) REVERT: B 19 THR cc_start: 0.8370 (p) cc_final: 0.8010 (t) REVERT: B 646 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8074 (ttp80) REVERT: B 1037 SER cc_start: 0.8982 (t) cc_final: 0.8713 (m) REVERT: C 19 THR cc_start: 0.8047 (p) cc_final: 0.7781 (t) REVERT: C 312 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.8846 (tt) REVERT: C 823 PHE cc_start: 0.8028 (t80) cc_final: 0.7788 (t80) REVERT: C 1037 SER cc_start: 0.9116 (t) cc_final: 0.8863 (m) REVERT: C 1043 CYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7598 (m) outliers start: 56 outliers final: 48 residues processed: 192 average time/residue: 0.3818 time to fit residues: 121.0191 Evaluate side-chains 176 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 124 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1042 PHE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 0.9980 chunk 313 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 328 optimal weight: 2.9990 chunk 302 optimal weight: 0.0980 chunk 261 optimal weight: 0.0040 chunk 27 optimal weight: 6.9990 chunk 202 optimal weight: 0.8980 chunk 160 optimal weight: 0.8980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28062 Z= 0.169 Angle : 0.506 7.716 38142 Z= 0.261 Chirality : 0.044 0.377 4563 Planarity : 0.003 0.038 4815 Dihedral : 6.138 97.894 5658 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.83 % Allowed : 10.51 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3309 helix: 1.75 (0.21), residues: 678 sheet: 0.24 (0.18), residues: 795 loop : -0.48 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.002 0.001 HIS C1048 PHE 0.023 0.001 PHE A 823 TYR 0.022 0.001 TYR C 707 ARG 0.011 0.000 ARG B 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 138 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.8055 (p) cc_final: 0.7717 (t) REVERT: A 312 ILE cc_start: 0.8953 (mm) cc_final: 0.8724 (tt) REVERT: A 1037 SER cc_start: 0.9150 (t) cc_final: 0.8773 (m) REVERT: A 1043 CYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7509 (m) REVERT: B 19 THR cc_start: 0.8334 (p) cc_final: 0.8006 (t) REVERT: B 646 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8071 (ttp80) REVERT: B 1037 SER cc_start: 0.8982 (t) cc_final: 0.8681 (m) REVERT: B 1043 CYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8017 (m) REVERT: C 19 THR cc_start: 0.7998 (p) cc_final: 0.7710 (t) REVERT: C 312 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8842 (tt) REVERT: C 823 PHE cc_start: 0.8010 (t80) cc_final: 0.7745 (t80) REVERT: C 1037 SER cc_start: 0.9114 (OUTLIER) cc_final: 0.8865 (m) REVERT: C 1043 CYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7618 (m) outliers start: 53 outliers final: 44 residues processed: 187 average time/residue: 0.3531 time to fit residues: 111.0171 Evaluate side-chains 177 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 127 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1042 PHE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 2.9990 chunk 278 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 241 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 262 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 269 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.110483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.090198 restraints weight = 45767.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.093785 restraints weight = 22793.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.096115 restraints weight = 14607.442| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28062 Z= 0.186 Angle : 0.511 7.686 38142 Z= 0.264 Chirality : 0.044 0.376 4563 Planarity : 0.003 0.039 4815 Dihedral : 6.072 98.414 5658 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.11 % Allowed : 10.44 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 3309 helix: 1.73 (0.21), residues: 678 sheet: 0.23 (0.18), residues: 795 loop : -0.50 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.002 0.001 HIS C1048 PHE 0.024 0.001 PHE A 823 TYR 0.022 0.001 TYR A 707 ARG 0.005 0.000 ARG A 847 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4516.37 seconds wall clock time: 85 minutes 15.72 seconds (5115.72 seconds total)