Starting phenix.real_space_refine on Tue Mar 19 16:28:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp1_11333/03_2024/6zp1_11333.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp1_11333/03_2024/6zp1_11333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp1_11333/03_2024/6zp1_11333.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp1_11333/03_2024/6zp1_11333.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp1_11333/03_2024/6zp1_11333.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp1_11333/03_2024/6zp1_11333.pdb" } resolution = 3.3 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= 0.005 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 108 5.16 5 C 15708 2.51 5 N 4029 2.21 5 O 4860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 442": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 467": "OD1" <-> "OD2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 578": "OD1" <-> "OD2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 614": "OD1" <-> "OD2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 765": "NH1" <-> "NH2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24705 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7941 Classifications: {'peptide': 1017} Link IDs: {'PTRANS': 49, 'TRANS': 967} Chain breaks: 7 Chain: "B" Number of atoms: 7941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7941 Classifications: {'peptide': 1017} Link IDs: {'PTRANS': 49, 'TRANS': 967} Chain breaks: 7 Chain: "C" Number of atoms: 7941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7941 Classifications: {'peptide': 1017} Link IDs: {'PTRANS': 49, 'TRANS': 967} Chain breaks: 7 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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 13.04, per 1000 atoms: 0.53 Number of scatterers: 24705 At special positions: 0 Unit cell: (133.686, 145.357, 162.333, 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 108 16.00 O 4860 8.00 N 4029 7.00 C 15708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.05 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1316 " - " ASN A1074 " " NAG A1321 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 709 " " NAG B1316 " - " ASN B1074 " " NAG B1321 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 657 " " NAG C1311 " - " ASN C 709 " " NAG C1316 " - " ASN C1074 " " NAG C1321 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Time building additional restraints: 8.63 Conformation dependent library (CDL) restraints added in 4.2 seconds 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 48 sheets defined 24.9% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.061A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.555A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.255A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.723A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.740A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.259A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.257A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.498A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.061A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.555A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.254A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.723A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.740A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.259A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.256A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.499A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.061A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.556A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.255A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.722A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.740A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.259A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.256A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