Starting phenix.real_space_refine on Tue Feb 20 06:21:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbl_24982/02_2024/7sbl_24982_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbl_24982/02_2024/7sbl_24982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbl_24982/02_2024/7sbl_24982.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbl_24982/02_2024/7sbl_24982.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbl_24982/02_2024/7sbl_24982_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbl_24982/02_2024/7sbl_24982_neut.pdb" } resolution = 3.4 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= 0.003 sd= 0.044 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 117 5.16 5 C 17157 2.51 5 N 4385 2.21 5 O 5367 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 178": "OD1" <-> "OD2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1014": "NH1" <-> "NH2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 178": "OD1" <-> "OD2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C ARG 452": "NH1" <-> "NH2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 627": "OD1" <-> "OD2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 808": "OD1" <-> "OD2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 995": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27026 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 8615 Classifications: {'peptide': 1102} Link IDs: {'PTRANS': 52, 'TRANS': 1049} Chain breaks: 4 Chain: "B" Number of atoms: 8472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8472 Classifications: {'peptide': 1081} Link IDs: {'PTRANS': 52, 'TRANS': 1028} Chain breaks: 5 Chain: "C" Number of atoms: 8637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8637 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 53, 'TRANS': 1049} Chain breaks: 4 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 14.58, per 1000 atoms: 0.54 Number of scatterers: 27026 At special positions: 0 Unit cell: (146.037, 142.737, 216.168, 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 117 16.00 O 5367 8.00 N 4385 7.00 C 17157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.06 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 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=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.06 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.01 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.06 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG L 2 " - " MAN L 3 " " NAG R 2 " - " MAN R 3 " " NAG S 2 " - " MAN S 3 " " NAG T 2 " - " MAN T 3 " " NAG c 2 " - " MAN c 3 " " NAG d 2 " - " MAN d 3 " " NAG e 2 " - " MAN e 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Q 1 " - " FUC Q 3 " " NAG b 1 " - " FUC b 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 149 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 657 " " NAG A1408 " - " ASN A 709 " " NAG A1409 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 149 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 331 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 657 " " NAG B1408 " - " ASN B 709 " " NAG B1409 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 603 " " NAG C1405 " - " ASN C 657 " " NAG C1406 " - " ASN C 709 " " NAG C1407 " - " ASN C1158 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 616 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN A 343 " " NAG M 1 " - " ASN B 282 " " NAG N 1 " - " ASN B 616 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1074 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN B 343 " " NAG U 1 " - " ASN B 165 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 122 " " NAG X 1 " - " ASN C 234 " " NAG Y 1 " - " ASN C 282 " " NAG Z 1 " - " ASN C 616 " " NAG a 1 " - " ASN C 801 " " NAG b 1 " - " ASN C1074 " " NAG c 1 " - " ASN C1098 " " NAG d 1 " - " ASN C1134 " " NAG e 1 " - " ASN C 343 " " NAG f 1 " - " ASN C 165 " Time building additional restraints: 11.92 Conformation dependent library (CDL) restraints added in 5.1 seconds 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6150 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 46 sheets defined 27.6% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.36 Creating SS restraints... Processing helix chain 'A' and resid 180 through 185 removed outlier: 4.429A pdb=" N ASN A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.602A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.879A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 removed outlier: 3.642A pdb=" N ILE A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 411' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 737 through 744 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: 4.023A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.509A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.624A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.909A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.652A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 889 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.590A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.930A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 987 through 1033 removed outlier: 4.278A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 4.127A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A1161 " --> pdb=" O LYS A1157 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.139A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.376A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.017A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.503A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.784A pdb=" N TYR B 636 " --> pdb=" O TRP B 633 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 633 through 638' 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: 4.875A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.089A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.630A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.537A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.127A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1159 removed outlier: 