Starting phenix.real_space_refine on Sun Mar 24 10:53:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj7_25156/03_2024/7sj7_25156.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj7_25156/03_2024/7sj7_25156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj7_25156/03_2024/7sj7_25156.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj7_25156/03_2024/7sj7_25156.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj7_25156/03_2024/7sj7_25156.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj7_25156/03_2024/7sj7_25156.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.425 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: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 6 5.21 5 S 282 5.16 5 C 25802 2.51 5 N 7026 2.21 5 O 7910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 160": "OD1" <-> "OD2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 160": "OD1" <-> "OD2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "C PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 160": "OD1" <-> "OD2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 390": "NH1" <-> "NH2" Residue "E PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 160": "OD1" <-> "OD2" Residue "J TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 390": "NH1" <-> "NH2" Residue "J PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 160": "OD1" <-> "OD2" Residue "K TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 390": "NH1" <-> "NH2" Residue "K PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 160": "OD1" <-> "OD2" Residue "L TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 390": "NH1" <-> "NH2" Residue "L PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 359": "NH1" <-> "NH2" Residue "F PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 41056 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3418 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Chain: "C" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.89, per 1000 atoms: 0.48 Number of scatterers: 41056 At special positions: 0 Unit cell: (170.2, 103.96, 211.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 282 16.00 P 30 15.00 Mg 6 11.99 O 7910 8.00 N 7026 7.00 C 25802 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 16.41 Conformation dependent library (CDL) restraints added in 7.0 seconds 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9624 Finding SS restraints... Secondary structure from input PDB file: 222 helices and 36 sheets defined 53.2% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.45 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.660A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.669A pdb=" N ILE A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.734A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.652A pdb=" N VAL A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.878A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.040A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.611A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 48 through 51 Processing helix chain 'C' and resid 71 through 81 removed outlier: 4.660A pdb=" N ILE C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 114 through 128 Processing helix chain 'C' and resid 143 through 161 Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 205 through 216 removed outlier: 3.668A pdb=" N ILE C 209 " --> pdb=" O ASP C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 244 removed outlier: 3.734A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.652A pdb=" N VAL C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 297 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 Processing helix chain 'C' and resid 383 through 401 removed outlier: 3.878A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 4.040A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.612A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 48 through 51 Processing helix chain 'E' and resid 71 through 81 removed outlier: 4.660A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 110 through 113 Processing helix chain 'E' and resid 114 through 128 Processing helix chain 'E' and resid 143 through 161 Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 205 through 216 removed outlier: 3.668A pdb=" N ILE E 209 " --> pdb=" O ASP E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.735A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 removed outlier: 3.651A pdb=" N VAL E 260 " --> pdb=" O GLN E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 297 Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 Processing helix chain 'E' and resid 383 through 401 removed outlier: 3.878A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 removed outlier: 4.040A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 437 removed outlier: 3.612A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL E 437 " --> pdb=" O GLU E 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 28 Processing helix chain 'J' and resid 48 through 51 Processing helix chain 'J' and resid 71 through 81 removed outlier: 4.660A pdb=" N ILE J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 108 Processing helix chain 'J' and resid 110 through 113 Processing helix chain 'J' and resid 114 through 128 Processing helix chain 'J' and resid 143 through 161 Processing helix chain 'J' and resid 182 through 195 Processing helix chain 'J' and resid 205 through 216 removed outlier: 3.669A pdb=" N ILE J 209 " --> pdb=" O ASP J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 244 removed outlier: 3.735A pdb=" N LEU J 227 " --> pdb=" O THR J 223 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 260 removed outlier: 3.651A pdb=" N VAL J 260 " --> pdb=" O GLN J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 297 Processing helix chain 'J' and resid 306 through 310 Processing helix chain 'J' and resid 324 through 338 Processing helix chain 'J' and resid 383 through 401 removed outlier: 3.878A pdb=" N ALA J 387 " --> pdb=" O ALA J 383 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS J 401 " --> pdb=" O LEU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 411 removed outlier: 4.039A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 437 removed outlier: 3.612A pdb=" N PHE J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL J 437 " --> pdb=" O GLU J 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 28 Processing helix chain 'K' and resid 48 through 51 Processing helix chain 'K' and resid 71 through 81 removed outlier: 4.659A pdb=" N ILE K 75 " --> pdb=" O GLU K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 110 through 113 Processing helix chain 'K' and resid 114 through 128 Processing helix chain 'K' and resid 143 through 161 Processing helix chain 'K' and resid 182 through 195 Processing helix chain 'K' and resid 205 through 216 removed outlier: 3.669A pdb=" N ILE K 209 " --> pdb=" O ASP K 205 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 244 removed outlier: 3.734A pdb=" N LEU K 227 " --> pdb=" O THR K 223 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 260 removed outlier: 3.652A pdb=" N VAL K 260 " --> pdb=" O GLN K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 297 Processing helix chain 'K' and resid 306 through 310 Processing helix chain 'K' and resid 324 through 338 Processing helix chain 'K' and resid 383 through 401 removed outlier: 3.878A pdb=" N ALA K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS K 401 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 411 removed outlier: 4.040A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 437 removed outlier: 3.611A pdb=" N PHE K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL K 437 " --> pdb=" O GLU K 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 28 Processing helix chain 'L' and resid 48 through 51 Processing helix chain 'L' and resid 71 through 81 removed outlier: 4.660A pdb=" N ILE L 75 " --> pdb=" O GLU L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 108 Processing helix chain 'L' and resid 110 through 113 Processing helix chain 'L' and resid 114 through 128 Processing helix chain 'L' and resid 143 through 161 Processing helix chain 'L' and resid 182 through 195 Processing helix chain 'L' and resid 205 through 216 removed outlier: 3.668A pdb=" N ILE L 209 " --> pdb=" O ASP L 205 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 244 removed outlier: 3.735A pdb=" N LEU L 227 " --> pdb=" O THR L 223 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 260 removed outlier: 3.652A pdb=" N VAL L 260 " --> pdb=" O GLN L 256 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 297 Processing helix chain 'L' and resid 306 through 310 Processing helix chain 'L' and resid 324 through 338 Processing helix chain 'L' and resid 383 through 401 removed outlier: 3.878A pdb=" N ALA L 387 " --> pdb=" O ALA L 383 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS L 401 " --> pdb=" O LEU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 411 removed outlier: 4.041A pdb=" N TYR L 408 " --> pdb=" O PHE L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 437 removed outlier: 3.612A pdb=" N PHE L 418 " --> pdb=" O GLU L 414 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL L 437 " --> pdb=" O GLU L 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 29 Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.979A pdb=" N ARG F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 69 through 79 removed outlier: 4.429A pdb=" N MET F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.546A pdb=" N PHE F 90 " --> pdb=" O PRO F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 108 through 127 removed outlier: 3.860A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 159 Processing helix chain 'F' and resid 180 through 196 removed outlier: 3.519A pdb=" N ASN F 184 " --> pdb=" O VAL F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 213 Processing helix chain 'F' and resid 221 through 242 removed outlier: 3.575A pdb=" N LEU F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER F 239 " --> pdb=" O GLY F 235 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU F 240 " --> pdb=" O VAL F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 258 Processing helix chain 'F' and resid 285 through 294 removed outlier: 3.700A pdb=" N PHE F 294 " --> pdb=" O THR F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 299 Processing helix chain 'F' and resid 304 through 308 Processing helix chain 'F' and resid 322 through 337 removed outlier: 3.634A pdb=" N ASN F 337 " --> pdb=" O ILE F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 341 Processing helix chain 'F' and resid 374 through 391 removed outlier: 3.633A pdb=" N ARG F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 400 removed outlier: 4.062A pdb=" N TYR F 398 " --> pdb=" O PHE F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 427 removed outlier: 3.866A pdb=" N PHE F 408 " --> pdb=" O ASP F 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 40 through 46 removed outlier: 4.179A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 69 through 79 removed outlier: 4.429A pdb=" N MET D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.547A pdb=" N PHE D 90 " --> pdb=" O PRO D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 108 through 127 removed outlier: 3.859A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 159 Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.518A pdb=" N ASN D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 213 Processing helix chain 'D' and resid 221 through 242 removed outlier: 3.575A pdb=" N LEU D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.700A pdb=" N PHE D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 299 Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 322 through 337 removed outlier: 3.634A pdb=" N ASN D 337 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 341 Processing helix chain 'D' and resid 374 through 391 removed outlier: 3.633A pdb=" N ARG D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 400 removed outlier: 4.063A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 427 removed outlier: 3.866A pdb=" N PHE D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 29 Processing helix chain 'G' and resid 41 through 46 removed outlier: 3.980A pdb=" N ARG G 46 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 69 through 79 removed outlier: 4.429A pdb=" N MET G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 removed outlier: 3.547A pdb=" N PHE G 90 " --> pdb=" O PRO G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 106 Processing helix chain 'G' and resid 108 through 127 removed outlier: 3.859A pdb=" N LEU G 112 " --> pdb=" O GLU G 108 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASP G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER G 115 " --> pdb=" O GLU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 159 Processing helix chain 'G' and resid 180 through 196 removed outlier: 3.518A pdb=" N ASN G 184 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 213 Processing helix chain 'G' and resid 221 through 242 removed outlier: 3.575A pdb=" N LEU G 225 " --> pdb=" O THR G 221 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER G 239 " --> pdb=" O GLY G 235 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU G 240 " --> pdb=" O VAL G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 258 Processing helix chain 'G' and resid 285 through 294 removed outlier: 3.700A pdb=" N PHE G 294 " --> pdb=" O THR G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 304 through 308 Processing helix chain 'G' and resid 322 through 337 removed outlier: 3.634A pdb=" N ASN G 337 " --> pdb=" O ILE G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 341 Processing helix chain 'G' and resid 374 through 391 removed outlier: 3.633A pdb=" N ARG G 391 " --> pdb=" O ALA G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 394 through 400 removed outlier: 4.062A pdb=" N TYR G 398 " --> pdb=" O PHE G 394 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 427 removed outlier: 3.866A pdb=" N PHE G 408 " --> pdb=" O ASP G 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 29 Processing helix chain 'H' and resid 40 through 46 removed outlier: 4.179A pdb=" N LEU H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG H 46 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 69 through 79 removed outlier: 4.429A pdb=" N MET H 73 " --> pdb=" O GLU H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.547A pdb=" N PHE H 90 " --> pdb=" O PRO H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 108 through 127 removed outlier: 3.860A pdb=" N LEU H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASP H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 159 Processing helix chain 'H' and resid 180 through 196 removed outlier: 3.518A pdb=" N ASN H 184 " --> pdb=" O VAL H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 213 Processing helix chain 'H' and resid 221 through 242 removed outlier: 3.575A pdb=" N LEU H 225 " --> pdb=" O THR H 221 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER H 239 " --> pdb=" O GLY H 235 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU H 240 " --> pdb=" O VAL H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 258 Processing helix chain 'H' and resid 285 through 294 removed outlier: 3.700A pdb=" N PHE H 294 " --> pdb=" O THR H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 299 Processing helix chain 'H' and resid 304 through 308 Processing helix chain 'H' and resid 322 through 337 removed outlier: 3.634A pdb=" N ASN H 337 " --> pdb=" O ILE H 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 341 Processing helix chain 'H' and resid 374 through 391 removed outlier: 3.633A pdb=" N ARG H 391 " --> pdb=" O ALA H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 394 through 400 removed outlier: 4.062A pdb=" N TYR H 398 " --> pdb=" O