.499A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.744A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.007A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.518A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.339A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.692A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.773A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.433A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.686A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.021A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.543A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.478A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.745A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.007A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.518A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.339A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.691A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.773A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.687A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.021A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.477A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.745A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.518A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.338A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.691A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.774A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.687A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.021A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.478A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1047 hydrogen bonds defined for protein. 2898 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: 10.69 Time building geometry restraints manager: 9.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 6274 1.33 - 1.47: 8002 1.47 - 1.60: 10831 1.60 - 1.74: 6 1.74 - 1.87: 129 Bond restraints: 25242 Sorted by residual: bond pdb=" CG1 ILE B 896 " pdb=" CD1 ILE B 896 " ideal model delta sigma weight residual 1.513 1.371 0.142 3.90e-02 6.57e+02 1.32e+01 bond pdb=" CG1 ILE C 896 " pdb=" CD1 ILE C 896 " ideal model delta sigma weight residual 1.513 1.371 0.142 3.90e-02 6.57e+02 1.32e+01 bond pdb=" CG1 ILE A 896 " pdb=" CD1 ILE A 896 " ideal model delta sigma weight residual 1.513 1.372 0.141 3.90e-02 6.57e+02 1.31e+01 bond pdb=" CA PHE B 106 " pdb=" CB PHE B 106 " ideal model delta sigma weight residual 1.533 1.591 -0.058 1.90e-02 2.77e+03 9.28e+00 bond pdb=" CG GLU B 990 " pdb=" CD GLU B 990 " ideal model delta sigma weight residual 1.516 1.440 0.076 2.50e-02 1.60e+03 9.27e+00 ... (remaining 25237 not shown) Histogram of bond angle deviations from ideal: 96.15 - 103.75: 321 103.75 - 111.35: 10433 111.35 - 118.94: 9923 118.94 - 126.54: 13373 126.54 - 134.14: 282 Bond angle restraints: 34332 Sorted by residual: angle pdb=" CA GLU C 990 " pdb=" CB GLU C 990 " pdb=" CG GLU C 990 " ideal model delta sigma weight residual 114.10 133.70 -19.60 2.00e+00 2.50e-01 9.60e+01 angle pdb=" CA GLU B 990 " pdb=" CB GLU B 990 " pdb=" CG GLU B 990 " ideal model delta sigma weight residual 114.10 133.67 -19.57 2.00e+00 2.50e-01 9.57e+01 angle pdb=" CA GLU A 990 " pdb=" CB GLU A 990 " pdb=" CG GLU A 990 " ideal model delta sigma weight residual 114.10 133.66 -19.56 2.00e+00 2.50e-01 9.57e+01 angle pdb=" C PHE A 429 " pdb=" CA PHE A 429 " pdb=" CB PHE A 429 " ideal model delta sigma weight residual 109.84 120.10 -10.26 1.50e+00 4.44e-01 4.68e+01 angle pdb=" C PHE C 429 " pdb=" CA PHE C 429 " pdb=" CB PHE C 429 " ideal model delta sigma weight residual 109.84 120.05 -10.21 1.50e+00 4.44e-01 4.64e+01 ... (remaining 34327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 14750 17.48 - 34.96: 757 34.96 - 52.45: 231 52.45 - 69.93: 81 69.93 - 87.41: 27 Dihedral angle restraints: 15846 sinusoidal: 6975 harmonic: 8871 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 