3.884A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B1152 " --> pdb=" O PHE B1148 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.526A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.025A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.032A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.726A 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 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 634 through 639 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: 4.015A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.465A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.544A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.694A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.505A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.529A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.898A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 4.260A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C1152 " --> pdb=" O PHE C1148 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR C1155 " --> pdb=" O GLU C1151 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER C1161 " --> pdb=" O LYS C1157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.858A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.640A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.668A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.948A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.834A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.144A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.487A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.551A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.846A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.584A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.584A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.182A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.133A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.658A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 49 removed outlier: 7.472A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.480A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.299A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.169A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.974A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.875A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.568A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.498A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.083A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.907A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.254A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.484A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 31 removed outlier: 8.915A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.988A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.167A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.456A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.985A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.183A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.507A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.550A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.236A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.615A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 2973 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: 13.03 Time building geometry restraints manager: 12.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5129 1.32 - 1.45: 7299 1.45 - 1.58: 15042 1.58 - 1.71: 2 1.71 - 1.84: 147 Bond restraints: 27619 Sorted by residual: bond pdb=" CA ASN A 81 " pdb=" C ASN A 81 " ideal model delta sigma weight residual 1.524 1.586 -0.062 1.26e-02 6.30e+03 2.44e+01 bond pdb=" CA PRO A 25 " pdb=" C PRO A 25 " ideal model delta sigma weight residual 1.517 1.550 -0.033 6.70e-03 2.23e+04 2.43e+01 bond pdb=" C5 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.413 1.508 -0.095 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.508 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C5 NAG A1409 " pdb=" O5 NAG A1409 " ideal model delta sigma weight residual 1.413 1.501 -0.088 2.00e-02 2.50e+03 1.94e+01 ... (remaining 27614 not shown) Histogram of bond angle deviations from ideal: 96.66 - 104.52: 391 104.52 - 112.38: 12481 112.38 - 120.24: 13605 120.24 - 128.11: 10972 128.11 - 135.97: 113 Bond angle restraints: 37562 Sorted by residual: angle pdb=" N ASN A 17 " pdb=" CA ASN A 17 " pdb=" C ASN A 17 " ideal model delta sigma weight residual 110.24 122.99 -12.75 1.41e+00 5.03e-01 8.18e+01 angle pdb=" N ASN C 17 " pdb=" CA ASN C 17 " pdb=" C ASN C 17 " ideal model delta sigma weight residual 110.23 123.01 -12.78 1.45e+00 4.76e-01 7.77e+01 angle pdb=" N ASN B 17 " pdb=" CA ASN B 17 " pdb=" C ASN B 17 " ideal model delta sigma weight residual 110.23 122.93 -12.70 1.45e+00 4.76e-01 7.67e+01 angle pdb=" N VAL A 143 " pdb=" CA VAL A 143 " pdb=" C VAL A 143 " ideal model delta sigma weight residual 108.89 98.80 10.09 1.32e+00 5.74e-01 5.84e+01 angle pdb=" N ARG A 19 " pdb=" CA ARG A 19 " pdb=" C ARG A 19 " ideal model delta sigma weight residual 110.68 100.07 10.61 1.39e+00 5.18e-01 5.83e+01 ... (remaining 37557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.23: 16937 25.23 - 50.46: 565 50.46 - 75.69: 128 75.69 - 100.92: 31 100.92 - 126.15: 34 Dihedral angle restraints: 17695 sinusoidal: 8130 harmonic: 9565 Sorted by residual: dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual -86.00 -154.93 68.93 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" C ASN A 603 " pdb=" N ASN A 603 " pdb=" CA ASN A 603 " pdb=" CB ASN A 603 " ideal model delta harmonic sigma weight residual -122.60 -141.47 18.87 0 2.50e+00 1.60e-01 5.70e+01 dihedral pdb=" N ASN A 603 " pdb=" C ASN A 603 " pdb=" CA ASN A 603 " pdb=" CB ASN A 603 " ideal model delta harmonic sigma weight residual 122.80 140.63 -17.83 0 2.50e+00 1.60e-01 5.09e+01 ... (remaining 17692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.339: 4467 0.339 - 0.678: 32 0.678 - 1.016: 10 1.016 - 1.355: 6 1.355 - 1.694: 3 Chirality restraints: 4518 Sorted by residual: chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.44e+02 chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.05e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.33e+01 ... (remaining 4515 not shown) Planarity restraints: 4785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " -0.181 2.00e-02 2.50e+03 1.96e-01 4.78e+02 pdb=" CG ASN B 343 " 0.114 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " 0.300 2.00e-02 2.50e+03 pdb=" C1 NAG T 1 " -0.235 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " 0.181 2.00e-02 2.50e+03 1.95e-01 4.78e+02 pdb=" CG ASN A 343 " -0.114 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " -0.300 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " 0.235 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 165 " -0.101 2.00e-02 2.50e+03 1.37e-01 2.36e+02 pdb=" CG ASN B 165 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN B 165 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN B 165 " 0.237 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.160 2.00e-02 2.50e+03 ... (remaining 4782 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1027 2.74 - 3.28: 27152 3.28 - 3.82: 40951 3.82 - 4.36: 54890 4.36 - 4.90: 88246 Nonbonded interactions: 212266 Sorted by model distance: nonbonded pdb=" N GLN A 23 " pdb=" OE1 GLN A 23 " model vdw 2.197 2.520 nonbonded pdb=" N GLU B 281 " pdb=" OE1 GLU B 281 " model vdw 2.210 2.520 nonbonded pdb=" N GLU A 154 " pdb=" OE1 GLU A 154 " model vdw 2.220 2.520 nonbonded pdb=" CB GLN C 173 " pdb=" CD PRO C 174 " model vdw 2.238 3.840 nonbonded pdb=" CG2 THR C 33 " pdb=" CE1 PHE C 58 " model vdw 2.255 3.760 ... (remaining 212261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 828 or resid 854 through 1162 or resid 1401 thr \ ough 1407)) selection = (chain 'B' and (resid 14 through 623 or resid 636 through 1162 or resid 1401 thr \ ough 1407)) selection = (chain 'C' and (resid 14 through 623 or resid 636 through 828 or resid 854 throu \ gh 1162 or resid 1401 through 1407)) } ncs_group { reference = (chain 'D' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.530 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: 0.010 Extract box with map and model: 23.230 Check model and map are aligned: 0.440 Set scattering table: 0.310 Process input model: 77.670 Find NCS groups from input model: 2.380 Set up NCS constraints: 0.280 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:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 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 : 0.014 0.095 27619 Z= 0.932 Angle : 1.876 12.782 37562 Z= 1.235 Chirality : 0.132 1.694 4518 Planarity : 0.013 0.124 4731 Dihedral : 14.917 126.149 11416 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.81 % Favored : 91.46 % Rotamer: Outliers : 2.72 % Allowed : 4.43 % Favored : 92.84 % Cbeta Deviations : 0.62 % 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: -1.91 (0.13), residues: 3254 helix: -1.41 (0.16), residues: 736 sheet: 0.31 (0.21), residues: 580 loop : -1.78 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.122 0.021 TRP C 353 HIS 0.017 0.006 HIS C1083 PHE 0.107 0.015 PHE C 898 TYR 0.120 0.020 TYR C 489 ARG 0.013 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1065 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 987 time to evaluate : 3.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8848 (t) cc_final: 0.8557 (m) REVERT: A 114 THR cc_start: 0.7769 (p) cc_final: 0.7529 (p) REVERT: A 271 GLN cc_start: 0.7640 (mt0) cc_final: 0.7094 (mt0) REVERT: A 320 VAL cc_start: 0.9002 (t) cc_final: 0.8705 (m) REVERT: A 362 VAL cc_start: 0.7352 (t) cc_final: 0.6906 (t) REVERT: A 505 TYR cc_start: 0.5791 (t80) cc_final: 0.5577 (t80) REVERT: A 533 LEU cc_start: 0.8657 (tp) cc_final: 0.8268 (tt) REVERT: A 571 ASP cc_start: 0.7577 (t0) cc_final: 0.7242 (t0) REVERT: A 697 MET cc_start: 0.8406 (ptm) cc_final: 0.8142 (ptm) REVERT: A 737 ASP cc_start: 0.8018 (t0) cc_final: 0.7527 (t0) REVERT: A 740 MET cc_start: 0.8777 (ttt) cc_final: 0.8566 (ttm) REVERT: A 745 ASP cc_start: 0.7173 (m-30) cc_final: 0.6745 (m-30) REVERT: A 818 ILE cc_start: 0.9295 (mt) cc_final: 0.9054 (mt) REVERT: A 904 TYR cc_start: 0.7788 (m-80) cc_final: 0.7450 (m-80) REVERT: A 985 ASP cc_start: 0.7406 (p0) cc_final: 0.6998 (p0) REVERT: B 62 VAL cc_start: 0.8650 (m) cc_final: 0.8446 (t) REVERT: B 96 GLU cc_start: 0.5674 (OUTLIER) cc_final: 0.5206 (tp30) REVERT: B 128 ILE cc_start: 0.8248 (mt) cc_final: 0.7970 (mm) REVERT: B 178 ASP cc_start: 0.5843 (OUTLIER) cc_final: 0.4588 (m-30) REVERT: B 274 THR cc_start: 0.8850 (m) cc_final: 0.8141 (m) REVERT: B 329 PHE cc_start: 0.7814 (m-10) cc_final: 0.7557 (m-80) REVERT: B 396 TYR cc_start: 0.7707 (m-80) cc_final: 0.6898 (m-80) REVERT: B 696 THR cc_start: 0.9149 (m) cc_final: 0.8888 (p) REVERT: B 697 MET cc_start: 0.8427 (ptm) cc_final: 0.8089 (ptp) REVERT: B 808 ASP cc_start: 0.7841 (t0) cc_final: 0.7197 (t70) REVERT: B 824 ASN cc_start: 0.8664 (m-40) cc_final: 0.8442 (m-40) REVERT: B 976 VAL cc_start: 0.8993 (t) cc_final: 0.8451 (p) REVERT: B 979 ASP cc_start: 0.7563 (m-30) cc_final: 0.6971 (m-30) REVERT: C 46 SER cc_start: 0.9077 (m) cc_final: 0.8811 (p) REVERT: C 117 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.7021 (pp) REVERT: C 154 GLU cc_start: 0.5639 (OUTLIER) cc_final: 0.4950 (mp0) REVERT: C 179 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.5702 (tp) REVERT: C 186 PHE cc_start: 0.6022 (OUTLIER) cc_final: 0.5620 (m-80) REVERT: C 265 TYR cc_start: 0.6364 (p90) cc_final: 0.6100 (p90) REVERT: C 306 PHE cc_start: 0.8049 (m-80) cc_final: 0.7454 (m-80) REVERT: C 314 GLN cc_start: 0.8090 (tp40) cc_final: 0.7817 (tp40) REVERT: C 569 ILE cc_start: 0.8419 (mm) cc_final: 0.8018 (mt) REVERT: C 633 TRP cc_start: 0.7924 (p-90) cc_final: 0.7649 (p-90) REVERT: C 737 ASP cc_start: 0.8305 (t0) cc_final: 0.8069 (t0) REVERT: C 913 GLN cc_start: 0.8033 (pt0) cc_final: 0.7820 (pt0) REVERT: C 994 ASP cc_start: 0.7583 (t70) cc_final: 0.6941 (t0) REVERT: C 1023 ASN cc_start: 0.8182 (m-40) cc_final: 0.7883 (m110) outliers start: 78 outliers final: 22 residues processed: 1027 average time/residue: 0.4151 time to fit residues: 645.5037 Evaluate side-chains 747 