PHE H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 427 removed outlier: 3.866A pdb=" N PHE H 408 " --> pdb=" O ASP H 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 29 Processing helix chain 'I' and resid 41 through 46 removed outlier: 3.979A pdb=" N ARG I 46 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'I' and resid 69 through 79 removed outlier: 4.430A pdb=" N MET I 73 " --> pdb=" O GLU I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 90 removed outlier: 3.546A pdb=" N PHE I 90 " --> pdb=" O PRO I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 106 Processing helix chain 'I' and resid 108 through 127 removed outlier: 3.859A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 159 Processing helix chain 'I' and resid 180 through 196 removed outlier: 3.518A pdb=" N ASN I 184 " --> pdb=" O VAL I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 213 Processing helix chain 'I' and resid 221 through 242 removed outlier: 3.575A pdb=" N LEU I 225 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER I 239 " --> pdb=" O GLY I 235 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU I 240 " --> pdb=" O VAL I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 258 Processing helix chain 'I' and resid 285 through 294 removed outlier: 3.700A pdb=" N PHE I 294 " --> pdb=" O THR I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 299 Processing helix chain 'I' and resid 304 through 308 Processing helix chain 'I' and resid 322 through 337 removed outlier: 3.633A pdb=" N ASN I 337 " --> pdb=" O ILE I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 341 Processing helix chain 'I' and resid 374 through 391 removed outlier: 3.633A pdb=" N ARG I 391 " --> pdb=" O ALA I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 400 removed outlier: 4.062A pdb=" N TYR I 398 " --> pdb=" O PHE I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 427 removed outlier: 3.865A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.979A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 79 removed outlier: 4.430A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.547A pdb=" N PHE B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 127 removed outlier: 3.859A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.518A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.575A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.700A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.634A pdb=" N ASN B 337 " --> pdb=" O ILE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 374 through 391 removed outlier: 3.633A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.062A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.866A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 removed outlier: 8.901A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 Processing sheet with id=AA4, first strand: chain 'C' and resid 93 through 94 removed outlier: 8.901A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'C' and resid 269 through 273 Processing sheet with id=AA7, first strand: chain 'E' and resid 93 through 94 removed outlier: 8.902A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AA9, first strand: chain 'E' and resid 269 through 273 Processing sheet with id=AB1, first strand: chain 'J' and resid 93 through 94 removed outlier: 8.901A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'J' and resid 269 through 273 Processing sheet with id=AB4, first strand: chain 'K' and resid 93 through 94 removed outlier: 8.901A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'K' and resid 269 through 273 Processing sheet with id=AB7, first strand: chain 'L' and resid 93 through 94 removed outlier: 8.902A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'L' and resid 269 through 273 Processing sheet with id=AC1, first strand: chain 'F' and resid 91 through 92 removed outlier: 8.191A pdb=" N ILE F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU F 65 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE F 163 " --> pdb=" O GLN F 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 91 through 92 removed outlier: 8.191A pdb=" N ILE F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU F 65 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE F 163 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N MET F 164 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N TYR F 200 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR F 166 " --> pdb=" O TYR F 200 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N THR F 199 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE F 265 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 51 through 54 Processing sheet with id=AC4, first strand: chain 'D' and resid 91 through 92 removed outlier: 8.191A pdb=" N ILE D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU D 65 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE D 163 " --> pdb=" O GLN D 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 91 through 92 removed outlier: 8.191A pdb=" N ILE D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU D 65 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE D 163 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N MET D 164 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N TYR D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR D 166 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 51 through 54 Processing sheet with id=AC7, first strand: chain 'G' and resid 91 through 92 removed outlier: 8.191A pdb=" N ILE G 91 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU G 65 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE G 64 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS G 6 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL G 66 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN G 8 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU G 3 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE G 133 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL G 5 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE G 7 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS G 137 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE G 163 " --> pdb=" O GLN G 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 91 through 92 removed outlier: 8.191A pdb=" N ILE G 91 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU G 65 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE G 64 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS G 6 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL G 66 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN G 8 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU G 3 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE G 133 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL G 5 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE G 7 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS G 137 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE G 163 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET G 164 " --> pdb=" O GLU G 198 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N TYR G 200 " --> pdb=" O MET G 164 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR G 166 " --> pdb=" O TYR G 200 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR G 199 " --> pdb=" O PHE G 266 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE G 265 " --> pdb=" O SER G 371 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER G 371 " --> pdb=" O PHE G 265 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AD1, first strand: chain 'H' and resid 91 through 92 removed outlier: 8.192A pdb=" N ILE H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU H 65 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL H 66 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLN H 8 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE H 163 " --> pdb=" O GLN H 131 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 91 through 92 removed outlier: 8.192A pdb=" N ILE H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU H 65 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL H 66 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLN H 8 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE H 163 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET H 164 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N TYR H 200 " --> pdb=" O MET H 164 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR H 166 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR H 199 " --> pdb=" O PHE H 266 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE H 265 " --> pdb=" O SER H 371 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER H 371 " --> pdb=" O PHE H 265 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 51 through 54 Processing sheet with id=AD4, first strand: chain 'I' and resid 91 through 92 removed outlier: 8.191A pdb=" N ILE I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU I 65 " --> pdb=" O ILE I 91 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE I 163 " --> pdb=" O GLN I 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 91 through 92 removed outlier: 8.191A pdb=" N ILE I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU I 65 " --> pdb=" O ILE I 91 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE I 163 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET I 164 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N TYR I 200 " --> pdb=" O MET I 164 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR I 166 " --> pdb=" O TYR I 200 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N THR I 199 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 51 through 54 Processing sheet with id=AD7, first strand: chain 'B' and resid 91 through 92 removed outlier: 8.191A pdb=" N ILE B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 163 " --> pdb=" O GLN B 131 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 91 through 92 removed outlier: 8.191A pdb=" N ILE B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 163 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 51 through 54 2160 hydrogen bonds defined for protein. 6192 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: 16.75 Time building geometry restraints manager: 17.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13615 1.34 - 1.46: 7555 1.46 - 1.57: 20336 1.57 - 1.69: 48 1.69 - 1.81: 444 Bond restraints: 41998 Sorted by residual: bond pdb=" N ARG I 359 " pdb=" CA ARG I 359 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 4.96e+00 bond pdb=" N ARG B 359 " pdb=" CA ARG B 359 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.30e+00 bond pdb=" N ARG G 359 " pdb=" CA ARG G 359 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 3.92e+00 bond pdb=" N ARG D 359 " pdb=" CA ARG D 359 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.21e+00 bond pdb=" C5 GDP I 501 " pdb=" C4 GDP I 501 " ideal model delta sigma weight residual 1.490 1.459 0.031 2.00e-02 2.50e+03 2.46e+00 ... (remaining 41993 not shown) Histogram of bond angle deviations from ideal: 99.42 - 106.79: 1433 106.79 - 114.17: 24363 114.17 - 121.55: 22055 121.55 - 128.92: 8871 128.92 - 136.30: 313 Bond angle restraints: 57035 Sorted by residual: angle pdb=" N ARG F 359 " pdb=" CA ARG F 359 " pdb=" C ARG F 359 " ideal model delta sigma weight residual 110.30 122.36 -12.06 1.50e+00 4.44e-01 6.47e+01 angle pdb=" C PRO H 357 " pdb=" N PRO H 358 " pdb=" CA PRO H 358 " ideal model delta sigma weight residual 119.84 126.58 -6.74 1.25e+00 6.40e-01 2.91e+01 angle pdb=" N PRO F 358 " pdb=" CA PRO F 358 " pdb=" C PRO F 358 " ideal model delta sigma weight residual 111.19 103.26 7.93 1.57e+00 4.06e-01 2.55e+01 angle pdb=" N VAL J 181 " pdb=" CA VAL J 181 " pdb=" C VAL J 181 " ideal model delta sigma weight residual 113.53 109.10 4.43 9.80e-01 1.04e+00 2.04e+01 angle pdb=" N VAL L 181 " pdb=" CA VAL L 181 " pdb=" C VAL L 181 " ideal model delta sigma weight residual 113.53 109.10 4.43 9.80e-01 1.04e+00 2.04e+01 ... (remaining 57030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.71: 24430 32.71 - 65.41: 455 65.41 - 98.12: 48 98.12 - 130.83: 6 130.83 - 163.53: 6 Dihedral angle restraints: 24945 sinusoidal: 9957 harmonic: 14988 Sorted by residual: dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -127.20 -163.53 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -127.24 -163.50 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" C5' GTP J 501 " pdb=" O5' GTP J 501 " pdb=" PA GTP J 501 " pdb=" O3A GTP J 501 " ideal model delta sinusoidal sigma weight residual 69.27 -127.24 -163.49 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 24942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 5514 0.071 - 0.142: 713 0.142 - 0.214: 6 0.214 - 0.285: 2 0.285 - 0.356: 5 Chirality restraints: 6240 Sorted by residual: chirality pdb=" CA ARG H 359 " pdb=" N ARG H 359 " pdb=" C ARG H 359 " pdb=" CB ARG H 359 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CA ARG I 359 " pdb=" N ARG I 359 " pdb=" C ARG I 359 " pdb=" CB ARG I 359 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA ARG D 359 " pdb=" N ARG D 359 " pdb=" C ARG D 359 " pdb=" CB ARG D 359 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 6237 not shown) Planarity restraints: 7411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO H 357 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C PRO H 357 " -0.038 2.00e-02 2.50e+03 pdb=" O PRO H 357 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO H 358 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO I 357 " -0.011 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C PRO I 357 " 0.036 2.00e-02 2.50e+03 pdb=" O PRO I 357 " -0.014 2.00e-02 2.50e+03 pdb=" N PRO I 358 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 357 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C PRO F 357 " -0.035 2.00e-02 2.50e+03 pdb=" O PRO F 357 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO F 358 " 0.012 2.00e-02 2.50e+03 ... (remaining 7408 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 566 2.54 - 3.13: 34585 3.13 - 3.72: 65253 3.72 - 4.31: 88992 4.31 - 4.90: 151927 Nonbonded interactions: 341323 Sorted by model distance: nonbonded pdb=" O3B GTP K 501 " pdb="MG MG K 502 " model vdw 1.947 2.170 nonbonded pdb=" O3B GTP J 501 " pdb="MG MG J 502 " model vdw 1.947 2.170 nonbonded pdb=" O3B GTP E 501 " pdb="MG MG E 502 " model vdw 1.947 2.170 nonbonded pdb=" O3B GTP A 501 " pdb="MG MG A 502 " model vdw 1.947 2.170 nonbonded pdb=" O3B GTP L 501 " pdb="MG MG L 502 " model vdw 1.948 2.170 ... (remaining 341318 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 1 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 441 or resid 501 through 502)) selection = chain 'C' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.620 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: 0.040 Extract box with map and model: 29.750 Check model and map are aligned: 0.600 Set scattering table: 0.370 Process input model: 103.160 Find NCS groups from input model: 3.500 Set up NCS constraints: 0.390 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: 0.020 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 : 0.006 0.064 41998 Z= 0.381 Angle : 0.665 12.064 57035 Z= 0.377 Chirality : 0.045 0.356 6240 Planarity : 0.004 0.032 7411 Dihedral : 13.533 163.533 15321 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.89 % Favored : 95.02 % Rotamer: Outliers : 5.43 % Allowed : 7.88 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -1.01 (0.12), residues: 5136 helix: 0.52 (0.10), residues: 2430 sheet: -1.76 (0.19), residues: 732 loop : -1.68 (0.15), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 21 HIS 0.004 0.001 HIS C 192 PHE 0.015 0.002 PHE B 20 TYR 0.011 0.001 TYR L 272 ARG 0.005 0.000 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1953 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1713 time to evaluate : 4.