173.60 -80.60 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 173.59 -80.59 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 173.54 -80.54 1 1.00e+01 1.00e-02 8.02e+01 ... (remaining 15843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 3699 0.121 - 0.242: 348 0.242 - 0.363: 15 0.363 - 0.484: 15 0.484 - 0.605: 3 Chirality restraints: 4080 Sorted by residual: chirality pdb=" CG LEU A 277 " pdb=" CB LEU A 277 " pdb=" CD1 LEU A 277 " pdb=" CD2 LEU A 277 " both_signs ideal model delta sigma weight residual False -2.59 -1.98 -0.60 2.00e-01 2.50e+01 9.15e+00 chirality pdb=" CG LEU C 277 " pdb=" CB LEU C 277 " pdb=" CD1 LEU C 277 " pdb=" CD2 LEU C 277 " both_signs ideal model delta sigma weight residual False -2.59 -1.99 -0.60 2.00e-01 2.50e+01 9.01e+00 chirality pdb=" CG LEU B 277 " pdb=" CB LEU B 277 " pdb=" CD1 LEU B 277 " pdb=" CD2 LEU B 277 " both_signs ideal model delta sigma weight residual False -2.59 -1.99 -0.60 2.00e-01 2.50e+01 8.99e+00 ... (remaining 4077 not shown) Planarity restraints: 4416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 986 " 0.040 2.00e-02 2.50e+03 7.79e-02 6.07e+01 pdb=" C PRO A 986 " -0.135 2.00e-02 2.50e+03 pdb=" O PRO A 986 " 0.048 2.00e-02 2.50e+03 pdb=" N PRO A 987 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 986 " -0.040 2.00e-02 2.50e+03 7.77e-02 6.04e+01 pdb=" C PRO C 986 " 0.135 2.00e-02 2.50e+03 pdb=" O PRO C 986 " -0.048 2.00e-02 2.50e+03 pdb=" N PRO C 987 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 986 " -0.040 2.00e-02 2.50e+03 7.76e-02 6.02e+01 pdb=" C PRO B 986 " 0.134 2.00e-02 2.50e+03 pdb=" O PRO B 986 " -0.048 2.00e-02 2.50e+03 pdb=" N PRO B 987 " -0.047 2.00e-02 2.50e+03 ... (remaining 4413 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2533 2.74 - 3.28: 24214 3.28 - 3.82: 40020 3.82 - 4.36: 48929 4.36 - 4.90: 83428 Nonbonded interactions: 199124 Sorted by model distance: nonbonded pdb=" OG SER A 813 " pdb=" OE2 GLU A 868 " model vdw 2.197 2.440 nonbonded pdb=" OG SER C 813 " pdb=" OE2 GLU C 868 " model vdw 2.197 2.440 nonbonded pdb=" OG SER B 813 " pdb=" OE2 GLU B 868 " model vdw 2.197 2.440 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.204 2.440 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.205 2.440 ... (remaining 199119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain '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' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 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: 4.990 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 65.550 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.270 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 : 0.011 0.142 25242 Z= 0.681 Angle : 1.287 19.597 34332 Z= 0.739 Chirality : 0.078 0.605 4080 Planarity : 0.008 0.086 4368 Dihedral : 12.573 87.411 10017 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.60 % Favored : 96.10 % Rotamer: Outliers : 0.34 % Allowed : 0.68 % Favored : 98.99 % Cbeta Deviations : 0.32 % 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: 0.13 (0.14), residues: 3003 helix: 0.66 (0.19), residues: 615 sheet: 0.91 (0.19), residues: 654 loop : -0.42 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP B 353 HIS 0.016 0.003 HIS C 519 PHE 0.126 0.006 PHE C 490 TYR 0.099 0.006 TYR B 495 ARG 0.030 0.002 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 248 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.9170 (tp) cc_final: 0.8942 (tt) REVERT: A 238 PHE cc_start: 0.7015 (p90) cc_final: 0.6763 (p90) REVERT: A 351 TYR cc_start: 0.8222 (p90) cc_final: 0.7786 (p90) REVERT: A 353 TRP cc_start: 0.8180 (p-90) cc_final: 0.7476 (p-90) REVERT: B 351 TYR cc_start: 0.8108 (p90) cc_final: 0.7706 (p90) REVERT: B 353 TRP cc_start: 0.8309 (p-90) cc_final: 0.7471 (p-90) REVERT: B 378 LYS cc_start: 0.8212 (tmmt) cc_final: 0.7596 (tmtt) REVERT: C 64 TRP cc_start: 0.7984 (t60) cc_final: 0.7630 (t60) REVERT: C 351 TYR cc_start: 