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 719 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 515 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 276 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 167 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 257 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 156 optimal weight: 0.5980 chunk 191 optimal weight: 0.6980 chunk 297 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 207 HIS A 563 GLN A 658 ASN A 954 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 125 ASN B 207 HIS B 211 ASN B 271 GLN B 437 ASN B 544 ASN B 563 GLN B 804 GLN B 856 ASN B 960 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN C 196 ASN C 271 GLN C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN C 955 ASN C 957 GLN C 969 ASN C1002 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27619 Z= 0.268 Angle : 0.810 9.090 37562 Z= 0.414 Chirality : 0.052 0.552 4518 Planarity : 0.005 0.069 4731 Dihedral : 11.823 105.725 5561 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.74 % Rotamer: Outliers : 4.29 % Allowed : 12.77 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.14), residues: 3254 helix: 0.57 (0.19), residues: 767 sheet: 0.16 (0.19), residues: 690 loop : -1.62 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 436 HIS 0.012 0.001 HIS B 207 PHE 0.038 0.002 PHE A 175 TYR 0.029 0.002 TYR C 904 ARG 0.008 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 718 time to evaluate : 3.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8120 (m) cc_final: 0.7795 (p) REVERT: A 80 ASP cc_start: 0.6099 (OUTLIER) cc_final: 0.5241 (m-30) REVERT: A 271 GLN cc_start: 0.7331 (mt0) cc_final: 0.7047 (mt0) REVERT: A 320 VAL cc_start: 0.9063 (t) cc_final: 0.8682 (m) REVERT: A 384 PRO cc_start: 0.8137 (Cg_endo) cc_final: 0.7888 (Cg_exo) REVERT: A 571 ASP cc_start: 0.7605 (t0) cc_final: 0.7284 (t0) REVERT: A 591 SER cc_start: 0.9102 (t) cc_final: 0.8615 (p) REVERT: A 763 LEU cc_start: 0.9007 (mt) cc_final: 0.8686 (mp) REVERT: A 764 ASN cc_start: 0.8386 (m-40) cc_final: 0.8099 (m110) REVERT: A 985 ASP cc_start: 0.7518 (p0) cc_final: 0.6962 (p0) REVERT: A 988 GLU cc_start: 0.7984 (tp30) cc_final: 0.7764 (tp30) REVERT: A 1037 SER cc_start: 0.8949 (t) cc_final: 0.8528 (p) REVERT: B 96 GLU cc_start: 0.6271 (OUTLIER) cc_final: 0.4616 (tt0) REVERT: B 131 CYS cc_start: 0.2533 (OUTLIER) cc_final: 0.1571 (m) REVERT: B 178 ASP cc_start: 0.6164 (OUTLIER) cc_final: 0.5731 (m-30) REVERT: B 215 ASP cc_start: 0.6130 (OUTLIER) cc_final: 0.5817 (p0) REVERT: B 353 TRP cc_start: 0.7730 (p-90) cc_final: 0.7525 (p-90) REVERT: B 437 ASN cc_start: 0.7247 (OUTLIER) cc_final: 0.6976 (m-40) REVERT: B 517 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6914 (mp) REVERT: B 696 THR cc_start: 0.9160 (m) cc_final: 0.8869 (p) REVERT: B 697 MET cc_start: 0.8432 (ptm) cc_final: 0.8068 (ptp) REVERT: B 740 MET cc_start: 0.8432 (ttp) cc_final: 0.8158 (ttp) REVERT: B 765 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.8077 (ttm110) REVERT: B 820 ASP cc_start: 0.8422 (m-30) cc_final: 0.8159 (m-30) REVERT: B 824 ASN cc_start: 0.8744 (m-40) cc_final: 0.8422 (m-40) REVERT: C 117 LEU cc_start: 0.7304 (pp) cc_final: 0.7050 (pp) REVERT: C 377 PHE cc_start: 0.7648 (t80) cc_final: 0.7359 (t80) REVERT: C 387 LEU cc_start: 0.9188 (mm) cc_final: 0.8986 (mt) REVERT: C 451 TYR cc_start: 0.6181 (m-10) cc_final: 0.5969 (m-10) REVERT: C 569 ILE cc_start: 0.8326 (mm) cc_final: 0.8102 (mt) REVERT: C 604 THR cc_start: 0.8648 (m) cc_final: 0.8392 (t) REVERT: C 900 MET cc_start: 0.8410 (tpp) cc_final: 0.8178 (mtp) outliers start: 123 outliers final: 70 residues processed: 785 average time/residue: 0.3975 time to fit residues: 483.7976 Evaluate side-chains 684 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 607 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 165 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 298 optimal weight: 0.9980 chunk 322 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 295 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 935 GLN A 955 ASN A1119 ASN A1135 ASN B 474 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 955 ASN B1088 HIS C 271 GLN C 314 GLN C 317 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27619 Z= 0.318 Angle : 0.770 12.183 37562 Z= 0.386 Chirality : 0.049 0.389 4518 Planarity : 0.005 0.065 4731 Dihedral : 10.906 104.750 5544 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.99 % Favored : 93.85 % Rotamer: Outliers : 4.85 % Allowed : 14.45 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.14), residues: 3254 helix: 1.07 (0.19), residues: 773 sheet: 0.02 (0.19), residues: 698 loop : -1.66 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 436 HIS 0.032 0.002 HIS B 207 PHE 0.027 0.002 PHE C 168 TYR 0.032 0.002 TYR C 904 ARG 0.006 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 655 time to evaluate : 3.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8143 (m) cc_final: 0.7842 (p) REVERT: A 144 TYR cc_start: 0.3063 (m-10) cc_final: 0.2847 (m-10) REVERT: A 238 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7951 (p90) REVERT: A 271 GLN cc_start: 0.7472 (mt0) cc_final: 0.7241 (mt0) REVERT: A 320 VAL cc_start: 0.9119 (t) cc_final: 0.8802 (m) REVERT: A 591 SER cc_start: 0.9151 (t) cc_final: 0.8855 (p) REVERT: A 763 LEU cc_start: 0.9015 (mt) cc_final: 0.8751 (mp) REVERT: A 764 ASN cc_start: 0.8562 (m-40) cc_final: 0.8307 (m110) REVERT: A 918 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7418 (mp0) REVERT: A 1019 ARG cc_start: 0.8372 (ttm110) cc_final: 0.8083 (ttm170) REVERT: A 1037 SER cc_start: 0.9042 (t) cc_final: 0.8704 (p) REVERT: A 1138 TYR cc_start: 0.7917 (t80) cc_final: 0.7557 (t80) REVERT: B 96 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.4918 (tt0) REVERT: B 154 GLU cc_start: 0.4921 (OUTLIER) cc_final: 0.4221 (mp0) REVERT: B 178 ASP cc_start: 0.6251 (OUTLIER) cc_final: 0.5822 (m-30) REVERT: B 215 ASP cc_start: 0.6362 (OUTLIER) cc_final: 0.6081 (p0) REVERT: B 304 LYS cc_start: 0.8940 (mmtp) cc_final: 0.8715 (mmmm) REVERT: B 353 TRP cc_start: 0.7675 (p-90) cc_final: 0.7369 (p-90) REVERT: B 398 ASP cc_start: 0.6904 (m-30) cc_final: 