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.7918 (m) cc_final: 0.7707 (m) REVERT: A 33 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7207 (p0) REVERT: A 90 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7924 (tp30) REVERT: A 198 SER cc_start: 0.8638 (p) cc_final: 0.8043 (p) REVERT: A 221 ARG cc_start: 0.7099 (mtt90) cc_final: 0.6715 (mtt90) REVERT: A 280 LYS cc_start: 0.8150 (ttmt) cc_final: 0.7924 (ttpt) REVERT: A 300 ASN cc_start: 0.8390 (m-40) cc_final: 0.8177 (t0) REVERT: A 318 LEU cc_start: 0.8957 (mt) cc_final: 0.8664 (mp) REVERT: A 336 LYS cc_start: 0.9038 (mtpm) cc_final: 0.8829 (mtpp) REVERT: A 382 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8409 (p) REVERT: A 392 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7643 (t0) REVERT: C 33 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6921 (p0) REVERT: C 50 ASN cc_start: 0.7804 (t0) cc_final: 0.7198 (t0) REVERT: C 103 TYR cc_start: 0.8833 (t80) cc_final: 0.8253 (t80) REVERT: C 121 ARG cc_start: 0.8142 (mmm160) cc_final: 0.7808 (tpt170) REVERT: C 154 MET cc_start: 0.8886 (mmm) cc_final: 0.8667 (mmm) REVERT: C 210 TYR cc_start: 0.8391 (m-10) cc_final: 0.8071 (m-80) REVERT: C 228 ASN cc_start: 0.8569 (m-40) cc_final: 0.8344 (m-40) REVERT: C 256 GLN cc_start: 0.8278 (pt0) cc_final: 0.7999 (pt0) REVERT: C 304 LYS cc_start: 0.9084 (tppt) cc_final: 0.8826 (tptt) REVERT: C 317 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8870 (mt) REVERT: C 322 ASP cc_start: 0.7820 (t0) cc_final: 0.7397 (t70) REVERT: C 382 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8244 (p) REVERT: C 392 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7645 (t0) REVERT: C 429 GLU cc_start: 0.8368 (tp30) cc_final: 0.8129 (tm-30) REVERT: E 30 ILE cc_start: 0.8493 (mm) cc_final: 0.8281 (mm) REVERT: E 33 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.6405 (p0) REVERT: E 71 GLU cc_start: 0.7263 (pt0) cc_final: 0.7017 (pt0) REVERT: E 103 TYR cc_start: 0.8698 (t80) cc_final: 0.8401 (t80) REVERT: E 121 ARG cc_start: 0.8127 (mmm160) cc_final: 0.7846 (tpt170) REVERT: E 219 ILE cc_start: 0.8472 (mt) cc_final: 0.7360 (pt) REVERT: E 256 GLN cc_start: 0.8327 (pt0) cc_final: 0.8086 (pt0) REVERT: E 269 LEU cc_start: 0.8867 (pp) cc_final: 0.8632 (pp) REVERT: E 305 CYS cc_start: 0.7958 (m) cc_final: 0.7293 (m) REVERT: E 322 ASP cc_start: 0.7834 (t0) cc_final: 0.7605 (t70) REVERT: E 336 LYS cc_start: 0.8971 (mtpm) cc_final: 0.8618 (mtpp) REVERT: E 352 LYS cc_start: 0.8635 (tttp) cc_final: 0.8201 (tppt) REVERT: E 382 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8197 (p) REVERT: E 386 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7934 (pm20) REVERT: E 392 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7928 (t0) REVERT: E 413 MET cc_start: 0.6545 (ttm) cc_final: 0.6075 (mtp) REVERT: J 3 GLU cc_start: 0.7216 (mp0) cc_final: 0.6792 (mm-30) REVERT: J 50 ASN cc_start: 0.7911 (t0) cc_final: 0.7187 (t0) REVERT: J 51 THR cc_start: 0.8536 (p) cc_final: 0.8284 (p) REVERT: J 75 ILE cc_start: 0.9124 (mm) cc_final: 0.8859 (mt) REVERT: J 103 TYR cc_start: 0.8840 (t80) cc_final: 0.8375 (t80) REVERT: J 109 THR cc_start: 0.9487 (m) cc_final: 0.8365 (p) REVERT: J 149 PHE cc_start: 0.9263 (t80) cc_final: 0.9014 (t80) REVERT: J 198 SER cc_start: 0.8461 (p) cc_final: 0.8043 (t) REVERT: J 207 GLU cc_start: 0.8365 (tt0) cc_final: 0.8160 (tt0) REVERT: J 290 GLU cc_start: 0.8344 (tt0) cc_final: 0.8060 (tm-30) REVERT: J 305 CYS cc_start: 0.7815 (m) cc_final: 0.7158 (m) REVERT: J 317 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8857 (mt) REVERT: J 326 LYS cc_start: 0.9030 (tttm) cc_final: 0.8648 (ptpt) REVERT: J 352 LYS cc_start: 0.8328 (tttp) cc_final: 0.8025 (tppt) REVERT: J 357 TYR cc_start: 0.8675 (m-80) cc_final: 0.8376 (m-80) REVERT: J 382 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8238 (p) REVERT: J 386 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8402 (pm20) REVERT: J 392 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8111 (t0) REVERT: J 417 GLU cc_start: 0.7891 (tt0) cc_final: 0.7609 (tt0) REVERT: J 434 GLU cc_start: 0.8950 (tt0) cc_final: 0.8738 (tt0) REVERT: K 50 ASN cc_start: 0.7881 (t0) cc_final: 0.7265 (t0) REVERT: K 90 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7813 (tp30) REVERT: K 110 ILE cc_start: 0.9314 (mm) cc_final: 0.8783 (mm) REVERT: K 151 SER cc_start: 0.9023 (m) cc_final: 0.8786 (p) REVERT: K 198 SER cc_start: 0.8378 (p) cc_final: 0.7846 (p) REVERT: K 207 GLU cc_start: 0.8084 (tt0) cc_final: 0.7842 (tt0) REVERT: K 280 LYS cc_start: 0.8618 (ttmt) cc_final: 0.8378 (ttpt) REVERT: K 326 LYS cc_start: 0.8899 (tttm) cc_final: 0.8655 (ptpt) REVERT: K 352 LYS cc_start: 0.8152 (tttp) cc_final: 0.7822 (tppt) REVERT: K 382 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8227 (p) REVERT: K 392 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7985 (t0) REVERT: K 429 GLU cc_start: 0.8544 (tp30) cc_final: 0.8273 (tp30) REVERT: L 90 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7613 (tm-30) REVERT: L 110 ILE cc_start: 0.9366 (mm) cc_final: 0.8906 (mm) REVERT: L 198 SER cc_start: 0.8409 (p) cc_final: 0.7492 (p) REVERT: L 205 ASP cc_start: 0.8447 (t0) cc_final: 0.8198 (t0) REVERT: L 206 ASN cc_start: 0.8754 (m110) cc_final: 0.8408 (m-40) REVERT: L 210 TYR cc_start: 0.8424 (m-10) cc_final: 0.7985 (m-80) REVERT: L 326 LYS cc_start: 0.8990 (tttm) cc_final: 0.8391 (mttt) REVERT: L 336 LYS cc_start: 0.8881 (mtpm) cc_final: 0.8531 (mtpp) REVERT: L 352 LYS cc_start: 0.8260 (tttp) cc_final: 0.7895 (tppt) REVERT: L 372 GLN cc_start: 0.7934 (mt0) cc_final: 0.7165 (pt0) REVERT: L 392 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8374 (t0) REVERT: F 22 GLU cc_start: 0.7711 (tt0) cc_final: 0.7444 (tm-30) REVERT: F 26 ASP cc_start: 0.8354 (m-30) cc_final: 0.6661 (m-30) REVERT: F 36 TYR cc_start: 0.8324 (t80) cc_final: 0.7628 (t80) REVERT: F 58 LYS cc_start: 0.7384 (mttt) cc_final: 0.7079 (mtpt) REVERT: F 106 TYR cc_start: 0.8743 (m-80) cc_final: 0.8429 (m-10) REVERT: F 108 GLU cc_start: 0.8470 (tp30) cc_final: 0.8220 (tm-30) REVERT: F 112 LEU cc_start: 0.8475 (mp) cc_final: 0.8165 (tp) REVERT: F 174 LYS cc_start: 0.8483 (mtpt) cc_final: 0.8213 (mtpt) REVERT: F 198 GLU cc_start: 0.8419 (pt0) cc_final: 0.8109 (pt0) REVERT: F 200 TYR cc_start: 0.9018 (m-80) cc_final: 0.8706 (m-10) REVERT: F 208 TYR cc_start: 0.8496 (m-10) cc_final: 0.7840 (m-80) REVERT: F 252 LYS cc_start: 0.8500 (mtpt) cc_final: 0.8162 (mtpt) REVERT: F 288 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7215 (tm-30) REVERT: F 304 ASP cc_start: 0.8261 (t0) cc_final: 0.8025 (t0) REVERT: F 327 ASP cc_start: 0.8403 (m-30) cc_final: 0.8087 (m-30) REVERT: D 26 ASP cc_start: 0.8488 (m-30) cc_final: 0.7105 (m-30) REVERT: D 108 GLU cc_start: 0.8435 (tp30) cc_final: 0.8206 (tp30) REVERT: D 111 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7089 (mt-10) REVERT: D 122 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8780 (ttmt) REVERT: D 198 GLU cc_start: 0.8279 (pt0) cc_final: 0.7965 (pt0) REVERT: D 208 TYR cc_start: 0.8506 (m-10) cc_final: 0.8123 (m-80) REVERT: D 379 LYS cc_start: 0.8825 (mtpt) cc_final: 0.7881 (ttmt) REVERT: G 31 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8449 (t0) REVERT: G 36 TYR cc_start: 0.8213 (t80) cc_final: 0.7695 (t80) REVERT: G 103 LYS cc_start: 0.8107 (mttt) cc_final: 0.7851 (mtpp) REVERT: G 159 TYR cc_start: 0.8731 (m-80) cc_final: 0.8433 (m-80) REVERT: G 198 GLU cc_start: 0.8403 (pt0) cc_final: 0.8040 (pt0) REVERT: G 298 ASN cc_start: 0.9187 (t0) cc_final: 0.8734 (t0) REVERT: G 299 MET cc_start: 0.8516 (mmp) cc_final: 0.8128 (mmp) REVERT: G 310 TYR cc_start: 0.9149 (m-80) cc_final: 0.8921 (m-80) REVERT: G 388 MET cc_start: 0.8314 (mtp) cc_final: 0.7921 (mmt) REVERT: G 397 TRP cc_start: 0.8688 (m100) cc_final: 0.8461 (m-10) REVERT: H 108 GLU cc_start: 0.8490 (tp30) cc_final: 0.8230 (tp30) REVERT: H 118 ASP cc_start: 0.8264 (m-30) cc_final: 0.8033 (m-30) REVERT: H 125 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7910 (mp0) REVERT: H 129 CYS cc_start: 0.7926 (t) cc_final: 0.7472 (t) REVERT: H 162 ARG cc_start: 0.9057 (mmt-90) cc_final: 0.8750 (mmp80) REVERT: H 177 ASP cc_start: 0.7769 (t70) cc_final: 0.7546 (t0) REVERT: H 200 TYR cc_start: 0.8923 (m-80) cc_final: 0.8719 (m-10) REVERT: H 291 GLN cc_start: 0.8795 (pt0) cc_final: 0.8588 (pm20) REVERT: H 325 GLU cc_start: 0.7807 (tt0) cc_final: 0.6782 (tt0) REVERT: H 397 TRP cc_start: 0.8570 (m100) cc_final: 0.7799 (m-10) REVERT: I 26 ASP cc_start: 0.8229 (m-30) cc_final: 0.7248 (m-30) REVERT: I 30 ILE cc_start: 0.8680 (mm) cc_final: 0.8368 (mm) REVERT: I 95 SER cc_start: 0.9326 (m) cc_final: 0.8976 (p) REVERT: I 103 LYS cc_start: 0.8176 (mttt) cc_final: 0.7942 (mtpp) REVERT: I 106 TYR cc_start: 0.8638 (m-80) cc_final: 0.8216 (m-10) REVERT: I 118 ASP cc_start: 0.8444 (m-30) cc_final: 0.8190 (m-30) REVERT: I 125 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8079 (mp0) REVERT: I 159 TYR cc_start: 0.8650 (m-80) cc_final: 0.8071 (m-80) REVERT: I 200 TYR cc_start: 0.9025 (m-80) cc_final: 0.8765 (m-10) REVERT: I 209 ASP cc_start: 0.8503 (t0) cc_final: 0.8291 (t0) REVERT: I 257 MET cc_start: 0.8452 (mmp) cc_final: 0.8106 (mmm) REVERT: I 304 ASP cc_start: 0.8646 (t0) cc_final: 0.8267 (t0) REVERT: I 419 VAL cc_start: 0.9325 (t) cc_final: 0.9020 (p) REVERT: I 422 TYR cc_start: 0.8167 (m-80) cc_final: 0.7939 (m-80) REVERT: B 31 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8564 (m-30) REVERT: B 37 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.7981 (p) REVERT: B 106 TYR cc_start: 0.8648 (m-80) cc_final: 0.8426 (m-80) REVERT: B 108 GLU cc_start: 0.8181 (tp30) cc_final: 0.7803 (tp30) REVERT: B 112 LEU cc_start: 0.8097 (mp) cc_final: 0.7823 (tp) REVERT: B 121 ARG cc_start: 0.8708 (ttm110) cc_final: 0.8459 (mtm-85) REVERT: B 122 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8703 (ttmt) REVERT: B 138 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8727 (m) REVERT: B 198 GLU cc_start: 0.8144 (pt0) cc_final: 0.7563 (pt0) REVERT: B 200 TYR cc_start: 0.8970 (m-80) cc_final: 0.8326 (m-10) outliers start: 240 outliers final: 92 residues processed: 1876 average time/residue: 0.5543 time to fit residues: 1663.6892 Evaluate side-chains 1358 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1239 time to evaluate : 4.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 317 LEU Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 339 ARG Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 382 THR Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 200 CYS Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 317 LEU Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 339 ARG Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 382 THR Chi-restraints excluded: chain K residue 392 ASP Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 392 ASP Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 421 GLU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 303 CYS Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 303 CYS Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 156 ARG Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 303 CYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 430 optimal weight: 9.9990 chunk 386 optimal weight: 3.9990 chunk 214 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 260 optimal weight: 6.9990 chunk 206 optimal weight: 1.9990 chunk 399 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 243 optimal weight: 0.9980 chunk 297 optimal weight: 9.9990 chunk 463 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN C 206 ASN C 300 ASN E 176 GLN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN J 176 GLN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN J 300 ASN K 186 ASN K 206 ASN L 88 HIS ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 300 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 ASN D 298 ASN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS H 334 GLN H 347 ASN H 375 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 HIS I 245 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 HIS B 89 ASN B 99 ASN B 134 GLN B 245 GLN B 279 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 41998 Z= 0.240 Angle : 0.611 6.880 57035 Z= 0.312 Chirality : 0.044 0.175 6240 Planarity : 0.004 0.062 7411 Dihedral : 11.440 163.912 5956 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.82 % Favored : 96.13 % Rotamer: Outliers : 4.80 % Allowed : 17.55 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.12), residues: 5136 helix: 1.25 (0.10), residues: 2418 sheet: -1.34 (0.19), residues: 732 loop : -1.40 (0.15), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 21 HIS 0.010 0.001 HIS I 6 PHE 0.035 0.002 PHE I 81 TYR 0.032 0.001 TYR F 425 ARG 0.007 0.001 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1581 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1369 time to evaluate : 4.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7577 (p0) REVERT: A 90 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7817 (tp30) REVERT: A 113 GLU cc_start: 0.7455 (mp0) cc_final: 0.7075 (mp0) REVERT: A 156 ARG cc_start: 0.8601 (mmt-90) cc_final: 0.8319 (mmt-90) REVERT: A 256 GLN cc_start: 0.8238 (pt0) cc_final: 0.7908 (pt0) REVERT: A 257 THR cc_start: 0.8811 (m) cc_final: 0.8477 (m) REVERT: A 300 ASN cc_start: 0.8486 (m-40) cc_final: 0.8260 (t0) REVERT: A 382 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8346 (p) REVERT: A 392 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7580 (t0) REVERT: A 411 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7096 (mm-30) REVERT: C 33 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7075 (p0) REVERT: C 50 ASN cc_start: 0.7797 (t0) cc_final: 0.7537 (t0) REVERT: C 103 TYR cc_start: 0.8803 (t80) cc_final: 0.8303 (t80) REVERT: C 121 ARG cc_start: 0.8057 (mmm160) cc_final: 0.7770 (tpt170) REVERT: C 154 MET cc_start: 0.8763 (mmm) cc_final: 0.8485 (mmm) REVERT: C 206 ASN cc_start: 0.8747 (m110) cc_final: 0.8343 (m-40) REVERT: C 210 TYR cc_start: 0.8319 (m-10) cc_final: 0.7950 (m-80) REVERT: C 228 ASN cc_start: 0.8585 (m-40) cc_final: 0.8364 (m-40) REVERT: C 300 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8293 (t0) REVERT: C 317 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8804 (mt) REVERT: C 322 ASP cc_start: 0.7730 (t0) cc_final: 0.7353 (t70) REVERT: C 392 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7504 (t0) REVERT: E 20 CYS cc_start: 0.8364 (m) cc_final: 0.8137 (t) REVERT: E 33 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7034 (p0) REVERT: E 50 ASN cc_start: 0.8316 (t0) cc_final: 0.7843 (t0) REVERT: E 203 MET cc_start: 0.8574 (mmp) cc_final: 0.8288 (mmm) REVERT: E 269 LEU cc_start: 0.8868 (pp) cc_final: 0.8556 (pp) REVERT: E 305 CYS cc_start: 0.7916 (m) cc_final: 0.7195 (m) REVERT: E 336 LYS cc_start: 0.8931 (mtpm) cc_final: 0.8605 (mtpp) REVERT: E 386 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7998 (pm20) REVERT: E 392 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7595 (t0) REVERT: E 417 GLU cc_start: 0.7817 (tt0) cc_final: 0.7350 (tt0) REVERT: J 75 ILE cc_start: 0.9089 (mm) cc_final: 0.8783 (mt) REVERT: J 90 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7885 (tp30) REVERT: J 103 TYR cc_start: 0.8836 (t80) cc_final: 0.8462 (t80) REVERT: J 286 LEU cc_start: 0.8572 (mt) cc_final: 0.8209 (pp) REVERT: J 305 CYS cc_start: 0.7794 (m) cc_final: 0.6988 (m) REVERT: J 317 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8785 (mt) REVERT: J 326 LYS cc_start: 0.8992 (tttm) cc_final: 0.8546 (ptpt) REVERT: J 352 LYS cc_start: 0.8185 (tttp) cc_final: 0.7799 (tppt) REVERT: J 357 TYR cc_start: 0.8603 (m-80) cc_final: 0.8246 (m-80) REVERT: J 377 MET cc_start: 0.8922 (ttp) cc_final: 0.8457 (tmm) REVERT: J 386 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8378 (pm20) REVERT: J 392 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.7989 (t0) REVERT: K 3 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6655 (mm-30) REVERT: K 50 ASN cc_start: 