0.8119 (p90) cc_final: 0.7727 (p90) REVERT: C 378 LYS cc_start: 0.8162 (tmmt) cc_final: 0.7722 (tmtt) outliers start: 9 outliers final: 3 residues processed: 249 average time/residue: 0.3232 time to fit residues: 133.1725 Evaluate side-chains 190 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 990 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 0.9980 chunk 229 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 154 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 237 optimal weight: 40.0000 chunk 91 optimal weight: 0.0870 chunk 144 optimal weight: 20.0000 chunk 176 optimal weight: 0.7980 chunk 275 optimal weight: 10.0000 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 66 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 66 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25242 Z= 0.192 Angle : 0.624 8.880 34332 Z= 0.330 Chirality : 0.049 0.370 4080 Planarity : 0.004 0.058 4368 Dihedral : 7.950 57.912 4590 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.03 % Favored : 97.87 % Rotamer: Outliers : 0.60 % Allowed : 4.43 % Favored : 94.96 % 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: 0.35 (0.14), residues: 3003 helix: 1.74 (0.21), residues: 669 sheet: 0.47 (0.18), residues: 684 loop : -0.48 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 104 HIS 0.003 0.001 HIS A 207 PHE 0.034 0.002 PHE B 429 TYR 0.021 0.002 TYR C 380 ARG 0.006 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 228 time to evaluate : 2.495 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 238 PHE cc_start: 0.6956 (p90) cc_final: 0.6668 (p90) REVERT: A 351 TYR cc_start: 0.8120 (p90) cc_final: 0.7837 (p90) REVERT: A 400 PHE cc_start: 0.9073 (p90) cc_final: 0.8781 (p90) REVERT: A 429 PHE cc_start: 0.8716 (t80) cc_final: 0.8261 (t80) REVERT: B 104 TRP cc_start: 0.7617 (m-90) cc_final: 0.7371 (m-90) REVERT: B 238 PHE cc_start: 0.7712 (p90) cc_final: 0.7264 (p90) REVERT: B 351 TYR cc_start: 0.7933 (p90) cc_final: 0.7704 (p90) REVERT: C 351 TYR cc_start: 0.7996 (p90) cc_final: 0.7750 (p90) outliers start: 16 outliers final: 6 residues processed: 232 average time/residue: 0.3174 time to fit residues: 123.4381 Evaluate side-chains 190 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 184 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 152 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 8.9990 chunk 187 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 275 optimal weight: 1.9990 chunk 297 optimal weight: 6.9990 chunk 245 optimal weight: 10.0000 chunk 273 optimal weight: 0.0980 chunk 93 optimal weight: 1.9990 chunk 221 optimal weight: 20.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25242 Z= 0.231 Angle : 0.577 9.336 34332 Z= 0.298 Chirality : 0.047 0.338 4080 Planarity : 0.004 0.049 4368 Dihedral : 6.907 58.123 4584 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.53 % Favored : 97.37 % Rotamer: Outliers : 0.86 % Allowed : 7.52 % Favored : 91.62 % 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: 0.31 (0.15), residues: 3003 helix: 1.80 (0.21), residues: 666 sheet: 0.23 (0.18), residues: 705 loop : -0.44 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 104 HIS 0.003 0.001 HIS B1064 PHE 0.030 0.001 PHE A 515 TYR 0.020 0.001 TYR A1138 ARG 0.003 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 200 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7102 (p90) cc_final: 0.6858 (p90) REVERT: A 351 TYR cc_start: 0.8143 (p90) cc_final: 0.7882 (p90) REVERT: A 400 PHE cc_start: 0.9036 (p90) cc_final: 0.8682 (p90) REVERT: A 429 PHE cc_start: 0.8638 (t80) cc_final: 0.8241 (t80) REVERT: B 104 TRP cc_start: 0.7698 (m-90) cc_final: 0.7419 (m-90) REVERT: B 238 PHE cc_start: 0.7724 (p90) cc_final: 0.6967 (p90) REVERT: B 351 TYR cc_start: 0.8069 (p90) cc_final: 0.7823 (p90) REVERT: B 436 TRP cc_start: 0.8587 (p90) cc_final: 0.8363 (p90) REVERT: C 351 TYR cc_start: 0.8055 (p90) cc_final: 0.7817 (p90) REVERT: C 453 TYR cc_start: 0.7465 (p90) cc_final: 