0.5716 (m-30) REVERT: B 697 MET cc_start: 0.8346 (ptm) cc_final: 0.8061 (ptp) REVERT: B 824 ASN cc_start: 0.8734 (m-40) cc_final: 0.8431 (m-40) REVERT: B 935 GLN cc_start: 0.7525 (tm-30) cc_final: 0.7260 (tm-30) REVERT: C 317 ASN cc_start: 0.7736 (m110) cc_final: 0.7504 (m110) REVERT: C 377 PHE cc_start: 0.7743 (t80) cc_final: 0.7476 (t80) REVERT: C 569 ILE cc_start: 0.8406 (mm) cc_final: 0.8197 (mt) REVERT: C 604 THR cc_start: 0.8667 (m) cc_final: 0.8373 (t) REVERT: C 780 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8264 (mm-30) REVERT: C 900 MET cc_start: 0.8422 (tpp) cc_final: 0.8211 (mmm) REVERT: C 1041 ASP cc_start: 0.8070 (t0) cc_final: 0.7866 (t0) outliers start: 139 outliers final: 86 residues processed: 741 average time/residue: 0.3833 time to fit residues: 445.3504 Evaluate side-chains 692 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 601 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 294 optimal weight: 0.0270 chunk 224 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 299 optimal weight: 0.9980 chunk 317 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 658 ASN A 751 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1011 GLN A1135 ASN B 66 HIS B 388 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 957 GLN C 271 GLN C 314 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 901 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 27619 Z= 0.302 Angle : 0.748 11.912 37562 Z= 0.371 Chirality : 0.048 0.351 4518 Planarity : 0.004 0.064 4731 Dihedral : 10.377 104.609 5539 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.96 % Favored : 93.95 % Rotamer: Outliers : 4.68 % Allowed : 17.42 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.14), residues: 3254 helix: 1.31 (0.19), residues: 773 sheet: -0.01 (0.18), residues: 706 loop : -1.77 (0.13), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 436 HIS 0.005 0.001 HIS C 655 PHE 0.020 0.002 PHE C 194 TYR 0.025 0.002 TYR C 904 ARG 0.006 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 616 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8512 (p0) REVERT: A 271 GLN cc_start: 0.7549 (mt0) cc_final: 0.7279 (mt0) REVERT: A 294 ASP cc_start: 0.7796 (p0) cc_final: 0.7489 (p0) REVERT: A 320 VAL cc_start: 0.9136 (t) cc_final: 0.8796 (m) REVERT: A 591 SER cc_start: 0.9128 (t) cc_final: 0.8895 (p) REVERT: A 763 LEU cc_start: 0.8999 (mt) cc_final: 0.8751 (mp) REVERT: A 764 ASN cc_start: 0.8543 (m-40) cc_final: 0.8268 (m110) REVERT: A 1019 ARG cc_start: 0.8344 (ttm110) cc_final: 0.8117 (ttm110) REVERT: A 1037 SER cc_start: 0.9031 (t) cc_final: 0.8727 (p) REVERT: A 1138 TYR cc_start: 0.8046 (t80) cc_final: 0.7765 (t80) REVERT: B 96 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.5043 (tt0) REVERT: B 154 GLU cc_start: 0.4990 (OUTLIER) cc_final: 0.4221 (mp0) REVERT: B 178 ASP cc_start: 0.6213 (OUTLIER) cc_final: 0.5750 (m-30) REVERT: B 215 ASP cc_start: 0.6308 (OUTLIER) cc_final: 0.6015 (p0) REVERT: B 304 LYS cc_start: 0.8952 (mmtp) cc_final: 0.8747 (mmmm) REVERT: B 353 TRP cc_start: 0.7676 (p-90) cc_final: 0.7235 (p-90) REVERT: B 398 ASP cc_start: 0.6900 (m-30) cc_final: 0.5595 (m-30) REVERT: B 436 TRP cc_start: 0.7271 (p90) cc_final: 0.6653 (p90) REVERT: B 697 MET cc_start: 0.8315 (ptm) cc_final: 0.8016 (ptm) REVERT: B 725 GLU cc_start: 0.7916 (tt0) cc_final: 0.7511 (tt0) REVERT: B 824 ASN cc_start: 0.8745 (m-40) cc_final: 0.8449 (m-40) REVERT: B 870 ILE cc_start: 0.9023 (mm) cc_final: 0.8794 (mt) REVERT: B 935 GLN cc_start: 0.7560 (tm-30) cc_final: 0.7332 (tm-30) REVERT: C 154 GLU cc_start: 0.6215 (OUTLIER) cc_final: 0.4285 (mm-30) REVERT: C 377 PHE cc_start: 0.7805 (t80) cc_final: 0.7110 (t80) REVERT: C 780 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8214 (mm-30) outliers start: 134 outliers final: 98 residues processed: 701 average time/residue: 0.3908 time to fit residues: 429.4589 Evaluate side-chains 692 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 588 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 264 optimal weight: 0.0670 chunk 179 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 236 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 388 ASN B 437 ASN B 658 ASN C 271 GLN C 314 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 27619 Z= 0.402 Angle : 0.776 9.721 37562 Z= 0.386 Chirality : 0.049 0.481 4518 Planarity : 0.005 0.059 4731 Dihedral : 10.359 105.683 5537 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.70 % Favored : 93.24 % Rotamer: Outliers : 5.24 % Allowed : 18.18 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3254 helix: 1.20 (0.19), residues: 781 sheet: -0.16 (0.18), residues: 692 loop : -1.86 (0.13), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 436 HIS 0.007 0.001 HIS C 655 PHE 0.029 0.002 PHE A 429 TYR 0.026 0.002 TYR C 904 ARG 0.009 0.001 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 610 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8222 (m) cc_final: 0.7877 (p) REVERT: A 229 LEU cc_start: 0.8147 (pt) cc_final: 0.7918 (pp) REVERT: A 294 ASP cc_start: 0.7831 (p0) cc_final: 0.7603 (p0) REVERT: A 320 VAL cc_start: 0.9158 (t) cc_final: 0.8814 (m) REVERT: A 362 VAL cc_start: 0.6735 (OUTLIER) cc_final: 0.6452 (p) REVERT: A 591 SER cc_start: 0.9176 (t) cc_final: 0.8970 (p) REVERT: A 763 LEU cc_start: 0.9038 (mt) cc_final: 0.8794 (mp) REVERT: A 764 ASN cc_start: 0.8579 (m-40) cc_final: 0.8298 (m110) REVERT: A 823 PHE cc_start: 0.7727 (m-10) cc_final: 0.7483 (m-10) REVERT: A 1019 ARG cc_start: 0.8340 (ttm110) cc_final: 0.8059 (ttm170) REVERT: A 1037 SER cc_start: 0.9074 (t) cc_final: 0.8795 (p) REVERT: B 90 VAL cc_start: 0.8501 (p) cc_final: 0.8024 (m) REVERT: B 96 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.4434 (tt0) REVERT: B 121 ASN cc_start: 0.8124 (p0) cc_final: 0.7737 (p0) REVERT: B 154 GLU cc_start: 0.5404 (OUTLIER) cc_final: 0.4012 (mp0) REVERT: B 178 ASP cc_start: 0.6155 (OUTLIER) cc_final: 0.5572 (m-30) REVERT: B 215 ASP cc_start: 0.6198 (OUTLIER) cc_final: 0.5878 (p0) REVERT: B 258 TRP cc_start: 0.5729 (OUTLIER) cc_final: 0.5286 (m100) REVERT: B 303 LEU cc_start: 0.9005 (tp) cc_final: 0.8726 (tp) REVERT: B 353 TRP cc_start: 0.7784 (p-90) cc_final: 0.7539 (p-90) REVERT: B 357 ARG cc_start: 0.8078 (tmm-80) cc_final: 0.7853 (ttp80) REVERT: B 736 VAL cc_start: 0.8973 (t) cc_final: 0.8524 (m) REVERT: B 824 ASN cc_start: 0.8760 (m-40) cc_final: 0.8456 (m-40) REVERT: B 870 ILE cc_start: 0.9015 (mm) cc_final: 0.8794 (mt) REVERT: B 935 GLN cc_start: 0.7599 (tm-30) cc_final: 0.7358 (tm-30) REVERT: C 154 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.4438 (mm-30) REVERT: C 377 PHE cc_start: 0.7907 (t80) cc_final: 0.7347 (t80) REVERT: C 396 TYR cc_start: 0.7806 (m-80) cc_final: 0.7490 (m-80) REVERT: C 562 PHE cc_start: 0.7841 (p90) cc_final: 0.7289 (p90) REVERT: C 904 TYR cc_start: 0.8304 (m-80) cc_final: 0.7990 (m-10) outliers start: 150 outliers final: 117 residues processed: 703 average time/residue: 0.3815 time to fit residues: 421.0709 Evaluate side-chains 703 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 579 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 106 optimal weight: 0.7980 chunk 285 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 186 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 317 optimal weight: 0.9980 chunk 263 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 chunk 104 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 784 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 388 ASN B 544 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27619 Z= 0.233 Angle : 0.717 10.428 37562 Z= 0.351 Chirality : 0.046 0.379 4518 Planarity : 0.004 0.063 4731 Dihedral : 9.781 102.451 5537 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.65 % Favored : 94.25 % Rotamer: Outliers : 4.71 % Allowed : 19.86 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.86 (0.14), residues: 3254 helix: 1.41 (0.19), residues: 780 sheet: 0.04 (0.18), residues: 688 loop : -1.83 (0.13), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 436 HIS 0.004 0.001 HIS C 655 PHE 0.030 0.002 PHE A 133 TYR 0.026 0.001 TYR A 904 ARG 0.010 0.001 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 621 time to evaluate : 3.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8240 (m) cc_final: 0.7921 (p) REVERT: A 238 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7838 (p90) REVERT: A 294 ASP cc_start: 0.7742 (p0) cc_final: 0.7477 (p0) REVERT: A 320 VAL cc_start: 0.9134 (t) cc_final: 0.8781 (m) REVERT: A 763 LEU cc_start: 0.8989 (mt) cc_final: 0.8748 (mp) REVERT: A 764 ASN cc_start: 0.8525 (m-40) cc_final: 0.8256 (m110) REVERT: A 1019 ARG cc_start: 0.8219 (ttm110) cc_final: 0.7787 (ttm110) REVERT: A 1029 MET cc_start: 0.8786 (tpp) cc_final: 0.8332 (tpp) REVERT: A 1037 SER cc_start: 0.9051 (t) cc_final: 0.8758 (p) REVERT: A 1138 TYR cc_start: 0.8085 (t80) cc_final: 0.7845 (t80) REVERT: B 81 ASN cc_start: 0.7217 (t0) cc_final: 0.6992 (t0) REVERT: B 96 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.4434 (tt0) REVERT: B 121 ASN cc_start: 0.7996 (p0) cc_final: 0.7557 (p0) REVERT: B 154 GLU cc_start: 0.5215 (OUTLIER) cc_final: 0.3741 (mp0) REVERT: B 178 ASP cc_start: 0.6174 (OUTLIER) cc_final: 0.5585 (m-30) REVERT: B 215 ASP cc_start: 0.6140 (OUTLIER) cc_final: 0.5832 (p0) REVERT: B 258 TRP cc_start: 0.5811 (OUTLIER) cc_final: 0.5437 (m100) REVERT: B 313 TYR cc_start: 0.8496 (m-80) cc_final: 0.8211 (m-80) REVERT: B 398 ASP cc_start: 0.6880 (m-30) cc_final: 0.6562 (m-30) REVERT: B 599 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8728 (p) REVERT: B 773 GLU cc_start: 0.8028 (tt0) cc_final: 0.7825 (tt0) REVERT: B 824 ASN cc_start: 0.8676 (m-40) cc_final: 0.8359 (m-40) REVERT: B 870 ILE cc_start: 0.8998 (mm) cc_final: 0.8779 (mt) REVERT: B 935 GLN cc_start: 0.7614 (tm-30) cc_final: 0.7389 (tm-30) REVERT: B 990 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8080 (mm-30) REVERT: C 154 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.4217 (mm-30) REVERT: C 780 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8228 (mm-30) REVERT: C 1017 GLU cc_start: 0.8545 (tp30) cc_final: 0.8069 (tp30) outliers start: 135 outliers final: 99 residues processed: 704 average time/residue: 0.3889 time to fit residues: 430.0414 Evaluate side-chains 690 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 583 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 305 optimal weight: 0.3980 chunk 35 optimal weight: 0.4980 chunk 180 optimal weight: 0.9990 chunk 231 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 316 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 751 ASN A 955 ASN B 125 ASN B 388 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 955 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 27619 Z= 0.297 Angle : 0.737 9.645 37562 Z= 0.362 Chirality : 0.047 0.344 4518 Planarity : 0.004 0.065 4731 Dihedral : 9.529 102.109 5535 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.52 % Favored : 93.36 % Rotamer: Outliers : 5.27 % Allowed : 20.07 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.14), residues: 3254 helix: 1.39 (0.19), residues: 781 sheet: -0.01 (0.19), residues: 669 loop : -1.84 (0.13), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 436 HIS 0.004 0.001 HIS C1083 PHE 0.025 0.002 PHE A 592 TYR 0.025 0.002 TYR A 904 ARG 0.012 0.001 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 595 time to evaluate : 3.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7839 (p90) REVERT: A 294 ASP cc_start: 0.7746 (p0) cc_final: 0.7503 (p0) REVERT: A 320 VAL cc_start: 0.9189 (t) cc_final: 0.8824 (m) REVERT: A 763 LEU cc_start: 0.9018 (mt) cc_final: 0.8782 (mp) REVERT: A 764 ASN cc_start: 0.8562 (m-40) cc_final: 0.8269 (m110) REVERT: A 790 LYS cc_start: 0.8232 (mttm) cc_final: 0.8032 (mttm) REVERT: A 823 PHE cc_start: 0.7717 (m-10) cc_final: 0.7508 (m-10) REVERT: A 957 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8128 (tm-30) REVERT: A 1019 ARG cc_start: 0.8233 (ttm110) cc_final: 0.7803 (ttm110) REVERT: A 1029 MET cc_start: 0.8736 (tpp) cc_final: 0.8279 (tpp) REVERT: A 1037 SER cc_start: 0.9078 (t) cc_final: 0.8797 (p) REVERT: A 1138 TYR cc_start: 0.8169 (t80) cc_final: 0.7909 (t80) REVERT: B 96 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.4800 (tt0) REVERT: B 121 ASN cc_start: 0.8029 (p0) cc_final: 0.7711 (p0) REVERT: B 154 GLU cc_start: 0.5529 (OUTLIER) cc_final: 0.4893 (mp0) REVERT: B 178 ASP cc_start: 0.6098 (OUTLIER) cc_final: 0.5517 (m-30) REVERT: B 215 ASP cc_start: 0.6109 (OUTLIER) cc_final: 0.5803 (p0) REVERT: B 218 GLN cc_start: 0.8238 (tt0) cc_final: 0.7914 (mt0) REVERT: B 398 ASP cc_start: 0.6857 (m-30) cc_final: 0.6588 (m-30) REVERT: B 599 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8730 (p) REVERT: B 824 ASN cc_start: 0.8687 (m-40) cc_final: 0.8378 (m-40) REVERT: B 858 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8226 (mm) REVERT: B 870 ILE cc_start: 0.9000 (mm) cc_final: 0.8791 (mt) REVERT: B 935 GLN cc_start: 0.7648 (tm-30) cc_final: 0.7446 (tm-30) REVERT: C 16 VAL cc_start: 0.7924 (OUTLIER) cc_final: 0.7678 (p) REVERT: C 154 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.4206 (mm-30) REVERT: C 633 TRP cc_start: 0.8015 (p-90) cc_final: 0.7495 (p-90) REVERT: C 904 TYR cc_start: 0.8289 (m-10) cc_final: 0.8032 (m-10) REVERT: C 1017 GLU cc_start: 0.8549 (tp30) cc_final: 0.8067 (tp30) outliers start: 151 outliers final: 116 residues processed: 686 average time/residue: 0.3911 time to fit residues: 425.7764 Evaluate side-chains 707 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 582 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 195 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 200 optimal weight: 0.5980 chunk 215 optimal weight: 0.4980 chunk 156 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN A 955 ASN B 519 HIS ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 949 GLN B 955 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27619 Z= 0.240 Angle : 0.723 9.570 37562 Z= 0.352 Chirality : 0.046 0.317 4518 Planarity : 0.004 0.067 4731 Dihedral : 8.944 99.212 5533 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.93 % Favored : 93.98 % Rotamer: Outliers : 5.20 % Allowed : 20.28 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3254 helix: 1.46 (0.19), residues: 779 sheet: -0.01 (0.19), residues: 677 loop : -1.80 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 436 HIS 0.003 0.001 HIS B 49 PHE 0.023 0.002 PHE A 592 TYR 0.027 0.001 TYR A 904 ARG 0.010 0.001 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 608 time to evaluate : 3.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8202 (m) cc_final: 0.7887 (p) REVERT: A 238 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7807 (p90) REVERT: A 294 ASP cc_start: 0.7685 (p0) cc_final: 0.7459 (p0) REVERT: A 320 VAL cc_start: 0.9179 (t) cc_final: 0.8814 (m) REVERT: A 763 LEU cc_start: 0.8998 (mt) cc_final: 0.8763 (mp) REVERT: A 764 ASN cc_start: 0.8539 (m-40) cc_final: 0.8247 (m110) REVERT: A 957 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8365 (tm-30) REVERT: A 1019 ARG cc_start: 0.8221 (ttm110) cc_final: 0.7801 (ttm110) REVERT: A 1029 MET cc_start: 0.8758 (tpp) cc_final: 0.8320 (tpp) REVERT: A 1138 TYR cc_start: 0.8174 (t80) cc_final: 0.7917 (t80) REVERT: B 121 ASN cc_start: 0.8007 (p0) cc_final: 0.7549 (p0) REVERT: B 154 GLU cc_start: 0.5497 (OUTLIER) cc_final: 0.4410 (mp0) REVERT: B 178 ASP cc_start: 0.6041 (OUTLIER) cc_final: 0.5481 (m-30) REVERT: B 215 ASP cc_start: 0.6055 (OUTLIER) cc_final: 0.5730 (p0) REVERT: B 218 GLN cc_start: 0.8216 (tt0) cc_final: 0.7973 (mt0) REVERT: B 258 TRP cc_start: 0.6294 (OUTLIER) cc_final: 0.5951 (m100) REVERT: B 313 TYR cc_start: 0.8496 (m-80) cc_final: 0.8276 (m-80) REVERT: B 398 ASP cc_start: 0.6792 (m-30) cc_final: 0.6451 (m-30) REVERT: B 418 ILE cc_start: 0.8001 (mp) cc_final: 0.7787 (mm) REVERT: B 599 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8739 (p) REVERT: B 695 TYR cc_start: 0.8448 (p90) cc_final: 0.8108 (p90) REVERT: B 824 ASN cc_start: 0.8659 (m-40) cc_final: 0.8345 (m-40) REVERT: B 858 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8195 (mm) REVERT: B 870 ILE cc_start: 0.9007 (mm) cc_final: 0.8787 (mt) REVERT: C 16 VAL cc_start: 0.7866 (OUTLIER) cc_final: 0.7634 (p) REVERT: C 154 GLU cc_start: 0.5777 (OUTLIER) cc_final: 0.3509 (mm-30) REVERT: C 633 TRP cc_start: 0.7993 (p-90) cc_final: 0.7480 (p-90) REVERT: C 904 TYR cc_start: 0.8252 (m-10) cc_final: 0.7996 (m-10) REVERT: C 1017 GLU cc_start: 0.8538 (tp30) cc_final: 0.8073 (tp30) outliers start: 149 outliers final: 119 residues processed: 698 average time/residue: 0.3923 time to fit residues: 428.6541 Evaluate side-chains 718 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 590 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 287 optimal weight: 0.7980 chunk 302 optimal weight: 0.9980 chunk 276 optimal weight: 0.9980 chunk 294 optimal weight: 0.8980 chunk 177 optimal weight: 0.0030 chunk 128 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 266 optimal weight: 0.6980 chunk 278 optimal weight: 2.9990 chunk 293 optimal weight: 0.7980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN B 81 ASN B 388 ASN B 519 HIS ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 907 ASN B 949 GLN B 955 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 901 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27619 Z= 0.226 Angle : 0.726 9.528 37562 Z= 0.353 Chirality : 0.046 0.309 4518 Planarity : 0.004 0.070 4731 Dihedral : 8.435 97.240 5533 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.18 % Favored : 93.70 % Rotamer: Outliers : 4.82 % Allowed : 21.40 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.79 (0.14), residues: 3254 helix: 1.51 (0.19), residues: 775 sheet: 0.02 (0.19), residues: 678 loop : -1.76 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 64 HIS 0.006 0.001 HIS B 519 PHE 0.025 0.002 PHE C 347 TYR 0.039 0.001 TYR A 904 ARG 0.008 0.001 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 613 time to evaluate : 2.