0.8076 (t0) cc_final: 0.7818 (t0) REVERT: K 90 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7572 (tm-30) REVERT: K 110 ILE cc_start: 0.9195 (mm) cc_final: 0.8989 (mm) REVERT: K 113 GLU cc_start: 0.8167 (mp0) cc_final: 0.7892 (mp0) REVERT: K 151 SER cc_start: 0.8946 (m) cc_final: 0.8736 (p) REVERT: K 199 ASP cc_start: 0.8249 (m-30) cc_final: 0.7955 (t0) REVERT: K 326 LYS cc_start: 0.8890 (tttm) cc_final: 0.8452 (ptpt) REVERT: K 352 LYS cc_start: 0.8136 (tttp) cc_final: 0.7762 (tppt) REVERT: K 357 TYR cc_start: 0.8368 (m-80) cc_final: 0.8009 (m-80) REVERT: K 377 MET cc_start: 0.8874 (ttp) cc_final: 0.8559 (tmm) REVERT: K 392 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7854 (t0) REVERT: L 50 ASN cc_start: 0.8553 (t0) cc_final: 0.8091 (t0) REVERT: L 76 ASP cc_start: 0.8650 (m-30) cc_final: 0.8192 (m-30) REVERT: L 90 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7691 (tp30) REVERT: L 103 TYR cc_start: 0.8733 (t80) cc_final: 0.8468 (t80) REVERT: L 197 HIS cc_start: 0.8578 (m90) cc_final: 0.8378 (m170) REVERT: L 205 ASP cc_start: 0.8327 (t0) cc_final: 0.8099 (t0) REVERT: L 206 ASN cc_start: 0.8571 (m110) cc_final: 0.8210 (m-40) REVERT: L 210 TYR cc_start: 0.8328 (m-10) cc_final: 0.7948 (m-80) REVERT: L 326 LYS cc_start: 0.8883 (tttm) cc_final: 0.8312 (pttt) REVERT: L 357 TYR cc_start: 0.8578 (m-80) cc_final: 0.8158 (m-80) REVERT: L 372 GLN cc_start: 0.7926 (mt0) cc_final: 0.7203 (pt0) REVERT: L 392 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8153 (t0) REVERT: F 14 ASN cc_start: 0.8547 (m-40) cc_final: 0.8161 (m-40) REVERT: F 19 LYS cc_start: 0.8951 (mmmt) cc_final: 0.8678 (mmmt) REVERT: F 36 TYR cc_start: 0.8225 (t80) cc_final: 0.7726 (t80) REVERT: F 46 ARG cc_start: 0.8668 (mmt-90) cc_final: 0.8363 (mmt-90) REVERT: F 106 TYR cc_start: 0.8588 (m-80) cc_final: 0.8324 (m-10) REVERT: F 112 LEU cc_start: 0.8453 (mp) cc_final: 0.8239 (tp) REVERT: F 136 THR cc_start: 0.9101 (m) cc_final: 0.8716 (p) REVERT: F 208 TYR cc_start: 0.8359 (m-10) cc_final: 0.7834 (m-80) REVERT: F 209 ASP cc_start: 0.8364 (t0) cc_final: 0.7675 (t0) REVERT: F 213 ARG cc_start: 0.8148 (ttm110) cc_final: 0.7770 (ttp-110) REVERT: F 252 LYS cc_start: 0.8312 (mtpt) cc_final: 0.8064 (mtpt) REVERT: F 323 MET cc_start: 0.7544 (mmm) cc_final: 0.7330 (mmm) REVERT: D 26 ASP cc_start: 0.8010 (m-30) cc_final: 0.7746 (m-30) REVERT: D 111 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6908 (mt-10) REVERT: D 112 LEU cc_start: 0.8217 (tp) cc_final: 0.7991 (tp) REVERT: D 122 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8737 (ttmt) REVERT: D 136 THR cc_start: 0.9078 (m) cc_final: 0.8585 (p) REVERT: D 198 GLU cc_start: 0.8173 (pt0) cc_final: 0.7874 (pt0) REVERT: D 208 TYR cc_start: 0.8323 (m-10) cc_final: 0.8030 (m-80) REVERT: D 298 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8675 (t0) REVERT: D 425 TYR cc_start: 0.8725 (m-80) cc_final: 0.7989 (m-80) REVERT: G 31 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8432 (t0) REVERT: G 36 TYR cc_start: 0.8103 (t80) cc_final: 0.7730 (t80) REVERT: G 116 VAL cc_start: 0.9130 (t) cc_final: 0.8914 (p) REVERT: G 180 VAL cc_start: 0.9108 (m) cc_final: 0.8772 (p) REVERT: G 299 MET cc_start: 0.8654 (mmp) cc_final: 0.8326 (mmp) REVERT: G 307 HIS cc_start: 0.8900 (m-70) cc_final: 0.8603 (m-70) REVERT: G 310 TYR cc_start: 0.9178 (m-80) cc_final: 0.8863 (m-80) REVERT: G 375 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7859 (pp30) REVERT: G 388 MET cc_start: 0.8296 (mtp) cc_final: 0.7837 (mmt) REVERT: G 397 TRP cc_start: 0.8689 (m100) cc_final: 0.8450 (m-10) REVERT: H 36 TYR cc_start: 0.8167 (t80) cc_final: 0.7766 (t80) REVERT: H 129 CYS cc_start: 0.8005 (t) cc_final: 0.7686 (t) REVERT: H 198 GLU cc_start: 0.7917 (pt0) cc_final: 0.7706 (pt0) REVERT: H 213 ARG cc_start: 0.8172 (ttm110) cc_final: 0.7698 (ttp-110) REVERT: H 257 MET cc_start: 0.8516 (mmp) cc_final: 0.8135 (mmm) REVERT: H 291 GLN cc_start: 0.8729 (pt0) cc_final: 0.8503 (pm20) REVERT: H 322 SER cc_start: 0.8148 (m) cc_final: 0.7827 (p) REVERT: H 397 TRP cc_start: 0.8640 (m100) cc_final: 0.7754 (m-10) REVERT: H 407 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8517 (mp0) REVERT: I 26 ASP cc_start: 0.7729 (m-30) cc_final: 0.7497 (m-30) REVERT: I 31 ASP cc_start: 0.8740 (t0) cc_final: 0.8113 (t0) REVERT: I 95 SER cc_start: 0.9326 (m) cc_final: 0.8993 (p) REVERT: I 103 LYS cc_start: 0.8177 (mttt) cc_final: 0.7935 (mtpp) REVERT: I 118 ASP cc_start: 0.8357 (m-30) cc_final: 0.8152 (m-30) REVERT: I 165 ASN cc_start: 0.8464 (m-40) cc_final: 0.8186 (m-40) REVERT: I 180 VAL cc_start: 0.8919 (m) cc_final: 0.8514 (p) REVERT: I 198 GLU cc_start: 0.8025 (pt0) cc_final: 0.6987 (pt0) REVERT: I 200 TYR cc_start: 0.8888 (m-80) cc_final: 0.8496 (m-10) REVERT: I 209 ASP cc_start: 0.8516 (t0) cc_final: 0.8300 (t0) REVERT: I 257 MET cc_start: 0.8588 (mmp) cc_final: 0.7884 (mmm) REVERT: I 267 MET cc_start: 0.8734 (mtp) cc_final: 0.8366 (mtt) REVERT: I 282 ARG cc_start: 0.8048 (mmm-85) cc_final: 0.7802 (ttt180) REVERT: I 299 MET cc_start: 0.8587 (mmp) cc_final: 0.8385 (mmp) REVERT: I 364 SER cc_start: 0.9306 (p) cc_final: 0.9098 (m) REVERT: I 419 VAL cc_start: 0.9294 (t) cc_final: 0.9024 (p) REVERT: B 31 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8582 (m-30) REVERT: B 37 VAL cc_start: 0.8359 (OUTLIER) cc_final: 0.7939 (p) REVERT: B 99 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8451 (m-40) REVERT: B 122 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8617 (ttmt) REVERT: B 425 TYR cc_start: 0.8868 (m-80) cc_final: 0.8613 (m-80) outliers start: 212 outliers final: 125 residues processed: 1516 average time/residue: 0.5390 time to fit residues: 1317.5263 Evaluate side-chains 1346 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1193 time to evaluate : 4.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 317 LEU Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain J residue 413 MET Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 317 LEU Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 392 ASP Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 245 ASP Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 392 ASP Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 303 CYS Chi-restraints excluded: chain G residue 333 ILE Chi-restraints excluded: chain G residue 375 GLN Chi-restraints excluded: chain G residue 407 GLU Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 303 CYS Chi-restraints excluded: chain H residue 407 GLU Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 190 HIS Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 381 ILE Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 372 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 257 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 385 optimal weight: 10.0000 chunk 315 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 463 optimal weight: 7.9990 chunk 501 optimal weight: 8.9990 chunk 413 optimal weight: 8.9990 chunk 460 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 372 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN C 256 GLN C 300 ASN E 256 GLN E 293 ASN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN J 300 ASN L 88 HIS L 226 ASN L 300 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 HIS F 99 ASN F 134 GLN F 245 GLN F 298 ASN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 ASN D 134 GLN D 279 GLN D 298 ASN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 GLN ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 423 GLN G 424 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS H 134 GLN H 298 ASN H 423 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 134 GLN I 190 HIS ** I 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 424 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 279 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 41998 Z= 0.475 Angle : 0.715 7.677 57035 Z= 0.367 Chirality : 0.048 0.170 6240 Planarity : 0.005 0.045 7411 Dihedral : 11.504 167.406 5905 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.78 % Favored : 94.16 % Rotamer: Outliers : 6.57 % Allowed : 19.47 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.12), residues: 5136 helix: 0.97 (0.10), residues: 2424 sheet: -1.38 (0.19), residues: 720 loop : -1.53 (0.15), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 21 HIS 0.024 0.001 HIS I 190 PHE 0.036 0.002 PHE D 167 TYR 0.022 0.002 TYR L 24 ARG 0.008 0.001 ARG L 339 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1486 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 1196 time to evaluate : 4.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7670 (p0) REVERT: A 90 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7998 (tp30) REVERT: A 221 ARG cc_start: 0.7045 (mtt90) cc_final: 0.6316 (mtt90) REVERT: A 256 GLN cc_start: 0.8007 (pt0) cc_final: 0.7279 (pt0) REVERT: A 300 ASN cc_start: 0.8559 (m-40) cc_final: 0.8265 (t0) REVERT: A 318 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8673 (mp) REVERT: A 392 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7635 (t0) REVERT: A 411 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7691 (tp30) REVERT: C 33 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7377 (p0) REVERT: C 90 GLU cc_start: 0.8173 (tp30) cc_final: 0.7930 (tp30) REVERT: C 121 ARG cc_start: 0.8134 (mmm160) cc_final: 0.7913 (tpt170) REVERT: C 206 ASN cc_start: 0.8792 (m110) cc_final: 0.8427 (m-40) REVERT: C 210 TYR cc_start: 0.8437 (m-10) cc_final: 0.8115 (m-80) REVERT: C 228 ASN cc_start: 0.8737 (m-40) cc_final: 0.8425 (m-40) REVERT: C 317 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8880 (mt) REVERT: C 322 ASP cc_start: 0.7834 (t0) cc_final: 0.7444 (t70) REVERT: C 377 MET cc_start: 0.8853 (tmm) cc_final: 0.8394 (tmm) REVERT: C 392 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7537 (t0) REVERT: C 429 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7968 (tm-30) REVERT: E 3 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7166 (mm-30) REVERT: E 90 GLU cc_start: 0.8254 (tp30) cc_final: 0.7900 (tp30) REVERT: E 305 CYS cc_start: 0.8015 (m) cc_final: 0.7545 (m) REVERT: E 336 LYS cc_start: 0.9061 (mtpm) cc_final: 0.8698 (mtpp) REVERT: E 357 TYR cc_start: 0.8486 (m-80) cc_final: 0.8257 (m-80) REVERT: E 377 MET cc_start: 0.8930 (tmm) cc_final: 0.8666 (tmm) REVERT: E 386 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: J 103 TYR cc_start: 0.8818 (t80) cc_final: 0.8452 (t80) REVERT: J 199 ASP cc_start: 0.8672 (m-30) cc_final: 0.8417 (t0) REVERT: J 220 GLU cc_start: 0.7479 (tp30) cc_final: 0.7222 (tp30) REVERT: J 286 LEU cc_start: 0.8664 (mt) cc_final: 0.8260 (pp) REVERT: J 300 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8470 (t0) REVERT: J 317 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8887 (mt) REVERT: J 326 LYS cc_start: 0.8992 (tttm) cc_final: 0.8467 (ptpt) REVERT: J 352 LYS cc_start: 0.8102 (tttp) cc_final: 0.7694 (tppt) REVERT: J 353 VAL cc_start: 0.9544 (t) cc_final: 0.9150 (p) REVERT: J 357 TYR cc_start: 0.8669 (m-80) cc_final: 0.8258 (m-80) REVERT: J 377 MET cc_start: 0.8906 (ttp) cc_final: 0.8647 (tmm) REVERT: J 392 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8073 (t0) REVERT: K 50 ASN cc_start: 0.8008 (t0) cc_final: 0.7736 (t0) REVERT: K 90 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7830 (tp30) REVERT: K 112 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8685 (tmmt) REVERT: K 113 GLU cc_start: 0.8170 (mp0) cc_final: 0.7894 (mp0) REVERT: K 156 ARG cc_start: 0.8339 (mmm-85) cc_final: 0.8104 (mmm-85) REVERT: K 199 ASP cc_start: 0.8373 (m-30) cc_final: 0.8103 (t0) REVERT: K 224 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: K 326 LYS cc_start: 0.8970 (tttm) cc_final: 0.8405 (ptpt) REVERT: K 352 LYS cc_start: 0.8138 (tttp) cc_final: 0.7647 (tppt) REVERT: K 357 TYR cc_start: 0.8523 (m-80) cc_final: 0.8275 (m-80) REVERT: K 392 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.7904 (t0) REVERT: L 103 TYR cc_start: 0.8774 (t80) cc_final: 0.8570 (t80) REVERT: L 203 MET cc_start: 0.9006 (mmm) cc_final: 0.8746 (mmm) REVERT: L 205 ASP cc_start: 0.8347 (t0) cc_final: 0.8108 (t0) REVERT: L 206 ASN cc_start: 0.8667 (m110) cc_final: 0.8398 (m-40) REVERT: L 210 TYR cc_start: 0.8539 (m-10) cc_final: 0.8047 (m-80) REVERT: L 322 ASP cc_start: 0.7739 (t0) cc_final: 0.7491 (t70) REVERT: L 326 LYS cc_start: 0.8866 (tttm) cc_final: 0.8182 (mttt) REVERT: L 352 LYS cc_start: 0.3681 (tppt) cc_final: 0.3165 (tppt) REVERT: L 357 TYR cc_start: 0.8589 (m-80) cc_final: 0.8290 (m-80) REVERT: L 377 MET cc_start: 0.8930 (tmm) cc_final: 0.8530 (tmm) REVERT: L 391 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9010 (mp) REVERT: L 392 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8192 (t0) REVERT: F 19 LYS cc_start: 0.8853 (mmmt) cc_final: 0.8566 (mmmt) REVERT: F 36 TYR cc_start: 0.8289 (t80) cc_final: 0.7742 (t80) REVERT: F 112 LEU cc_start: 0.8591 (mp) cc_final: 0.8304 (tp) REVERT: F 208 TYR cc_start: 0.8496 (m-10) cc_final: 0.8009 (m-80) REVERT: F 323 MET cc_start: 0.7675 (mmm) cc_final: 0.7431 (mmm) REVERT: D 22 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7630 (tm-30) REVERT: D 26 ASP cc_start: 0.8085 (m-30) cc_final: 0.7760 (m-30) REVERT: D 108 GLU cc_start: 0.8300 (tp30) cc_final: 0.7985 (tp30) REVERT: D 122 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8789 (ttmt) REVERT: D 198 GLU cc_start: 0.8278 (pt0) cc_final: 0.7900 (pt0) REVERT: D 208 TYR cc_start: 0.8440 (m-10) cc_final: 0.8138 (m-80) REVERT: G 31 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8599 (t0) REVERT: G 103 LYS cc_start: 0.8222 (mttt) cc_final: 0.7976 (mtpp) REVERT: G 116 VAL cc_start: 0.9167 (t) cc_final: 0.8935 (p) REVERT: G 299 MET cc_start: 0.8744 (mmp) cc_final: 0.8353 (mmp) REVERT: G 307 HIS cc_start: 0.8968 (m-70) cc_final: 0.8661 (m-70) REVERT: G 388 MET cc_start: 0.8291 (mtp) cc_final: 0.7854 (mmt) REVERT: H 129 CYS cc_start: 0.8142 (t) cc_final: 0.7780 (t) REVERT: H 167 PHE cc_start: 0.8303 (m-80) cc_final: 0.8051 (m-80) REVERT: H 198 GLU cc_start: 0.8071 (pt0) cc_final: 0.7860 (pt0) REVERT: H 255 VAL cc_start: 0.9160 (p) cc_final: 0.8952 (p) REVERT: H 257 MET cc_start: 0.8686 (mmp) cc_final: 0.8341 (mmm) REVERT: H 291 GLN cc_start: 0.8801 (pt0) cc_final: 0.8542 (pm20) REVERT: H 298 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8716 (t0) REVERT: H 325 GLU cc_start: 0.7704 (tt0) cc_final: 0.7160 (tt0) REVERT: H 388 MET cc_start: 0.8107 (mtp) cc_final: 0.7375 (mmt) REVERT: H 407 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8545 (mp0) REVERT: I 26 ASP cc_start: 0.7862 (m-30) cc_final: 0.7639 (m-30) REVERT: I 31 ASP cc_start: 0.8814 (t0) cc_final: 0.8219 (t70) REVERT: I 50 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.8273 (m-80) REVERT: I 95 SER cc_start: 0.9313 (m) cc_final: 0.9010 (p) REVERT: I 180 VAL cc_start: 0.9100 (m) cc_final: 0.8668 (p) REVERT: I 198 GLU cc_start: 0.8248 (pt0) cc_final: 0.7762 (pt0) REVERT: I 200 TYR cc_start: 0.9086 (m-80) cc_final: 0.8672 (m-10) REVERT: I 209 ASP cc_start: 0.8528 (t0) cc_final: 0.8325 (t0) REVERT: I 267 MET cc_start: 0.8883 (mtp) cc_final: 0.8665 (mtt) REVERT: I 299 MET cc_start: 0.8671 (mmp) cc_final: 0.8456 (mmp) REVERT: I 364 SER cc_start: 0.9345 (p) cc_final: 0.9138 (m) REVERT: B 31 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8651 (m-30) REVERT: B 37 VAL cc_start: 0.8412 (OUTLIER) cc_final: 0.8004 (p) REVERT: B 46 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8428 (tpp80) REVERT: B 198 GLU cc_start: 0.8170 (pt0) cc_final: 0.7933 (pt0) outliers start: 290 outliers final: 206 residues processed: 1400 average time/residue: 0.5098 time to fit residues: 1164.9021 Evaluate side-chains 1357 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1128 time to evaluate : 4.