0.7231 (p90) REVERT: C 495 TYR cc_start: 0.5288 (m-80) cc_final: 0.5019 (m-80) REVERT: C 572 THR cc_start: 0.9230 (p) cc_final: 0.8945 (t) outliers start: 23 outliers final: 10 residues processed: 213 average time/residue: 0.3138 time to fit residues: 112.0069 Evaluate side-chains 187 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 177 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 272 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 143 optimal weight: 50.0000 chunk 30 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 276 optimal weight: 2.9990 chunk 292 optimal weight: 1.9990 chunk 144 optimal weight: 30.0000 chunk 262 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 487 ASN A1002 GLN A1005 GLN B 487 ASN B1002 GLN B1005 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 957 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25242 Z= 0.256 Angle : 0.566 9.397 34332 Z= 0.291 Chirality : 0.047 0.319 4080 Planarity : 0.004 0.042 4368 Dihedral : 6.421 59.721 4584 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.73 % Allowed : 8.53 % Favored : 89.74 % 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: 0.28 (0.15), residues: 3003 helix: 1.78 (0.21), residues: 663 sheet: 0.29 (0.18), residues: 660 loop : -0.48 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 104 HIS 0.003 0.001 HIS C1048 PHE 0.025 0.001 PHE B 429 TYR 0.018 0.001 TYR A1067 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 191 time to evaluate : 2.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8183 (p90) cc_final: 0.7919 (p90) REVERT: A 429 PHE cc_start: 0.8710 (t80) cc_final: 0.8368 (t80) REVERT: B 104 TRP cc_start: 0.7814 (m-90) cc_final: 0.7594 (m-90) REVERT: B 351 TYR cc_start: 0.8098 (p90) cc_final: 0.7884 (p90) REVERT: B 436 TRP cc_start: 0.8567 (p90) cc_final: 0.8339 (p90) REVERT: B 515 PHE cc_start: 0.8277 (m-80) cc_final: 0.7999 (m-80) REVERT: B 964 LYS cc_start: 0.8795 (mmmm) cc_final: 0.8474 (ttmm) REVERT: C 351 TYR cc_start: 0.8055 (p90) cc_final: 0.7844 (p90) REVERT: C 453 TYR cc_start: 0.7515 (p90) cc_final: 0.7275 (p90) REVERT: C 495 TYR cc_start: 0.5400 (m-80) cc_final: 0.5047 (m-80) outliers start: 46 outliers final: 18 residues processed: 218 average time/residue: 0.3277 time to fit residues: 118.6119 Evaluate side-chains 196 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 178 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 243 optimal weight: 30.0000 chunk 166 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 218 optimal weight: 40.0000 chunk 120 optimal weight: 0.9980 chunk 249 optimal weight: 2.9990 chunk 202 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 262 optimal weight: 0.0050 chunk 73 optimal weight: 7.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1005 GLN B 87 ASN B1002 GLN B1005 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25242 Z= 0.194 Angle : 0.543 9.961 34332 Z= 0.279 Chirality : 0.046 0.313 4080 Planarity : 0.003 0.039 4368 Dihedral : 6.023 58.883 4581 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.39 % Allowed : 9.32 % Favored : 89.29 % 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: 0.31 (0.15), residues: 3003 helix: 2.01 (0.21), residues: 645 sheet: 0.23 (0.18), residues: 690 loop : -0.51 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 104 HIS 0.003 0.001 HIS C1048 PHE 0.021 0.001 PHE C 515 TYR 0.022 0.001 TYR B1138 ARG 0.004 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 192 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7208 (p90) cc_final: 0.6853 (p90) REVERT: A 351 TYR cc_start: 0.8224 (p90) cc_final: 0.7950 (p90) REVERT: A 429 PHE cc_start: 0.8663 (t80) cc_final: 0.8349 (t80) REVERT: A 964 LYS cc_start: 0.8721 (mmmm) cc_final: 0.8411 (mttp) REVERT: B 104 TRP cc_start: 0.7809 (m-90) cc_final: 0.7581 (m-90) REVERT: B 351 TYR cc_start: 0.8123 (p90) cc_final: 0.7919 (p90) REVERT: B 436 TRP cc_start: 0.8539 (p90) cc_final: 0.8300 (p90) REVERT: B 515 PHE