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8227 (m) cc_final: 0.7883 (p) REVERT: A 238 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7825 (p90) REVERT: A 294 ASP cc_start: 0.7671 (p0) cc_final: 0.7460 (p0) REVERT: A 320 VAL cc_start: 0.9165 (t) cc_final: 0.8784 (m) REVERT: A 763 LEU cc_start: 0.8983 (mt) cc_final: 0.8746 (mp) REVERT: A 764 ASN cc_start: 0.8519 (m-40) cc_final: 0.8235 (m110) REVERT: A 1019 ARG cc_start: 0.8213 (ttm110) cc_final: 0.7832 (ttm110) REVERT: A 1029 MET cc_start: 0.8751 (tpp) cc_final: 0.8311 (tpp) REVERT: A 1138 TYR cc_start: 0.8147 (t80) cc_final: 0.7914 (t80) REVERT: B 121 ASN cc_start: 0.8018 (p0) cc_final: 0.7545 (p0) REVERT: B 154 GLU cc_start: 0.5398 (OUTLIER) cc_final: 0.4416 (mp0) REVERT: B 178 ASP cc_start: 0.5933 (OUTLIER) cc_final: 0.5364 (m-30) REVERT: B 215 ASP cc_start: 0.6143 (OUTLIER) cc_final: 0.4974 (p0) REVERT: B 218 GLN cc_start: 0.8213 (tt0) cc_final: 0.7943 (mt0) REVERT: B 258 TRP cc_start: 0.6328 (OUTLIER) cc_final: 0.6017 (m100) REVERT: B 313 TYR cc_start: 0.8480 (m-80) cc_final: 0.8215 (m-80) REVERT: B 398 ASP cc_start: 0.6756 (m-30) cc_final: 0.6507 (m-30) REVERT: B 418 ILE cc_start: 0.7981 (mp) cc_final: 0.7716 (mm) REVERT: B 599 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8743 (p) REVERT: B 695 TYR cc_start: 0.8429 (p90) cc_final: 0.8104 (p90) REVERT: B 824 ASN cc_start: 0.8608 (m-40) cc_final: 0.8306 (m-40) REVERT: B 858 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8173 (mm) REVERT: B 870 ILE cc_start: 0.9001 (mm) cc_final: 0.8782 (mt) REVERT: B 933 LYS cc_start: 0.7992 (mmmm) cc_final: 0.7780 (mtpp) REVERT: C 16 VAL cc_start: 0.7879 (OUTLIER) cc_final: 0.7631 (p) REVERT: C 154 GLU cc_start: 0.6023 (OUTLIER) cc_final: 0.4530 (mp0) REVERT: C 298 GLU cc_start: 0.7873 (tt0) cc_final: 0.7454 (tt0) REVERT: C 457 ARG cc_start: 0.6896 (OUTLIER) cc_final: 0.6671 (mmm160) REVERT: C 633 TRP cc_start: 0.7976 (p-90) cc_final: 0.7378 (p-90) REVERT: C 901 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: C 1017 GLU cc_start: 0.8523 (tp30) cc_final: 0.8085 (tp30) outliers start: 138 outliers final: 113 residues processed: 696 average time/residue: 0.3956 time to fit residues: 434.2914 Evaluate side-chains 715 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 591 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 193 optimal weight: 0.1980 chunk 311 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 147 optimal weight: 0.0970 chunk 216 optimal weight: 0.9990 chunk 326 optimal weight: 0.6980 chunk 300 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 81 ASN B 271 GLN B 519 HIS ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 907 ASN B 955 ASN C 99 ASN C 271 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 901 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27619 Z= 0.221 Angle : 0.739 11.524 37562 Z= 0.359 Chirality : 0.047 0.736 4518 Planarity : 0.004 0.068 4731 Dihedral : 7.796 95.451 5530 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.84 % Favored : 94.04 % Rotamer: Outliers : 4.61 % Allowed : 21.99 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3254 helix: 1.58 (0.19), residues: 770 sheet: 0.03 (0.19), residues: 679 loop : -1.72 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 436 HIS 0.010 0.001 HIS B 519 PHE 0.031 0.002 PHE C 497 TYR 0.038 0.001 TYR A 904 ARG 0.007 0.001 ARG A 995 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 618 time to evaluate : 3.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7818 (p90) REVERT: A 763 LEU cc_start: 0.8971 (mt) cc_final: 0.8733 (mp) REVERT: A 764 ASN cc_start: 0.8516 (m-40) cc_final: 0.8234 (m110) REVERT: A 1019 ARG cc_start: 0.8213 (ttm110) cc_final: 0.7831 (ttm110) REVERT: A 1029 MET cc_start: 0.8733 (tpp) cc_final: 0.8267 (tpp) REVERT: A 1138 TYR cc_start: 0.8175 (t80) cc_final: 0.7929 (t80) REVERT: B 154 GLU cc_start: 0.5311 (OUTLIER) cc_final: 0.4145 (mp0) REVERT: B 178 ASP cc_start: 0.5975 (OUTLIER) cc_final: 0.5375 (m-30) REVERT: B 215 ASP cc_start: 0.6160 (OUTLIER) cc_final: 0.4984 (p0) REVERT: B 218 GLN cc_start: 0.8201 (tt0) cc_final: 0.7960 (mt0) REVERT: B 258 TRP cc_start: 0.6290 (OUTLIER) cc_final: 0.5988 (m100) REVERT: B 313 TYR cc_start: 0.8488 (m-80) cc_final: 0.8181 (m-80) REVERT: B 398 ASP cc_start: 0.6695 (m-30) cc_final: 0.6461 (m-30) REVERT: B 417 LYS cc_start: 0.7063 (tptm) cc_final: 0.6836 (tptp) REVERT: B 599 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8743 (p) REVERT: B 824 ASN cc_start: 0.8610 (m-40) cc_final: 0.8310 (m-40) REVERT: B 858 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8170 (mm) REVERT: B 870 ILE cc_start: 0.9006 (mm) cc_final: 0.8775 (mt) REVERT: B 933 LYS cc_start: 0.7968 (mmmm) cc_final: 0.7754 (mtpp) REVERT: C 16 VAL cc_start: 0.7873 (OUTLIER) cc_final: 0.7630 (p) REVERT: C 154 GLU cc_start: 0.5776 (OUTLIER) cc_final: 0.4947 (mp0) REVERT: C 633 TRP cc_start: 0.7950 (p-90) cc_final: 0.7392 (p-90) REVERT: C 1017 GLU cc_start: 0.8515 (tp30) cc_final: 0.8074 (tp30) outliers start: 132 outliers final: 111 residues processed: 697 average time/residue: 0.3997 time to fit residues: 442.4164 Evaluate side-chains 724 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 604 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 206 optimal weight: 1.9990 chunk 277 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 239 optimal weight: 3.9990 chunk 38 optimal weight: 0.0870 chunk 72 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 32 optimal weight: 0.0270 chunk 48 optimal weight: 0.1980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN A 856 ASN A 955 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 901 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.097827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.078142 restraints weight = 69656.924| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.86 r_work: 0.3075 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27619 Z= 0.208 Angle : 0.737 12.809 37562 Z= 0.359 Chirality : 0.047 0.675 4518 Planarity : 0.004 0.068 4731 Dihedral : 7.399 94.060 5530 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.13 % Rotamer: Outliers : 4.22 % Allowed : 23.11 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.70 (0.14), residues: 3254 helix: 1.64 (0.19), residues: 763 sheet: 0.10 (0.19), residues: 675 loop : -1.70 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 886 HIS 0.024 0.001 HIS B 519 PHE 0.029 0.001 PHE C 497 TYR 0.035 0.002 TYR A 904 ARG 0.012 0.001 ARG B 765 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8755.93 seconds wall clock time: 158 minutes 16.90 seconds (9496.90 seconds total)