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 317 LEU Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 379 SER Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain J residue 413 MET Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 112 LYS Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 200 CYS Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 224 TYR Chi-restraints excluded: chain K residue 232 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 304 LYS Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 317 LEU Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 392 ASP Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 198 SER Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 232 SER Chi-restraints excluded: chain L residue 237 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 392 ASP Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 211 CYS Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 407 GLU Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 298 ASN Chi-restraints excluded: chain H residue 407 GLU Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 347 ASN Chi-restraints excluded: chain I residue 381 ILE Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 424 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 458 optimal weight: 2.9990 chunk 348 optimal weight: 10.0000 chunk 240 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 221 optimal weight: 1.9990 chunk 311 optimal weight: 5.9990 chunk 465 optimal weight: 3.9990 chunk 492 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 441 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN J 300 ASN L 300 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 ASN ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN G 423 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 ASN H 347 ASN ** H 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 423 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 424 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 424 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 41998 Z= 0.280 Angle : 0.621 8.355 57035 Z= 0.316 Chirality : 0.045 0.167 6240 Planarity : 0.004 0.051 7411 Dihedral : 11.105 167.494 5876 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.69 % Favored : 95.25 % Rotamer: Outliers : 5.86 % Allowed : 21.37 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.12), residues: 5136 helix: 1.21 (0.11), residues: 2412 sheet: -1.21 (0.19), residues: 732 loop : -1.36 (0.15), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 21 HIS 0.005 0.001 HIS C 61 PHE 0.025 0.002 PHE D 167 TYR 0.025 0.001 TYR B 425 ARG 0.009 0.001 ARG K 339 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1509 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1250 time to evaluate : 4.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7716 (p0) REVERT: A 90 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7946 (tp30) REVERT: A 221 ARG cc_start: 0.7099 (mtt90) cc_final: 0.6667 (mtt-85) REVERT: A 256 GLN cc_start: 0.7935 (pt0) cc_final: 0.7208 (pt0) REVERT: A 392 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7742 (t0) REVERT: A 411 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7661 (tp30) REVERT: C 121 ARG cc_start: 0.8151 (mmm160) cc_final: 0.7909 (tpt170) REVERT: C 206 ASN cc_start: 0.8683 (m110) cc_final: 0.8349 (m-40) REVERT: C 210 TYR cc_start: 0.8374 (m-10) cc_final: 0.8074 (m-80) REVERT: C 228 ASN cc_start: 0.8714 (m-40) cc_final: 0.8450 (m-40) REVERT: C 256 GLN cc_start: 0.8352 (pt0) cc_final: 0.8092 (pt0) REVERT: C 317 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8781 (mt) REVERT: C 322 ASP cc_start: 0.7757 (t0) cc_final: 0.7369 (t70) REVERT: C 377 MET cc_start: 0.8874 (tmm) cc_final: 0.8464 (tmm) REVERT: C 392 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7530 (t0) REVERT: E 3 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7058 (mm-30) REVERT: E 90 GLU cc_start: 0.8222 (tp30) cc_final: 0.7815 (tp30) REVERT: E 210 TYR cc_start: 0.8473 (m-10) cc_final: 0.7925 (m-80) REVERT: E 269 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8593 (pp) REVERT: E 336 LYS cc_start: 0.9038 (mtpm) cc_final: 0.8643 (mtpp) REVERT: E 377 MET cc_start: 0.8835 (tmm) cc_final: 0.8620 (tmm) REVERT: E 413 MET cc_start: 0.7501 (mmm) cc_final: 0.6369 (mmm) REVERT: J 3 GLU cc_start: 0.6933 (mp0) cc_final: 0.6711 (mm-30) REVERT: J 50 ASN cc_start: 0.8353 (t0) cc_final: 0.8084 (t0) REVERT: J 169 PHE cc_start: 0.8890 (m-80) cc_final: 0.8520 (m-10) REVERT: J 199 ASP cc_start: 0.8672 (m-30) cc_final: 0.8447 (t0) REVERT: J 286 LEU cc_start: 0.8643 (mt) cc_final: 0.8253 (pp) REVERT: J 305 CYS cc_start: 0.7643 (m) cc_final: 0.7239 (m) REVERT: J 326 LYS cc_start: 0.8924 (tttm) cc_final: 0.8414 (ptpt) REVERT: J 352 LYS cc_start: 0.8042 (tttp) cc_final: 0.7690 (tppt) REVERT: J 353 VAL cc_start: 0.9513 (t) cc_final: 0.9124 (p) REVERT: J 377 MET cc_start: 0.8855 (ttp) cc_final: 0.8587 (tmm) REVERT: J 386 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7605 (pm20) REVERT: J 392 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.7978 (t0) REVERT: K 90 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7773 (tp30) REVERT: K 113 GLU cc_start: 0.8193 (mp0) cc_final: 0.7923 (mp0) REVERT: K 169 PHE cc_start: 0.8818 (m-80) cc_final: 0.8501 (m-10) REVERT: K 199 ASP cc_start: 0.8318 (m-30) cc_final: 0.8020 (t0) REVERT: K 224 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.8100 (m-80) REVERT: K 300 ASN cc_start: 0.8749 (t0) cc_final: 0.8394 (t0) REVERT: K 326 LYS cc_start: 0.8943 (tttm) cc_final: 0.8418 (ptpt) REVERT: K 352 LYS cc_start: 0.8115 (tttp) cc_final: 0.7698 (tppt) REVERT: K 353 VAL cc_start: 0.9417 (t) cc_final: 0.9155 (m) REVERT: K 357 TYR cc_start: 0.8500 (m-80) cc_final: 0.8242 (m-80) REVERT: K 377 MET cc_start: 0.8950 (tmm) cc_final: 0.8533 (tmm) REVERT: K 386 GLU cc_start: 0.8115 (pp20) cc_final: 0.7746 (pp20) REVERT: K 392 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.7967 (t0) REVERT: L 76 ASP cc_start: 0.8700 (m-30) cc_final: 0.8283 (m-30) REVERT: L 90 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7695 (tp30) REVERT: L 203 MET cc_start: 0.8963 (mmm) cc_final: 0.8711 (mmm) REVERT: L 206 ASN cc_start: 0.8539 (m110) cc_final: 0.8274 (m-40) REVERT: L 210 TYR cc_start: 0.8525 (m-10) cc_final: 0.7971 (m-80) REVERT: L 322 ASP cc_start: 0.7778 (t0) cc_final: 0.7494 (t70) REVERT: L 326 LYS cc_start: 0.8856 (tttm) cc_final: 0.8161 (mttt) REVERT: L 352 LYS cc_start: 0.3848 (tppt) cc_final: 0.3255 (tppt) REVERT: L 357 TYR cc_start: 0.8587 (m-80) cc_final: 0.8315 (m-80) REVERT: L 377 MET cc_start: 0.8857 (tmm) cc_final: 0.8526 (tmm) REVERT: L 392 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8102 (t0) REVERT: F 14 ASN cc_start: 0.8467 (m-40) cc_final: 0.8180 (m-40) REVERT: F 19 LYS cc_start: 0.8917 (mmmt) cc_final: 0.8624 (mmmt) REVERT: F 36 TYR cc_start: 0.8278 (t80) cc_final: 0.7834 (t80) REVERT: F 50 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.7914 (m-10) REVERT: F 106 TYR cc_start: 0.8548 (m-80) cc_final: 0.8341 (m-10) REVERT: F 112 LEU cc_start: 0.8506 (mp) cc_final: 0.8290 (tp) REVERT: F 136 THR cc_start: 0.8995 (m) cc_final: 0.8726 (p) REVERT: F 208 TYR cc_start: 0.8447 (m-10) cc_final: 0.8162 (m-10) REVERT: F 323 MET cc_start: 0.7622 (mmm) cc_final: 0.6994 (mmm) REVERT: F 327 ASP cc_start: 0.8346 (m-30) cc_final: 0.7732 (m-30) REVERT: F 397 TRP cc_start: 0.8867 (m100) cc_final: 0.8644 (m100) REVERT: F 425 TYR cc_start: 0.8995 (m-80) cc_final: 0.8726 (m-80) REVERT: D 22 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7537 (tm-30) REVERT: D 26 ASP cc_start: 0.8116 (m-30) cc_final: 0.7634 (m-30) REVERT: D 108 GLU cc_start: 0.8193 (tp30) cc_final: 0.7785 (tp30) REVERT: D 112 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8080 (tp) REVERT: D 122 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8783 (ttmt) REVERT: D 208 TYR cc_start: 0.8415 (m-10) cc_final: 0.8082 (m-80) REVERT: D 307 HIS cc_start: 0.8676 (m-70) cc_final: 0.8363 (m90) REVERT: D 323 MET cc_start: 0.7837 (mmm) cc_final: 0.7475 (mmm) REVERT: D 327 ASP cc_start: 0.8251 (m-30) cc_final: 0.7983 (m-30) REVERT: G 14 ASN cc_start: 0.8655 (m-40) cc_final: 0.8434 (m-40) REVERT: G 31 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8592 (t0) REVERT: G 103 LYS cc_start: 0.8128 (mttt) cc_final: 0.7870 (mtpp) REVERT: G 116 VAL cc_start: 0.9140 (t) cc_final: 0.8904 (p) REVERT: G 198 GLU cc_start: 0.8608 (pt0) cc_final: 0.8082 (pt0) REVERT: G 205 GLU cc_start: 0.8356 (pt0) cc_final: 0.8119 (pt0) REVERT: G 257 MET cc_start: 0.8494 (mmp) cc_final: 0.8061 (mmm) REVERT: G 299 MET cc_start: 0.8626 (mmp) cc_final: 0.8372 (mmp) REVERT: G 375 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.8093 (pp30) REVERT: G 397 TRP cc_start: 0.8645 (m100) cc_final: 0.8260 (m-10) REVERT: H 129 CYS cc_start: 0.8172 (t) cc_final: 0.7769 (t) REVERT: H 167 PHE cc_start: 0.8011 (m-80) cc_final: 0.7572 (m-80) REVERT: H 291 GLN cc_start: 0.8787 (pt0) cc_final: 0.8513 (pm20) REVERT: H 322 SER cc_start: 0.8029 (m) cc_final: 0.7748 (p) REVERT: H 325 GLU cc_start: 0.7838 (tt0) cc_final: 0.7572 (tt0) REVERT: H 388 MET cc_start: 0.8073 (mtp) cc_final: 0.7360 (mmt) REVERT: H 407 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8446 (mp0) REVERT: I 26 ASP cc_start: 0.7856 (m-30) cc_final: 0.7628 (m-30) REVERT: I 31 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8222 (t70) REVERT: I 50 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.8207 (m-80) REVERT: I 198 GLU cc_start: 0.8117 (pt0) cc_final: 0.7702 (pt0) REVERT: I 200 TYR cc_start: 0.9057 (m-80) cc_final: 0.8704 (m-10) REVERT: I 267 MET cc_start: 0.8918 (mtp) cc_final: 0.8616 (mtt) REVERT: I 299 MET cc_start: 0.8723 (mmp) cc_final: 0.8489 (mmp) REVERT: I 364 SER cc_start: 0.9315 (p) cc_final: 0.9089 (m) REVERT: B 31 ASP cc_start: 0.8880 (OUTLIER) cc_final: 0.8634 (m-30) REVERT: B 37 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.7964 (p) REVERT: B 136 THR cc_start: 0.9031 (m) cc_final: 0.8662 (p) outliers start: 259 outliers final: 192 residues processed: 1422 average time/residue: 0.5105 time to fit residues: 1184.5822 Evaluate side-chains 1372 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1158 time to evaluate : 4.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 280 LYS Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 304 LYS Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 379 SER Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain J residue 413 MET Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 200 CYS Chi-restraints excluded: chain K residue 224 TYR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 304 LYS Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 392 ASP Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 198 SER Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 237 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 392 ASP Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 46 ARG Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 298 ASN Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 211 CYS Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 375 GLN Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 407 GLU Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 407 GLU Chi-restraints excluded: chain H residue 423 GLN Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 83 HIS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 381 ILE Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 372 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 410 optimal weight: 2.9990 chunk 279 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 367 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 chunk 420 optimal weight: 6.9990 chunk 340 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 251 optimal weight: 20.0000 chunk 442 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 ASN ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 300 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 ASN F 424 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 ASN H 298 ASN H 347 ASN ** H 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 423 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 423 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 41998 Z= 0.277 Angle : 0.617 8.947 57035 Z= 0.312 Chirality : 0.045 0.171 6240 Planarity : 0.004 0.050 7411 Dihedral : 10.932 167.464 5868 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.61 % Favored : 95.33 % Rotamer: Outliers : 6.25 % Allowed : 22.32 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.12), residues: 5136 helix: 1.29 (0.11), residues: 2412 sheet: -1.09 (0.19), residues: 732 loop : -1.28 (0.15), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 21 HIS 0.009 0.001 HIS I 6 PHE 0.043 0.002 PHE I 167 TYR 0.022 0.001 TYR J 210 ARG 0.007 0.001 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1485 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1209 time to evaluate : 4.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6856 (mm-30) REVERT: A 90 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7896 (tp30) REVERT: A 214 ARG cc_start: 0.8588 (tmm-80) cc_final: 0.8040 (tmm-80) REVERT: A 221 ARG cc_start: 0.7129 (mtt90) cc_final: 0.6400 (mtt90) REVERT: A 293 ASN cc_start: 0.8728 (m110) cc_final: 0.8463 (m110) REVERT: A 392 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7446 (t0) REVERT: A 411 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7633 (tp30) REVERT: C 121 ARG cc_start: 0.8144 (mmm160) cc_final: 0.7919 (tpt170) REVERT: C 153 LEU cc_start: 0.9343 (tp) cc_final: 0.9113 (tp) REVERT: C 206 ASN cc_start: 0.8681 (m110) cc_final: 0.8348 (m-40) REVERT: C 210 TYR cc_start: 0.8390 (m-10) cc_final: 0.8047 (m-80) REVERT: C 228 ASN cc_start: 0.8793 (m-40) cc_final: 0.8510 (m-40) REVERT: C 256 GLN cc_start: 0.8166 (pt0) cc_final: 0.7653 (pt0) REVERT: C 317 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8738 (mt) REVERT: C 322 ASP cc_start: 0.7783 (t0) cc_final: 0.7402 (t70) REVERT: C 377 MET cc_start: 0.8884 (tmm) cc_final: 0.8616 (tmm) REVERT: C 392 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7300 (t0) REVERT: E 3 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7024 (mm-30) REVERT: E 90 GLU cc_start: 0.8233 (tp30) cc_final: 0.7790 (tp30) REVERT: E 210 TYR cc_start: 0.8491 (m-10) cc_final: 0.7942 (m-80) REVERT: E 336 LYS cc_start: 0.9120 (mtpm) cc_final: 0.8678 (mtpp) REVERT: E 377 MET cc_start: 0.8802 (tmm) cc_final: 0.8593 (tmm) REVERT: E 413 MET cc_start: 0.7539 (mmm) cc_final: 0.6943 (mmm) REVERT: J 149 PHE cc_start: 0.9265 (t80) cc_final: 0.9059 (t80) REVERT: J 169 PHE cc_start: 0.8891 (m-80) cc_final: 0.8516 (m-10) REVERT: J 199 ASP cc_start: 0.8672 (m-30) cc_final: 0.8452 (t0) REVERT: J 286 LEU cc_start: 0.8631 (mt) cc_final: 0.8258 (pp) REVERT: J 305 CYS cc_start: 0.7651 (m) cc_final: 0.7223 (m) REVERT: J 326 LYS cc_start: 0.8940 (tttm) cc_final: 0.8187 (mttt) REVERT: J 352 LYS cc_start: 0.8026 (tttp) cc_final: 0.7628 (tppt) REVERT: J 353 VAL cc_start: 0.9483 (t) cc_final: 0.9111 (p) REVERT: J 386 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7676 (pm20) REVERT: J 392 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8060 (t0) REVERT: K 3 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6636 (mm-30) REVERT: K 199 ASP cc_start: 0.8391 (m-30) cc_final: 0.8098 (t0) REVERT: K 300 ASN cc_start: 0.8753 (t0) cc_final: 0.8323 (t0) REVERT: K 326 LYS cc_start: 0.8890 (tttm) cc_final: 0.8334 (ptpt) REVERT: K 352 LYS cc_start: 0.8056 (tttp) cc_final: 0.7573 (tppt) REVERT: K 353 VAL cc_start: 0.9418 (t) cc_final: 0.9182 (m) REVERT: K 357 TYR cc_start: 0.8486 (m-80) cc_final: 0.8269 (m-80) REVERT: K 377 MET cc_start: 0.8934 (tmm) cc_final: 0.8524 (tmm) REVERT: K 386 GLU cc_start: 0.8035 (pp20) cc_final: 0.7690 (pp20) REVERT: K 392 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7924 (t0) REVERT: K 425 MET cc_start: 0.8748 (mmp) cc_final: 0.8503 (mmp) REVERT: L 76 ASP cc_start: 0.8767 (m-30) cc_final: 0.8344 (m-30) REVERT: L 90 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7701 (tp30) REVERT: L 203 MET cc_start: 0.8944 (mmm) cc_final: 0.8738 (mmm) REVERT: L 206 ASN cc_start: 0.8434 (m110) cc_final: 0.8091 (m-40) REVERT: L 210 TYR cc_start: 0.8470 (m-10) cc_final: 0.8037 (m-80) REVERT: L 322 ASP cc_start: 0.7826 (t0) cc_final: 0.7524 (t70) REVERT: L 326 LYS cc_start: 0.8892 (tttm) cc_final: 0.8128 (mttt) REVERT: L 352 LYS cc_start: 0.3695 (tppt) cc_final: 0.2642 (mmtt) REVERT: L 357 TYR cc_start: 0.8622 (m-80) cc_final: 0.8387 (m-80) REVERT: L 377 MET cc_start: 0.8819 (tmm) cc_final: 0.8413 (tmm) REVERT: L 392 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8068 (t0) REVERT: F 19 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8707 (mmmt) REVERT: F 36 TYR cc_start: 0.8284 (t80) cc_final: 0.7753 (t80) REVERT: F 50 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.7951 (m-10) REVERT: F 112 LEU cc_start: 0.8516 (mp) cc_final: 0.8312 (tp) REVERT: F 208 TYR cc_start: 0.8470 (m-10) cc_final: 0.8233 (m-10) REVERT: F 323 MET cc_start: 0.7650 (mmm) cc_final: 0.6959 (mmm) REVERT: F 327 ASP cc_start: 0.8331 (m-30) cc_final: 0.7661 (m-30) REVERT: D 22 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7413 (tm-30) REVERT: D 26 ASP cc_start: 0.8065 (m-30) cc_final: 0.7542 (m-30) REVERT: D 45 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: D 46 ARG cc_start: 0.8610 (mmt-90) cc_final: 0.8299 (tpp80) REVERT: D 108 GLU cc_start: 0.8261 (tp30) cc_final: 0.7844 (tp30) REVERT: D 122 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8786 (ttmt) REVERT: D 208 TYR cc_start: 0.8403 (m-10) cc_final: 0.8037 (m-80) REVERT: D 279 GLN cc_start: 0.8490 (pm20) cc_final: 0.8108 (pt0) REVERT: D 307 HIS cc_start: 0.8674 (m-70) cc_final: 0.8394 (m90) REVERT: D 333 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8815 (tp) REVERT: D 414 ASN cc_start: 0.8234 (t0) cc_final: 0.7964 (t0) REVERT: G 31 ASP cc_start: 0.8991 (OUTLIER) cc_final: 0.8601 (t0) REVERT: G 121 ARG cc_start: 0.8676 (ttm110) cc_final: 0.7809 (mtm-85) REVERT: G 198 GLU cc_start: 0.8684 (pt0) cc_final: 0.8267 (pt0) REVERT: G 205 GLU cc_start: 0.8362 (pt0) cc_final: 0.8158 (pt0) REVERT: G 257 MET cc_start: 0.8401 (mmp) cc_final: 0.7918 (mmm) REVERT: G 397 TRP cc_start: 0.8550 (m100) cc_final: 0.8259 (m-10) REVERT: H 31 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8241 (t0) REVERT: H 125 GLU cc_start: 0.8227 (mp0) cc_final: 0.7710 (mp0) REVERT: H 129 CYS cc_start: 0.8203 (t) cc_final: 0.7815 (t) REVERT: H 213 ARG cc_start: 0.8244 (ttm110) cc_final: 0.7886 (ttp-110) REVERT: H 291 GLN cc_start: 0.8800 (pt0) cc_final: 0.8514 (pm20) REVERT: H 322 SER cc_start: 0.8017 (m) cc_final: 0.7701 (p) REVERT: H 325 GLU cc_start: 0.7827 (tt0) cc_final: 0.7504 (tt0) REVERT: H 388 MET cc_start: 0.8092 (mtp) cc_final: 0.7369 (mmt) REVERT: H 407 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8453 (mp0) REVERT: I 26 ASP cc_start: 0.7888 (m-30) cc_final: 0.7657 (m-30) REVERT: I 31 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8254 (t70) REVERT: I 50 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.7937 (m-80) REVERT: I 198 GLU cc_start: 0.8077 (pt0) cc_final: 0.7648 (pt0) REVERT: I 205 GLU cc_start: 0.8547 (tt0) cc_final: 0.8255 (pp20) REVERT: I 267 MET cc_start: 0.8911 (mtp) cc_final: 0.8603 (mtt) REVERT: I 299 MET cc_start: 0.8723 (mmp) cc_final: 0.8483 (mmp) REVERT: I 364 SER cc_start: 0.9325 (p) cc_final: 0.9065 (m) REVERT: B 31 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8645 (m-30) REVERT: B 37 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.7976 (p) REVERT: B 136 THR cc_start: 0.8970 (m) cc_final: 0.8691 (p) REVERT: B 333 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.8848 (tp) outliers start: 276 outliers final: 215 residues processed: 1384 average time/residue: 0.5130 time to fit residues: 1162.5929 Evaluate side-chains 1384 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1148 time to evaluate : 4.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 280 LYS Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 304 LYS Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 379 SER Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain J residue 413 MET Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 304 LYS Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 392 ASP Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 198 SER Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 232 SER Chi-restraints excluded: chain L residue 237 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 392 ASP Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 211 CYS Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 334 GLN Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 407 GLU Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 407 GLU Chi-restraints excluded: chain H residue 423 GLN Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 83 HIS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 347 ASN Chi-restraints excluded: chain I residue 381 ILE Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 372 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 165 optimal weight: 0.0570 chunk 443 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 289 optimal weight: 4.9990 chunk 121 optimal weight: 0.0050 chunk 493 optimal weight: 0.8980 chunk 409 optimal weight: 0.0980 chunk 228 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 259 optimal weight: 1.9990 overall best weight: 0.6114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN ** J 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 ASN K 206 ASN K 293 ASN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 ASN ** H 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 423 GLN I 204 ASN I 423 GLN B 165 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 41998 Z= 0.160 Angle : 0.580 9.989 57035 Z= 0.289 Chirality : 0.043 0.172 6240 Planarity : 0.004 0.047 7411 Dihedral : 10.492 167.693 5856 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.10 % Favored : 96.87 % Rotamer: Outliers : 4.28 % Allowed : 24.56 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.12), residues: 5136 helix: 1.40 (0.11), residues: 2448 sheet: -0.83 (0.19), residues: 756 loop : -1.13 (0.15), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 397 HIS 0.007 0.001 HIS I 6 PHE 0.021 0.001 PHE E 169 TYR 0.024 0.001 TYR J 210 ARG 0.007 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1522 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1333 time to evaluate : 5.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6771 (mm-30) REVERT: A 75 ILE cc_start: 0.8609 (mm) cc_final: 0.8325 (mm) REVERT: A 90 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7836 (tp30) REVERT: A 214 ARG cc_start: 0.8560 (tmm-80) cc_final: 0.8033 (tmm-80) REVERT: A 221 ARG cc_start: 0.7142 (mtt90) cc_final: 0.6138 (mtt90) REVERT: A 293 ASN cc_start: 0.8692 (m110) cc_final: 0.8408 (m110) REVERT: C 76 ASP cc_start: 0.8571 (m-30) cc_final: 0.8166 (m-30) REVERT: C 121 ARG cc_start: 0.8037 (mmm160) cc_final: 0.7815 (tpt170) REVERT: C 206 ASN cc_start: 0.8607 (m110) cc_final: 0.8198 (m-40) REVERT: C 210 TYR cc_start: 0.8342 (m-10) cc_final: 0.7944 (m-80) REVERT: C 212 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8626 (mp) REVERT: C 317 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8556 (mt) REVERT: C 322 ASP cc_start: 0.7700 (t0) cc_final: 0.7271 (t70) REVERT: C 377 MET cc_start: 0.8843 (tmm) cc_final: 0.8437 (tmm) REVERT: C 392 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.7749 (t0) REVERT: C 430 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8706 (ptmm) REVERT: E 3 GLU cc_start: 0.7567 (mm-30) cc_final: 0.6995 (mm-30) REVERT: E 33 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7181 (p0) REVERT: E 210 TYR cc_start: 0.8369 (m-10) cc_final: 0.7888 (m-80) REVERT: E 269 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8475 (pp) REVERT: E 336 LYS cc_start: 0.9055 (mtpm) cc_final: 0.8642 (mtpp) REVERT: E 413 MET cc_start: 0.7184 (mmm) cc_final: 0.6929 (mtm) REVERT: J 3 GLU cc_start: 0.6830 (mp0) cc_final: 0.6612 (mm-30) REVERT: J 169 PHE cc_start: 0.8843 (m-80) cc_final: 0.8509 (m-10) REVERT: J 199 ASP cc_start: 0.8562 (m-30) cc_final: 0.8326 (t0) REVERT: J 286 LEU cc_start: 0.8554 (mt) cc_final: 0.8183 (pp) REVERT: J 305 CYS cc_start: 0.7581 (m) cc_final: 0.7204 (m) REVERT: J 326 LYS cc_start: 0.8893 (tttm) cc_final: 0.8381 (ptpt) REVERT: J 352 LYS cc_start: 0.7947 (tttp) cc_final: 0.7574 (tppt) REVERT: J 353 VAL cc_start: 0.9454 (t) cc_final: 0.9084 (p) REVERT: J 357 TYR cc_start: 0.8595 (m-80) cc_final: 0.8188 (m-80) REVERT: J 377 MET cc_start: 0.8924 (ttp) cc_final: 0.8309 (tmm) REVERT: J 386 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7695 (pp20) REVERT: J 392 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8162 (t0) REVERT: K 3 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6651 (mm-30) REVERT: K 75 ILE cc_start: 0.9002 (mm) cc_final: 0.8646 (mm) REVERT: K 90 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: K 169 PHE cc_start: 0.8605 (m-80) cc_final: 0.8370 (m-10) REVERT: K 199 ASP cc_start: 0.8367 (m-30) cc_final: 0.8069 (t0) REVERT: K 300 ASN cc_start: 0.8693 (t0) cc_final: 0.8328 (t0) REVERT: K 326 LYS cc_start: 0.8849 (tttm) cc_final: 0.8317 (ptpt) REVERT: K 352 LYS cc_start: 0.7992 (tttp) cc_final: 0.7547 (tppt) REVERT: K 357 TYR cc_start: 0.8419 (m-80) cc_final: 0.8164 (m-80) REVERT: K 377 MET cc_start: 0.8949 (tmm) cc_final: 0.8535 (tmm) REVERT: K 392 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.7991 (t0) REVERT: L 3 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6958 (mm-30) REVERT: L 75 ILE cc_start: 0.8998 (mm) cc_final: 0.8746 (mm) REVERT: L 76 ASP cc_start: 0.8652 (m-30) cc_final: 0.8179 (m-30) REVERT: L 90 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7610 (tp30) REVERT: L 203 MET cc_start: 0.8903 (mmm) cc_final: 0.8617 (mmm) REVERT: L 206 ASN cc_start: 0.8087 (m110) cc_final: 0.7787 (m-40) REVERT: L 210 TYR cc_start: 0.8467 (m-10) cc_final: 0.7964 (m-80) REVERT: L 322 ASP cc_start: 0.7753 (t0) cc_final: 0.7447 (t70) REVERT: L 326 LYS cc_start: 0.8847 (tttm) cc_final: 0.8069 (mttt) REVERT: L 352 LYS cc_start: 0.3804 (tppt) cc_final: 0.2845 (mmtt) REVERT: L 357 TYR cc_start: 0.8607 (m-80) cc_final: 0.8388 (m-80) REVERT: L 377 MET cc_start: 0.8806 (tmm) cc_final: 0.8372 (tmm) REVERT: L 392 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8118 (t0) REVERT: L 425 MET cc_start: 0.8660 (mmp) cc_final: 0.8322 (tpp) REVERT: F 36 TYR cc_start: 0.8195 (t80) cc_final: 0.7693 (t80) REVERT: F 50 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7894 (m-80) REVERT: F 112 LEU cc_start: 0.8463 (mp) cc_final: 0.8243 (tp) REVERT: F 121 ARG cc_start: 0.8790 (ttm110) cc_final: 0.8514 (mtm-85) REVERT: F 252 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7930 (mtpt) REVERT: F 300 MET cc_start: 0.8330 (mtt) cc_final: 0.8107 (mtt) REVERT: F 323 MET cc_start: 0.7664 (mmm) cc_final: 0.6862 (mmm) REVERT: F 327 ASP cc_start: 0.8325 (m-30) cc_final: 0.7573 (m-30) REVERT: F 379 LYS cc_start: 0.9127 (ttpt) cc_final: 0.8736 (ptpt) REVERT: D 22 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7402 (tm-30) REVERT: D 26 ASP cc_start: 0.8012 (m-30) cc_final: 0.7430 (m-30) REVERT: D 45 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: D 46 ARG cc_start: 0.8422 (mmt-90) cc_final: 0.8149 (tpp80) REVERT: D 86 ARG cc_start: 0.6915 (ttp80) cc_final: 0.6407 (ttp80) REVERT: D 108 GLU cc_start: 0.8312 (tp30) cc_final: 0.7855 (tp30) REVERT: D 122 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8785 (ttpt) REVERT: D 208 TYR cc_start: 0.8370 (m-10) cc_final: 0.8098 (m-80) REVERT: D 279 GLN cc_start: 0.8375 (pm20) cc_final: 0.8056 (pt0) REVERT: D 307 HIS cc_start: 0.8660 (m-70) cc_final: 0.8420 (m90) REVERT: D 406 MET cc_start: 0.7908 (mmm) cc_final: 0.7525 (mmm) REVERT: D 414 ASN cc_start: 0.8089 (t0) cc_final: 0.7848 (t0) REVERT: G 31 ASP cc_start: 0.8947 (OUTLIER) cc_final: 0.8551 (t0) REVERT: G 121 ARG cc_start: 0.8686 (ttm110) cc_final: 0.7845 (mtm-85) REVERT: G 180 VAL cc_start: 0.9071 (m) cc_final: 0.8715 (p) REVERT: G 198 GLU cc_start: 0.8582 (pt0) cc_final: 0.8161 (pt0) REVERT: G 257 MET cc_start: 0.8179 (mmp) cc_final: 0.7309 (mmp) REVERT: G 312 THR cc_start: 0.7956 (p) cc_final: 0.7709 (p) REVERT: G 375 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7962 (pp30) REVERT: G 397 TRP cc_start: 0.8617 (m100) cc_final: 0.8335 (m-10) REVERT: G 419 VAL cc_start: 0.9259 (t) cc_final: 0.9053 (p) REVERT: H 31 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8236 (t0) REVERT: H 129 CYS cc_start: 0.8166 (t) cc_final: 0.7750 (t) REVERT: H 209 ASP cc_start: 0.8561 (t0) cc_final: 0.8353 (t0) REVERT: H 291 GLN cc_start: 0.8787 (pt0) cc_final: 0.8474 (pm20) REVERT: H 325 GLU cc_start: 0.7798 (tt0) cc_final: 0.7251 (tt0) REVERT: H 388 MET cc_start: 0.8038 (mtp) cc_final: 0.7321 (mmt) REVERT: H 407 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8329 (mp0) REVERT: I 26 ASP cc_start: 0.7856 (m-30) cc_final: 0.7603 (m-30) REVERT: I 31 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8247 (t0) REVERT: I 50 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7683 (m-80) REVERT: I 73 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8253 (mpp) REVERT: I 180 VAL cc_start: 0.9098 (m) cc_final: 0.8606 (p) REVERT: I 198 GLU cc_start: 0.7896 (pt0) cc_final: 0.7644 (pt0) REVERT: I 267 MET cc_start: 0.8793 (mtp) cc_final: 0.8502 (mtt) REVERT: I 291 GLN cc_start: 0.8824 (pt0) cc_final: 0.8525 (mm-40) REVERT: I 299 MET cc_start: 0.8745 (mmp) cc_final: 0.8480 (mmp) REVERT: I 322 SER cc_start: 0.7772 (m) cc_final: 0.7534 (p) REVERT: B 22 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7090 (tm-30) REVERT: B 26 ASP cc_start: 0.8438 (t0) cc_final: 0.8083 (m-30) REVERT: B 147 MET cc_start: 0.7882 (ttp) cc_final: 0.7528 (ttp) REVERT: B 255 VAL cc_start: 0.9069 (p) cc_final: 0.8783 (p) REVERT: B 329 GLN cc_start: 0.9182 (mm-40) cc_final: 0.8910 (mm-40) REVERT: B 359 ARG cc_start: 0.7077 (ttp-170) cc_final: 0.6731 (tmm160) outliers start: 189 outliers final: 126 residues processed: 1446 average time/residue: 0.5363 time to fit residues: 1264.8564 Evaluate side-chains 1384 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1236 time to evaluate : 4.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 280 LYS Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 392 ASP Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 392 ASP Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 334 GLN Chi-restraints excluded: chain G residue 375 GLN Chi-restraints excluded: chain G residue 407 GLU Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 298 ASN Chi-restraints excluded: chain H residue 407 GLU Chi-restraints excluded: chain H residue 423 GLN Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 83 HIS Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 372 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 475 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 281 optimal weight: 0.9980 chunk 360 optimal weight: 6.9990 chunk 279 optimal weight: 4.9990 chunk 415 optimal weight: 0.7980 chunk 275 optimal weight: 1.9990 chunk 491 optimal weight: 7.9990 chunk 307 optimal weight: 3.9990 chunk 299 optimal weight: 9.9990 chunk 226 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN ** J 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 ASN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 ASN H 298 ASN H 375 GLN H 423 GLN I 291 GLN I 423 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41998 Z= 0.192 Angle : 0.603 17.216 57035 Z= 0.298 Chirality : 0.044 0.234 6240 Planarity : 0.004 0.047 7411 Dihedral : 10.328 167.845 5846 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.62 % Favored : 96.34 % Rotamer: Outliers : 4.37 % Allowed : 25.58 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.12), residues: 5136 helix: 1.42 (0.11), residues: 2448 sheet: -0.77 (0.19), residues: 756 loop : -1.08 (0.15), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 397 HIS 0.010 0.001 HIS I 6 PHE 0.040 0.002 PHE H 20 TYR 0.021 0.001 TYR J 210 ARG 0.012 0.000 ARG J 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1450 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1257 time to evaluate : 4.