cc_start: 0.8401 (m-80) cc_final: 0.8091 (m-80) REVERT: C 351 TYR cc_start: 0.8048 (p90) cc_final: 0.7838 (p90) REVERT: C 453 TYR cc_start: 0.7438 (p90) cc_final: 0.7208 (p90) REVERT: C 495 TYR cc_start: 0.5455 (m-80) cc_final: 0.5193 (m-80) outliers start: 37 outliers final: 17 residues processed: 216 average time/residue: 0.3183 time to fit residues: 115.2081 Evaluate side-chains 189 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 98 optimal weight: 0.8980 chunk 263 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 293 optimal weight: 0.7980 chunk 243 optimal weight: 40.0000 chunk 135 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 153 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1005 GLN C 196 ASN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25242 Z= 0.230 Angle : 0.548 9.663 34332 Z= 0.282 Chirality : 0.046 0.309 4080 Planarity : 0.004 0.036 4368 Dihedral : 5.856 59.179 4581 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.09 % Allowed : 9.85 % Favored : 89.06 % 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: 0.38 (0.15), residues: 3003 helix: 2.20 (0.21), residues: 627 sheet: 0.27 (0.18), residues: 681 loop : -0.48 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 104 HIS 0.003 0.001 HIS A1048 PHE 0.020 0.001 PHE C 515 TYR 0.019 0.001 TYR B 495 ARG 0.003 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 180 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7202 (p90) cc_final: 0.6811 (p90) REVERT: A 351 TYR cc_start: 0.8224 (p90) cc_final: 0.7948 (p90) REVERT: A 429 PHE cc_start: 0.8634 (t80) cc_final: 0.8334 (t80) REVERT: A 964 LYS cc_start: 0.8728 (mmmm) cc_final: 0.8415 (mttp) REVERT: B 104 TRP cc_start: 0.7824 (m-90) cc_final: 0.7607 (m-90) REVERT: B 351 TYR cc_start: 0.8140 (p90) cc_final: 0.7937 (p90) REVERT: B 436 TRP cc_start: 0.8519 (p90) cc_final: 0.8285 (p90) REVERT: C 453 TYR cc_start: 0.7437 (p90) cc_final: 0.7216 (p90) REVERT: C 495 TYR cc_start: 0.5479 (m-80) cc_final: 0.5239 (m-80) outliers start: 29 outliers final: 22 residues processed: 199 average time/residue: 0.3071 time to fit residues: 103.6695 Evaluate side-chains 193 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 171 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 282 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 214 optimal weight: 10.0000 chunk 165 optimal weight: 0.9980 chunk 246 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 292 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 901 GLN B1002 GLN B1005 GLN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25242 Z= 0.212 Angle : 0.540 9.452 34332 Z= 0.277 Chirality : 0.046 0.309 4080 Planarity : 0.004 0.038 4368 Dihedral : 5.675 55.557 4581 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.24 % Allowed : 10.26 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 3003 helix: 2.22 (0.21), residues: 627 sheet: 0.25 (0.18), residues: 663 loop : -0.50 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 104 HIS 0.003 0.001 HIS A1048 PHE 0.020 0.001 PHE C 515 TYR 0.025 0.001 TYR A1138 ARG 0.004 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 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: A 238 PHE cc_start: 0.7298 (p90) cc_final: 0.6889 (p90) REVERT: A 351 TYR cc_start: 0.8305 (p90) cc_final: 0.8053 (p90) REVERT: A 429 PHE cc_start: 0.8643 (t80) cc_final: 0.8329 (t80) REVERT: A 436 TRP cc_start: 0.8776 (p90) cc_final: 0.8514 (p90) REVERT: A 964 LYS cc_start: 0.8737 (mmmm) cc_final: 0.8438 (mttp) REVERT: B 52 GLN cc_start: 0.8896 (tt0) cc_final: 0.8478 (tm-30) REVERT: B 351 TYR cc_start: 0.8150 (p90) cc_final: 0.7946 (p90) REVERT: B 436 TRP cc_start: 0.8494 (p90) cc_final: 0.8052 (p90) REVERT: B 964 LYS cc_start: 0.8797 (mmmm) cc_final: 0.8495 (ttmm) REVERT: C 104 TRP cc_start: 0.7656 (m-90) cc_final: 0.7399 (m-90) REVERT: C 453 TYR cc_start: 0.7478 (p90) cc_final: 0.7264 (p90) outliers start: 33 outliers final: 22 residues processed: 205 average time/residue: 