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6669 (mm-30) REVERT: A 90 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7786 (tp30) REVERT: A 214 ARG cc_start: 0.8562 (tmm-80) cc_final: 0.8030 (tmm-80) REVERT: A 221 ARG cc_start: 0.7143 (mtt90) cc_final: 0.6125 (mtt90) REVERT: A 293 ASN cc_start: 0.8704 (m110) cc_final: 0.8438 (m110) REVERT: C 1 MET cc_start: 0.8426 (ppp) cc_final: 0.8207 (ppp) REVERT: C 76 ASP cc_start: 0.8612 (m-30) cc_final: 0.8219 (m-30) REVERT: C 199 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7491 (t0) REVERT: C 206 ASN cc_start: 0.8627 (m110) cc_final: 0.8167 (m-40) REVERT: C 210 TYR cc_start: 0.8356 (m-10) cc_final: 0.7923 (m-80) REVERT: C 212 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8546 (mp) REVERT: C 317 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8576 (mt) REVERT: C 322 ASP cc_start: 0.7748 (t0) cc_final: 0.7333 (t70) REVERT: C 392 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7818 (t0) REVERT: E 3 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7061 (mm-30) REVERT: E 269 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8467 (pp) REVERT: E 377 MET cc_start: 0.8878 (tmm) cc_final: 0.8625 (tmm) REVERT: E 386 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7546 (pm20) REVERT: E 413 MET cc_start: 0.7248 (mmm) cc_final: 0.6441 (mtp) REVERT: J 169 PHE cc_start: 0.8831 (m-80) cc_final: 0.8481 (m-10) REVERT: J 199 ASP cc_start: 0.8571 (m-30) cc_final: 0.8345 (t0) REVERT: J 286 LEU cc_start: 0.8542 (mt) cc_final: 0.8183 (pp) REVERT: J 300 ASN cc_start: 0.8697 (t160) cc_final: 0.8445 (t0) REVERT: J 305 CYS cc_start: 0.7697 (m) cc_final: 0.7252 (m) REVERT: J 326 LYS cc_start: 0.8893 (tttm) cc_final: 0.8426 (ptpt) REVERT: J 352 LYS cc_start: 0.8015 (tttp) cc_final: 0.7117 (mmtt) REVERT: J 353 VAL cc_start: 0.9463 (t) cc_final: 0.9231 (m) REVERT: J 357 TYR cc_start: 0.8648 (m-80) cc_final: 0.8257 (m-80) REVERT: J 377 MET cc_start: 0.8901 (ttp) cc_final: 0.8336 (tmm) REVERT: J 386 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7760 (pm20) REVERT: J 392 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8172 (t0) REVERT: K 3 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6534 (mm-30) REVERT: K 75 ILE cc_start: 0.8999 (mm) cc_final: 0.8621 (mm) REVERT: K 90 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: K 169 PHE cc_start: 0.8652 (m-80) cc_final: 0.8377 (m-10) REVERT: K 199 ASP cc_start: 0.8376 (m-30) cc_final: 0.8074 (t0) REVERT: K 300 ASN cc_start: 0.8700 (t0) cc_final: 0.8289 (t0) REVERT: K 326 LYS cc_start: 0.8820 (tttm) cc_final: 0.8323 (ptpt) REVERT: K 352 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7435 (tppt) REVERT: K 377 MET cc_start: 0.8955 (tmm) cc_final: 0.8532 (tmm) REVERT: K 392 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.7970 (t0) REVERT: L 75 ILE cc_start: 0.9021 (mm) cc_final: 0.8768 (mm) REVERT: L 76 ASP cc_start: 0.8689 (m-30) cc_final: 0.8237 (m-30) REVERT: L 90 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7588 (tp30) REVERT: L 117 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8693 (tt) REVERT: L 203 MET cc_start: 0.8888 (mmm) cc_final: 0.8652 (mmm) REVERT: L 210 TYR cc_start: 0.8451 (m-10) cc_final: 0.8133 (m-80) REVERT: L 322 ASP cc_start: 0.7768 (t0) cc_final: 0.7445 (t70) REVERT: L 326 LYS cc_start: 0.8861 (tttm) cc_final: 0.8071 (mttt) REVERT: L 352 LYS cc_start: 0.3728 (tppt) cc_final: 0.2807 (mmtt) REVERT: L 377 MET cc_start: 0.8809 (tmm) cc_final: 0.8313 (tmm) REVERT: L 392 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8101 (t0) REVERT: L 425 MET cc_start: 0.8650 (mmp) cc_final: 0.8346 (tpp) REVERT: F 36 TYR cc_start: 0.8149 (t80) cc_final: 0.7686 (t80) REVERT: F 50 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: F 112 LEU cc_start: 0.8505 (mp) cc_final: 0.8288 (tp) REVERT: F 121 ARG cc_start: 0.8803 (ttm110) cc_final: 0.8504 (mtm-85) REVERT: F 197 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7973 (t0) REVERT: F 300 MET cc_start: 0.8376 (mtt) cc_final: 0.8129 (mtt) REVERT: F 323 MET cc_start: 0.7639 (mmm) cc_final: 0.6739 (mmm) REVERT: F 327 ASP cc_start: 0.8341 (m-30) cc_final: 0.7559 (m-30) REVERT: F 379 LYS cc_start: 0.9134 (ttpt) cc_final: 0.8690 (ptpt) REVERT: D 22 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7326 (tm-30) REVERT: D 26 ASP cc_start: 0.8045 (m-30) cc_final: 0.7449 (m-30) REVERT: D 45 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: D 46 ARG cc_start: 0.8480 (mmt-90) cc_final: 0.8185 (tpp80) REVERT: D 108 GLU cc_start: 0.8308 (tp30) cc_final: 0.7804 (tp30) REVERT: D 122 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8794 (ttpt) REVERT: D 198 GLU cc_start: 0.8309 (pt0) cc_final: 0.7986 (pt0) REVERT: D 208 TYR cc_start: 0.8341 (m-10) cc_final: 0.8093 (m-80) REVERT: D 279 GLN cc_start: 0.8378 (pm20) cc_final: 0.8046 (pt0) REVERT: D 307 HIS cc_start: 0.8683 (m-70) cc_final: 0.8440 (m90) REVERT: D 406 MET cc_start: 0.7870 (mmm) cc_final: 0.7496 (mmm) REVERT: D 414 ASN cc_start: 0.8185 (t0) cc_final: 0.7961 (t0) REVERT: G 14 ASN cc_start: 0.8517 (m-40) cc_final: 0.8241 (m110) REVERT: G 31 ASP cc_start: 0.8947 (OUTLIER) cc_final: 0.8590 (t0) REVERT: G 121 ARG cc_start: 0.8685 (ttm110) cc_final: 0.7854 (mtm-85) REVERT: G 180 VAL cc_start: 0.9084 (m) cc_final: 0.8736 (p) REVERT: G 196 THR cc_start: 0.7679 (m) cc_final: 0.7444 (m) REVERT: G 198 GLU cc_start: 0.8517 (pt0) cc_final: 0.8124 (pt0) REVERT: G 257 MET cc_start: 0.8198 (mmp) cc_final: 0.7304 (mmp) REVERT: G 312 THR cc_start: 0.7950 (p) cc_final: 0.7700 (p) REVERT: G 363 MET cc_start: 0.8317 (ptp) cc_final: 0.8070 (ptp) REVERT: G 397 TRP cc_start: 0.8626 (m100) cc_final: 0.8333 (m-10) REVERT: G 407 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8520 (mp0) REVERT: H 31 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8239 (t0) REVERT: H 129 CYS cc_start: 0.8181 (t) cc_final: 0.7824 (t) REVERT: H 291 GLN cc_start: 0.8808 (pt0) cc_final: 0.8500 (pm20) REVERT: H 304 ASP cc_start: 0.8511 (t0) cc_final: 0.8299 (t70) REVERT: H 325 GLU cc_start: 0.7835 (tt0) cc_final: 0.7247 (tt0) REVERT: H 388 MET cc_start: 0.8065 (mtp) cc_final: 0.7356 (mmt) REVERT: H 407 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8298 (mp0) REVERT: I 26 ASP cc_start: 0.7872 (m-30) cc_final: 0.7548 (m-30) REVERT: I 31 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8243 (t0) REVERT: I 50 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.7708 (m-80) REVERT: I 73 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8179 (mpp) REVERT: I 180 VAL cc_start: 0.9100 (m) cc_final: 0.8605 (p) REVERT: I 198 GLU cc_start: 0.7904 (pt0) cc_final: 0.7631 (pt0) REVERT: I 267 MET cc_start: 0.8799 (mtp) cc_final: 0.8492 (mtt) REVERT: I 291 GLN cc_start: 0.8804 (pt0) cc_final: 0.8604 (mm-40) REVERT: I 299 MET cc_start: 0.8711 (mmp) cc_final: 0.8465 (mmp) REVERT: I 322 SER cc_start: 0.7824 (m) cc_final: 0.7579 (p) REVERT: I 334 GLN cc_start: 0.8983 (mt0) cc_final: 0.8700 (mt0) REVERT: B 88 ASP cc_start: 0.7163 (p0) cc_final: 0.6637 (p0) REVERT: B 147 MET cc_start: 0.8050 (ttp) cc_final: 0.7802 (ttt) REVERT: B 255 VAL cc_start: 0.9101 (p) cc_final: 0.8857 (p) REVERT: B 329 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8899 (mm-40) REVERT: B 359 ARG cc_start: 0.7040 (ttp-170) cc_final: 0.6755 (tmm160) outliers start: 193 outliers final: 134 residues processed: 1371 average time/residue: 0.5177 time to fit residues: 1152.9992 Evaluate side-chains 1353 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1193 time to evaluate : 5.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 280 LYS Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 317 LEU Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 352 LYS Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 392 ASP Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 392 ASP Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 211 CYS Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 334 GLN Chi-restraints excluded: chain G residue 407 GLU Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 407 GLU Chi-restraints excluded: chain H residue 423 GLN Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 423 GLN Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 372 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 304 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 293 optimal weight: 0.4980 chunk 148 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 312 optimal weight: 8.9990 chunk 334 optimal weight: 7.9990 chunk 243 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 386 optimal weight: 1.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN ** J 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 ASN ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 300 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 HIS ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 ASN H 375 GLN H 423 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 291 GLN I 423 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 41998 Z= 0.298 Angle : 0.655 14.942 57035 Z= 0.327 Chirality : 0.045 0.219 6240 Planarity : 0.004 0.050 7411 Dihedral : 10.453 169.671 5840 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.44 % Favored : 95.54 % Rotamer: Outliers : 4.48 % Allowed : 25.90 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.12), residues: 5136 helix: 1.30 (0.11), residues: 2448 sheet: -0.96 (0.19), residues: 774 loop : -1.09 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 397 HIS 0.008 0.001 HIS F 6 PHE 0.037 0.002 PHE F 167 TYR 0.021 0.002 TYR J 103 ARG 0.010 0.001 ARG K 339 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1395 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1197 time to evaluate : 4.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6627 (mm-30) REVERT: A 90 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7875 (tp30) REVERT: A 214 ARG cc_start: 0.8581 (tmm-80) cc_final: 0.8035 (tmm-80) REVERT: A 221 ARG cc_start: 0.7217 (mtt90) cc_final: 0.6363 (mtt90) REVERT: A 293 ASN cc_start: 0.8745 (m110) cc_final: 0.8496 (m110) REVERT: A 300 ASN cc_start: 0.8649 (t0) cc_final: 0.8217 (t0) REVERT: C 1 MET cc_start: 0.8367 (ppp) cc_final: 0.8129 (ppp) REVERT: C 76 ASP cc_start: 0.8655 (m-30) cc_final: 0.8261 (m-30) REVERT: C 199 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7489 (t0) REVERT: C 206 ASN cc_start: 0.8683 (m110) cc_final: 0.8142 (m-40) REVERT: C 210 TYR cc_start: 0.8358 (m-10) cc_final: 0.7888 (m-80) REVERT: C 212 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8600 (mp) REVERT: C 293 ASN cc_start: 0.8743 (m110) cc_final: 0.8505 (m110) REVERT: C 317 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8616 (mt) REVERT: C 322 ASP cc_start: 0.7753 (t0) cc_final: 0.7381 (t70) REVERT: E 3 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7102 (mm-30) REVERT: E 33 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7332 (p0) REVERT: E 103 TYR cc_start: 0.8607 (t80) cc_final: 0.8356 (t80) REVERT: E 199 ASP cc_start: 0.7389 (m-30) cc_final: 0.6949 (m-30) REVERT: E 210 TYR cc_start: 0.8464 (m-10) cc_final: 0.7952 (m-80) REVERT: E 357 TYR cc_start: 0.8397 (m-80) cc_final: 0.8192 (m-80) REVERT: E 377 MET cc_start: 0.8873 (tmm) cc_final: 0.8579 (tmm) REVERT: E 386 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7525 (pm20) REVERT: J 286 LEU cc_start: 0.8591 (mt) cc_final: 0.8229 (pp) REVERT: J 300 ASN cc_start: 0.8842 (t160) cc_final: 0.8611 (t0) REVERT: J 305 CYS cc_start: 0.7733 (m) cc_final: 0.7295 (m) REVERT: J 319 TYR cc_start: 0.9083 (m-80) cc_final: 0.8819 (m-80) REVERT: J 326 LYS cc_start: 0.8949 (tttm) cc_final: 0.8428 (ptpt) REVERT: J 352 LYS cc_start: 0.8005 (tttp) cc_final: 0.7676 (tppt) REVERT: J 357 TYR cc_start: 0.8666 (m-80) cc_final: 0.8261 (m-80) REVERT: J 377 MET cc_start: 0.8890 (ttp) cc_final: 0.8541 (tmm) REVERT: J 386 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7717 (pm20) REVERT: J 392 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8082 (t0) REVERT: K 3 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6620 (mm-30) REVERT: K 75 ILE cc_start: 0.9074 (mm) cc_final: 0.8693 (mm) REVERT: K 169 PHE cc_start: 0.8699 (m-80) cc_final: 0.8407 (m-10) REVERT: K 199 ASP cc_start: 0.8433 (m-30) cc_final: 0.8158 (t0) REVERT: K 300 ASN cc_start: 0.8785 (t0) cc_final: 0.8338 (t0) REVERT: K 326 LYS cc_start: 0.8835 (tttm) cc_final: 0.8348 (ptpt) REVERT: K 352 LYS cc_start: 0.7942 (tttp) cc_final: 0.7421 (tppt) REVERT: K 377 MET cc_start: 0.8983 (tmm) cc_final: 0.8553 (tmm) REVERT: K 386 GLU cc_start: 0.8112 (pp20) cc_final: 0.7842 (pp20) REVERT: K 392 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.7781 (t0) REVERT: L 76 ASP cc_start: 0.8724 (m-30) cc_final: 0.8218 (m-30) REVERT: L 90 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7610 (tp30) REVERT: L 117 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8723 (tt) REVERT: L 203 MET cc_start: 0.8950 (mmm) cc_final: 0.8687 (mmm) REVERT: L 210 TYR cc_start: 0.8515 (m-10) cc_final: 0.8027 (m-80) REVERT: L 322 ASP cc_start: 0.7769 (t0) cc_final: 0.7459 (t70) REVERT: L 326 LYS cc_start: 0.8894 (tttm) cc_final: 0.8141 (mttt) REVERT: L 352 LYS cc_start: 0.3665 (tppt) cc_final: 0.2809 (mmtt) REVERT: L 377 MET cc_start: 0.8824 (tmm) cc_final: 0.8353 (tmm) REVERT: F 36 TYR cc_start: 0.8184 (t80) cc_final: 0.7782 (t80) REVERT: F 50 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7875 (m-80) REVERT: F 213 ARG cc_start: 0.8044 (ttp-110) cc_final: 0.7557 (ptp-170) REVERT: F 323 MET cc_start: 0.7045 (mmm) cc_final: 0.6687 (mmm) REVERT: F 327 ASP cc_start: 0.8371 (m-30) cc_final: 0.7774 (m-30) REVERT: D 22 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7396 (tm-30) REVERT: D 26 ASP cc_start: 0.8085 (m-30) cc_final: 0.7454 (m-30) REVERT: D 108 GLU cc_start: 0.8331 (tp30) cc_final: 0.7877 (tp30) REVERT: D 122 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8799 (ttpt) REVERT: D 208 TYR cc_start: 0.8454 (m-10) cc_final: 0.8164 (m-80) REVERT: D 279 GLN cc_start: 0.8406 (pm20) cc_final: 0.8073 (pt0) REVERT: D 333 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.8780 (tp) REVERT: D 397 TRP cc_start: 0.8880 (m100) cc_final: 0.8675 (m100) REVERT: D 406 MET cc_start: 0.7911 (mmm) cc_final: 0.7568 (mmm) REVERT: D 414 ASN cc_start: 0.8313 (t0) cc_final: 0.8088 (t0) REVERT: G 31 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8628 (t0) REVERT: G 121 ARG cc_start: 0.8716 (ttm110) cc_final: 0.7856 (mtm-85) REVERT: G 180 VAL cc_start: 0.9095 (m) cc_final: 0.8749 (p) REVERT: G 196 THR cc_start: 0.7740 (m) cc_final: 0.7521 (m) REVERT: G 198 GLU cc_start: 0.8570 (pt0) cc_final: 0.8094 (pt0) REVERT: G 257 MET cc_start: 0.8271 (mmp) cc_final: 0.7604 (mmp) REVERT: G 282 ARG cc_start: 0.8234 (tpt170) cc_final: 0.7998 (tpt90) REVERT: G 375 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8081 (pp30) REVERT: G 397 TRP cc_start: 0.8565 (m100) cc_final: 0.8290 (m-10) REVERT: H 31 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8363 (t0) REVERT: H 108 GLU cc_start: 0.8310 (tp30) cc_final: 0.8091 (tm-30) REVERT: H 129 CYS cc_start: 0.8234 (t) cc_final: 0.7889 (t) REVERT: H 291 GLN cc_start: 0.8812 (pt0) cc_final: 0.8494 (pm20) REVERT: H 322 SER cc_start: 0.8019 (m) cc_final: 0.7740 (p) REVERT: H 325 GLU cc_start: 0.7840 (tt0) cc_final: 0.7389 (tt0) REVERT: H 388 MET cc_start: 0.8089 (mtp) cc_final: 0.7370 (mmt) REVERT: H 407 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8370 (mp0) REVERT: I 31 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8307 (t70) REVERT: I 73 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8264 (mpp) REVERT: I 180 VAL cc_start: 0.9151 (m) cc_final: 0.8624 (p) REVERT: I 198 GLU cc_start: 0.7921 (pt0) cc_final: 0.7684 (pt0) REVERT: I 267 MET cc_start: 0.8800 (mtp) cc_final: 0.8496 (mtt) REVERT: I 291 GLN cc_start: 0.8848 (pt0) cc_final: 0.8582 (mp10) REVERT: I 299 MET cc_start: 0.8763 (mmp) cc_final: 0.8503 (mmp) REVERT: I 322 SER cc_start: 0.7910 (m) cc_final: 0.7684 (p) REVERT: I 334 GLN cc_start: 0.9000 (mt0) cc_final: 0.8787 (mt0) REVERT: I 364 SER cc_start: 0.9249 (p) cc_final: 0.9035 (m) REVERT: B 88 ASP cc_start: 0.7081 (p0) cc_final: 0.6843 (p0) REVERT: B 147 MET cc_start: 0.8094 (ttp) cc_final: 0.7815 (ttt) REVERT: B 359 ARG cc_start: 0.7031 (ttp-170) cc_final: 0.6739 (tmm160) outliers start: 198 outliers final: 147 residues processed: 1318 average time/residue: 0.5106 time to fit residues: 1102.1965 Evaluate side-chains 1321 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1154 time to evaluate : 4.