0.3253 time to fit residues: 111.4131 Evaluate side-chains 194 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 172 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 180 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 185 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 144 optimal weight: 30.0000 chunk 27 optimal weight: 0.9980 chunk 229 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1005 GLN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25242 Z= 0.228 Angle : 0.541 9.465 34332 Z= 0.277 Chirality : 0.046 0.307 4080 Planarity : 0.004 0.039 4368 Dihedral : 5.552 55.767 4581 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.01 % Allowed : 10.56 % Favored : 88.43 % 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: 0.37 (0.15), residues: 3003 helix: 2.22 (0.21), residues: 627 sheet: 0.26 (0.18), residues: 663 loop : -0.50 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 353 HIS 0.003 0.001 HIS C1048 PHE 0.019 0.001 PHE C 515 TYR 0.018 0.001 TYR B 495 ARG 0.003 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 174 time to evaluate : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7223 (p90) cc_final: 0.6804 (p90) REVERT: A 351 TYR cc_start: 0.8250 (p90) cc_final: 0.7849 (p90) REVERT: A 429 PHE cc_start: 0.8639 (t80) cc_final: 0.8339 (t80) REVERT: A 436 TRP cc_start: 0.8781 (p90) cc_final: 0.8529 (p90) REVERT: A 964 LYS cc_start: 0.8742 (mmmm) cc_final: 0.8442 (mttp) REVERT: B 52 GLN cc_start: 0.8870 (tt0) cc_final: 0.8459 (tm-30) REVERT: B 104 TRP cc_start: 0.7738 (m-90) cc_final: 0.7524 (m-90) REVERT: B 436 TRP cc_start: 0.8506 (p90) cc_final: 0.8042 (p90) REVERT: B 964 LYS cc_start: 0.8801 (mmmm) cc_final: 0.8502 (ttmm) REVERT: C 436 TRP cc_start: 0.8684 (p90) cc_final: 0.8480 (p90) outliers start: 27 outliers final: 23 residues processed: 192 average time/residue: 0.3212 time to fit residues: 103.7230 Evaluate side-chains 192 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 169 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 265 optimal weight: 0.9990 chunk 279 optimal weight: 0.9980 chunk 255 optimal weight: 3.9990 chunk 272 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 213 optimal weight: 30.0000 chunk 83 optimal weight: 4.9990 chunk 245 optimal weight: 50.0000 chunk 257 optimal weight: 1.9990 chunk 271 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1005 GLN B1135 ASN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25242 Z= 0.180 Angle : 0.530 9.473 34332 Z= 0.272 Chirality : 0.045 0.306 4080 Planarity : 0.003 0.040 4368 Dihedral : 5.419 55.558 4581 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.13 % Allowed : 10.60 % Favored : 88.28 % 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: 0.42 (0.15), residues: 3003 helix: 2.29 (0.21), residues: 627 sheet: 0.27 (0.18), residues: 669 loop : -0.47 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 353 HIS 0.003 0.001 HIS A1048 PHE 0.020 0.001 PHE A 133 TYR 0.023 0.001 TYR A1138 ARG 0.002 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7176 (p90) cc_final: 0.6759 (p90) REVERT: A 351 TYR cc_start: 0.8273 (p90) cc_final: 0.7898 (p90) REVERT: A 429 PHE cc_start: 0.8641 (t80) cc_final: 0.8341 (t80) REVERT: A 436 TRP cc_start: 0.8720 (p90) cc_final: 0.8457 (p90) REVERT: A 964 LYS cc_start: 0.8734 (mmmm) cc_final: 0.8440 (mttp) REVERT: B 52 GLN cc_start: 0.8873 (tt0) cc_final: 0.8459 (tm-30) REVERT: B 104 TRP cc_start: 0.7748 (m-90) cc_final: 0.7512 (m-90) REVERT: B 133 PHE cc_start: 0.6899 (OUTLIER) cc_final: 0.5565 (m-80) REVERT: B 436 TRP cc_start: 0.8478 (p90) cc_final: 0.8222 (p90) REVERT: B 964 LYS cc_start: 0.8777 (mmmm) cc_final: 0.8490 (ttmm) REVERT: B 990 GLU cc_start: 0.7919 (pm20) cc_final: 0.7582 (pm20) REVERT: C 133 PHE cc_start: 0.6998 (OUTLIER) cc_final: 0.5454 (m-80) REVERT: C 436 TRP cc_start: 0.8649 (p90) cc_final: 0.8442 (p90) REVERT: C 453 TYR cc_start: 0.8204 (p90) cc_final: 0.7786 (p90) REVERT: C 964 LYS cc_start: 0.8762 (mmmm) cc_final: 0.8477 (ttmm) outliers start: 30 outliers final: 23 residues processed: 198 average time/residue: 0.3319 time to fit residues: 109.7595 Evaluate side-chains 200 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 175 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 178 optimal weight: 3.9990 chunk 287 optimal weight: 3.9990 chunk 175 optimal weight: 0.0060 chunk 136 optimal weight: 40.0000 chunk 200 optimal weight: 0.0570 chunk 301 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 chunk 240 optimal weight: 30.0000 chunk 24 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 147 optimal weight: 0.3980 overall best weight: 1.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1002 GLN B1005 GLN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25242 Z= 0.191 Angle : 0.531 9.679 34332 Z= 0.272 Chirality : 0.045 0.303 4080 Planarity : 0.003 0.046 4368 Dihedral : 5.302 55.571 4581 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.94 % Allowed : 10.75 % Favored : 88.31 % 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: 0.46 (0.15), residues: 3003 helix: 2.32 (0.21), residues: 627 sheet: 0.35 (0.18), residues: 681 loop : -0.47 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 353 HIS 0.003 0.001 HIS C1048 PHE 0.017 0.001 PHE C 515 TYR 0.019 0.001 TYR B 495 ARG 0.004 0.000 ARG B 765 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 174 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7235 (p90) cc_final: 0.6813 (p90) REVERT: A 351 TYR cc_start: 0.8304 (p90) cc_final: 0.7937 (p90) REVERT: A 429 PHE cc_start: 0.8670 (t80) cc_final: 0.8374 (t80) REVERT: A 436 TRP cc_start: 0.8697 (p90) cc_final: 0.8364 (p90) REVERT: A 964 LYS cc_start: 0.8711 (mmmm) cc_final: 0.8407 (mttp) REVERT: B 52 GLN cc_start: 0.8867 (tt0) cc_final: 0.8459 (tm-30) REVERT: B 104 TRP cc_start: 0.7771 (m-90) cc_final: 0.7554 (m-90) REVERT: B 133 PHE cc_start: 0.6858 (OUTLIER) cc_final: 0.5614 (m-80) REVERT: B 428 ASP cc_start: 0.9129 (p0) cc_final: 0.8924 (p0) REVERT: B 436 TRP cc_start: 0.8465 (p90) cc_final: 0.8020 (p90) REVERT: B 964 LYS cc_start: 0.8783 (mmmm) cc_final: 0.8490 (ttmm) REVERT: C 133 PHE cc_start: 0.7094 (OUTLIER) cc_final: 0.5428 (m-80) REVERT: C 436 TRP cc_start: 0.8628 (p90) cc_final: 0.8422 (p90) REVERT: C 1138 TYR cc_start: 0.7882 (t80) cc_final: 0.7680 (t80) outliers start: 25 outliers final: 21 residues processed: 189 average time/residue: 0.3044 time to fit residues: 96.1759 Evaluate side-chains 194 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 171 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 190 optimal weight: 2.9990 chunk 256 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 221 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 240 optimal weight: 40.0000 chunk 100 optimal weight: 2.9990 chunk 247 optimal weight: 0.8980 chunk 30 optimal weight: 20.0000 chunk 44 optimal weight: 30.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1005 GLN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C 901 GLN C 957 GLN C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.132208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.078296 restraints weight = 48949.527| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.02 r_work: 0.2771 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 25242 Z= 0.313 Angle : 0.568 9.516 34332 Z= 0.290 Chirality : 0.046 0.296 4080 Planarity : 0.004 0.045 4368 Dihedral : 5.396 55.045 4581 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.09 % Allowed : 10.86 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 3003 helix: 2.17 (0.21), residues: 630 sheet: 0.30 (0.18), residues: 699 loop : -0.51 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 353 HIS 0.005 0.001 HIS C1048 PHE 0.026 0.001 PHE A 133 TYR 0.024 0.001 TYR A1138 ARG 0.003 0.000 ARG B 765 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4736.81 seconds wall clock time: 86 minutes 50.86 seconds (5210.86 seconds total)