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain J residue 25 CYS Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 290 GLU Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 392 ASP Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 211 CYS Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 334 GLN Chi-restraints excluded: chain G residue 375 GLN Chi-restraints excluded: chain G residue 403 MET Chi-restraints excluded: chain G residue 407 GLU Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 407 GLU Chi-restraints excluded: chain H residue 423 GLN Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 381 ILE Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 423 GLN Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 372 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 447 optimal weight: 8.9990 chunk 470 optimal weight: 0.9980 chunk 429 optimal weight: 0.0770 chunk 458 optimal weight: 3.9990 chunk 275 optimal weight: 0.0970 chunk 199 optimal weight: 0.0470 chunk 359 optimal weight: 0.5980 chunk 140 optimal weight: 4.9990 chunk 413 optimal weight: 0.9990 chunk 433 optimal weight: 3.9990 chunk 456 optimal weight: 30.0000 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 133 GLN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 ASN K 293 ASN F 298 ASN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN H 298 ASN ** H 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 423 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 423 GLN I 424 GLN B 14 ASN B 89 ASN B 204 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 41998 Z= 0.172 Angle : 0.631 15.434 57035 Z= 0.312 Chirality : 0.044 0.279 6240 Planarity : 0.004 0.052 7411 Dihedral : 10.192 171.568 5834 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.02 % Favored : 96.96 % Rotamer: Outliers : 2.97 % Allowed : 27.58 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.12), residues: 5136 helix: 1.35 (0.11), residues: 2448 sheet: -0.70 (0.19), residues: 768 loop : -1.05 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 388 HIS 0.009 0.001 HIS F 6 PHE 0.035 0.001 PHE H 20 TYR 0.023 0.001 TYR J 210 ARG 0.008 0.000 ARG J 339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1425 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1294 time to evaluate : 4.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6570 (mm-30) REVERT: A 90 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7809 (tp30) REVERT: A 214 ARG cc_start: 0.8564 (tmm-80) cc_final: 0.8103 (tmm-80) REVERT: A 221 ARG cc_start: 0.7148 (mtt90) cc_final: 0.6171 (mtt90) REVERT: A 257 THR cc_start: 0.8945 (m) cc_final: 0.8683 (m) REVERT: C 1 MET cc_start: 0.8347 (ppp) cc_final: 0.8133 (ppp) REVERT: C 76 ASP cc_start: 0.8561 (m-30) cc_final: 0.8142 (m-30) REVERT: C 103 TYR cc_start: 0.8637 (t80) cc_final: 0.8281 (t80) REVERT: C 199 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7338 (t0) REVERT: C 206 ASN cc_start: 0.8585 (m110) cc_final: 0.8034 (m-40) REVERT: C 210 TYR cc_start: 0.8275 (m-10) cc_final: 0.7824 (m-80) REVERT: C 212 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8562 (mp) REVERT: C 293 ASN cc_start: 0.8645 (m110) cc_final: 0.8405 (m110) REVERT: C 317 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8487 (mt) REVERT: C 322 ASP cc_start: 0.7733 (t0) cc_final: 0.7264 (t70) REVERT: C 432 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7065 (t80) REVERT: E 3 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7092 (mm-30) REVERT: E 33 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7282 (p0) REVERT: E 103 TYR cc_start: 0.8553 (t80) cc_final: 0.8286 (t80) REVERT: E 199 ASP cc_start: 0.7338 (m-30) cc_final: 0.6932 (m-30) REVERT: E 210 TYR cc_start: 0.8363 (m-10) cc_final: 0.7870 (m-80) REVERT: E 237 SER cc_start: 0.8998 (m) cc_final: 0.8698 (t) REVERT: E 243 ARG cc_start: 0.9058 (mtm110) cc_final: 0.8173 (ttm110) REVERT: E 269 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8412 (pp) REVERT: E 377 MET cc_start: 0.8881 (tmm) cc_final: 0.8636 (tmm) REVERT: E 386 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7608 (pm20) REVERT: E 392 ASP cc_start: 0.8536 (t0) cc_final: 0.8024 (t70) REVERT: J 286 LEU cc_start: 0.8548 (mt) cc_final: 0.8175 (pp) REVERT: J 300 ASN cc_start: 0.8799 (t160) cc_final: 0.8590 (t0) REVERT: J 305 CYS cc_start: 0.7696 (m) cc_final: 0.7163 (m) REVERT: J 326 LYS cc_start: 0.8891 (tttm) cc_final: 0.8422 (ptpt) REVERT: J 352 LYS cc_start: 0.7975 (tttp) cc_final: 0.7605 (tppt) REVERT: J 357 TYR cc_start: 0.8575 (m-80) cc_final: 0.8217 (m-80) REVERT: J 377 MET cc_start: 0.8757 (ttp) cc_final: 0.8520 (tmm) REVERT: J 386 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7867 (pm20) REVERT: J 392 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8236 (t0) REVERT: J 425 MET cc_start: 0.8586 (mmp) cc_final: 0.8170 (tpp) REVERT: K 3 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6519 (mm-30) REVERT: K 75 ILE cc_start: 0.8864 (mm) cc_final: 0.8456 (mm) REVERT: K 90 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: K 199 ASP cc_start: 0.8334 (m-30) cc_final: 0.8036 (t0) REVERT: K 300 ASN cc_start: 0.8687 (t0) cc_final: 0.8293 (t0) REVERT: K 326 LYS cc_start: 0.8876 (tttm) cc_final: 0.8364 (ptpt) REVERT: K 352 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.6900 (mmtt) REVERT: K 377 MET cc_start: 0.8993 (tmm) cc_final: 0.8588 (tmm) REVERT: K 392 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.7853 (t0) REVERT: K 417 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7699 (tm-30) REVERT: L 75 ILE cc_start: 0.8953 (mm) cc_final: 0.8690 (mm) REVERT: L 76 ASP cc_start: 0.8709 (m-30) cc_final: 0.8203 (m-30) REVERT: L 90 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7541 (tp30) REVERT: L 117 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8674 (tt) REVERT: L 210 TYR cc_start: 0.8414 (m-10) cc_final: 0.8114 (m-80) REVERT: L 322 ASP cc_start: 0.7701 (t0) cc_final: 0.7400 (t70) REVERT: L 326 LYS cc_start: 0.8883 (tttm) cc_final: 0.8142 (mttt) REVERT: L 352 LYS cc_start: 0.3628 (tppt) cc_final: 0.2991 (mmtp) REVERT: L 377 MET cc_start: 0.8807 (tmm) cc_final: 0.8384 (tmm) REVERT: L 425 MET cc_start: 0.8541 (mmp) cc_final: 0.8335 (tpp) REVERT: F 36 TYR cc_start: 0.8088 (t80) cc_final: 0.7699 (t80) REVERT: F 50 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: F 121 ARG cc_start: 0.8766 (ttm110) cc_final: 0.8563 (mtm-85) REVERT: F 180 VAL cc_start: 0.9060 (m) cc_final: 0.8721 (p) REVERT: F 282 ARG cc_start: 0.7979 (ptm160) cc_final: 0.7717 (ttp-110) REVERT: F 364 SER cc_start: 0.9074 (p) cc_final: 0.8857 (m) REVERT: F 379 LYS cc_start: 0.9114 (ttpt) cc_final: 0.8782 (ptpt) REVERT: F 423 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8515 (pp30) REVERT: D 22 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7331 (tm-30) REVERT: D 26 ASP cc_start: 0.8040 (m-30) cc_final: 0.7386 (m-30) REVERT: D 112 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7806 (tp) REVERT: D 122 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8768 (ttpt) REVERT: D 359 ARG cc_start: 0.7576 (tmm160) cc_final: 0.7296 (tmt170) REVERT: D 406 MET cc_start: 0.7790 (mmm) cc_final: 0.7480 (mmm) REVERT: G 31 ASP cc_start: 0.8931 (OUTLIER) cc_final: 0.8572 (t0) REVERT: G 121 ARG cc_start: 0.8705 (ttm110) cc_final: 0.7937 (mtm-85) REVERT: G 147 MET cc_start: 0.8636 (ttp) cc_final: 0.8421 (ttt) REVERT: G 158 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7904 (tt0) REVERT: G 165 ASN cc_start: 0.8993 (m-40) cc_final: 0.8676 (m-40) REVERT: G 180 VAL cc_start: 0.9048 (m) cc_final: 0.8689 (p) REVERT: G 257 MET cc_start: 0.8124 (mmp) cc_final: 0.7266 (mmp) REVERT: G 375 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7868 (pp30) REVERT: G 397 TRP cc_start: 0.8615 (m100) cc_final: 0.8257 (m-10) REVERT: G 407 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: G 419 VAL cc_start: 0.9284 (t) cc_final: 0.9017 (p) REVERT: H 31 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8288 (t0) REVERT: H 108 GLU cc_start: 0.8303 (tp30) cc_final: 0.8088 (tm-30) REVERT: H 129 CYS cc_start: 0.8237 (t) cc_final: 0.7863 (t) REVERT: H 213 ARG cc_start: 0.8340 (ttp-110) cc_final: 0.7916 (ptp-170) REVERT: H 291 GLN cc_start: 0.8792 (pt0) cc_final: 0.8239 (mp10) REVERT: H 304 ASP cc_start: 0.8518 (t0) cc_final: 0.7984 (t70) REVERT: H 325 GLU cc_start: 0.7783 (tt0) cc_final: 0.7228 (tt0) REVERT: H 388 MET cc_start: 0.8032 (mtp) cc_final: 0.7342 (mmt) REVERT: H 407 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8282 (mp0) REVERT: I 31 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8247 (t0) REVERT: I 50 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: I 69 GLU cc_start: 0.7759 (pt0) cc_final: 0.7430 (mp0) REVERT: I 73 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8233 (mpp) REVERT: I 106 TYR cc_start: 0.8294 (m-80) cc_final: 0.8038 (m-80) REVERT: I 180 VAL cc_start: 0.9054 (m) cc_final: 0.8555 (p) REVERT: I 198 GLU cc_start: 0.7807 (pt0) cc_final: 0.7604 (pt0) REVERT: I 216 LYS cc_start: 0.8902 (mmtp) cc_final: 0.8617 (mtmm) REVERT: I 267 MET cc_start: 0.8709 (mtp) cc_final: 0.8428 (mtt) REVERT: I 299 MET cc_start: 0.8744 (mmp) cc_final: 0.8453 (mmp) REVERT: I 322 SER cc_start: 0.7548 (m) cc_final: 0.7341 (p) REVERT: B 22 GLU cc_start: 0.7691 (tm-30) cc_final: 0.6992 (tm-30) REVERT: B 24 ILE cc_start: 0.8294 (mm) cc_final: 0.7606 (mt) REVERT: B 26 ASP cc_start: 0.8444 (t0) cc_final: 0.8091 (m-30) REVERT: B 88 ASP cc_start: 0.7185 (p0) cc_final: 0.6879 (p0) REVERT: B 147 MET cc_start: 0.8034 (ttp) cc_final: 0.7777 (ttt) REVERT: B 324 LYS cc_start: 0.9164 (tmtp) cc_final: 0.8952 (tttm) REVERT: B 329 GLN cc_start: 0.9189 (mm-40) cc_final: 0.8962 (mm-40) REVERT: B 359 ARG cc_start: 0.6864 (ttp-170) cc_final: 0.6630 (tmm160) outliers start: 131 outliers final: 91 residues processed: 1370 average time/residue: 0.5255 time to fit residues: 1171.1300 Evaluate side-chains 1334 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1217 time to evaluate : 4.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 352 LYS Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 392 ASP Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain G residue 14 ASN Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 375 GLN Chi-restraints excluded: chain G residue 407 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 407 GLU Chi-restraints excluded: chain H residue 423 GLN Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 300 optimal weight: 10.0000 chunk 484 optimal weight: 9.9990 chunk 295 optimal weight: 6.9990 chunk 229 optimal weight: 9.9990 chunk 336 optimal weight: 3.9990 chunk 508 optimal weight: 3.9990 chunk 467 optimal weight: 10.0000 chunk 404 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 312 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN ** J 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 ASN L 300 ASN L 393 HIS F 11 GLN F 298 ASN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 ASN ** H 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 423 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 298 ASN B 14 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 41998 Z= 0.267 Angle : 0.674 14.212 57035 Z= 0.336 Chirality : 0.045 0.204 6240 Planarity : 0.004 0.079 7411 Dihedral : 10.198 172.401 5827 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.12 % Allowed : 28.30 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.12), residues: 5136 helix: 1.34 (0.11), residues: 2442 sheet: -0.76 (0.19), residues: 768 loop : -1.06 (0.15), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 397 HIS 0.012 0.001 HIS D 6 PHE 0.043 0.002 PHE F 167 TYR 0.022 0.001 TYR J 103 ARG 0.018 0.001 ARG G 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1342 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1204 time to evaluate : 4.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6633 (mm-30) REVERT: A 90 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7867 (tp30) REVERT: A 121 ARG cc_start: 0.8120 (mmm160) cc_final: 0.7914 (tpt170) REVERT: A 214 ARG cc_start: 0.8555 (tmm-80) cc_final: 0.8115 (tmm-80) REVERT: A 293 ASN cc_start: 0.8728 (m110) cc_final: 0.8484 (m110) REVERT: A 300 ASN cc_start: 0.8618 (t0) cc_final: 0.8166 (t0) REVERT: C 1 MET cc_start: 0.8383 (ppp) cc_final: 0.8139 (ppp) REVERT: C 3 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6921 (mm-30) REVERT: C 199 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7457 (t0) REVERT: C 206 ASN cc_start: 0.8631 (m110) cc_final: 0.8028 (m-40) REVERT: C 210 TYR cc_start: 0.8351 (m-10) cc_final: 0.7859 (m-80) REVERT: C 212 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8556 (mp) REVERT: C 317 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8603 (mt) REVERT: C 322 ASP cc_start: 0.7781 (t0) cc_final: 0.7354 (t70) REVERT: E 3 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7057 (mm-30) REVERT: E 33 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7412 (p0) REVERT: E 199 ASP cc_start: 0.7304 (m-30) cc_final: 0.6914 (m-30) REVERT: E 210 TYR cc_start: 0.8458 (m-10) cc_final: 0.7953 (m-80) REVERT: E 269 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8493 (pp) REVERT: E 377 MET cc_start: 0.8868 (tmm) cc_final: 0.8569 (tmm) REVERT: E 386 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7587 (pm20) REVERT: J 3 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7072 (mm-30) REVERT: J 71 GLU cc_start: 0.7248 (pt0) cc_final: 0.7006 (tt0) REVERT: J 286 LEU cc_start: 0.8540 (mt) cc_final: 0.8197 (pp) REVERT: J 300 ASN cc_start: 0.8864 (t160) cc_final: 0.8637 (t0) REVERT: J 305 CYS cc_start: 0.7790 (m) cc_final: 0.7348 (m) REVERT: J 319 TYR cc_start: 0.9107 (m-80) cc_final: 0.8844 (m-80) REVERT: J 326 LYS cc_start: 0.8946 (tttm) cc_final: 0.8471 (ptpt) REVERT: J 352 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7651 (tppt) REVERT: J 357 TYR cc_start: 0.8643 (m-80) cc_final: 0.8268 (m-80) REVERT: J 386 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7892 (pm20) REVERT: J 392 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8179 (t0) REVERT: K 3 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6612 (mm-30) REVERT: K 75 ILE cc_start: 0.9012 (mm) cc_final: 0.8585 (mm) REVERT: K 199 ASP cc_start: 0.8410 (m-30) cc_final: 0.8129 (t0) REVERT: K 300 ASN cc_start: 0.8765 (t0) cc_final: 0.8312 (t0) REVERT: K 326 LYS cc_start: 0.8910 (tttm) cc_final: 0.8399 (ptpt) REVERT: K 352 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7431 (tppt) REVERT: K 377 MET cc_start: 0.8977 (tmm) cc_final: 0.8535 (tmm) REVERT: K 392 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.7833 (t0) REVERT: L 76 ASP cc_start: 0.8729 (m-30) cc_final: 0.8239 (m-30) REVERT: L 90 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7560 (tp30) REVERT: L 117 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8719 (tt) REVERT: L 203 MET cc_start: 0.8890 (mmm) cc_final: 0.8617 (mmm) REVERT: L 210 TYR cc_start: 0.8404 (m-10) cc_final: 0.8126 (m-80) REVERT: L 322 ASP cc_start: 0.7770 (t0) cc_final: 0.7464 (t70) REVERT: L 326 LYS cc_start: 0.8998 (tttm) cc_final: 0.8244 (mttt) REVERT: L 352 LYS cc_start: 0.3622 (tppt) cc_final: 0.2971 (mmtp) REVERT: L 357 TYR cc_start: 0.8586 (m-80) cc_final: 0.8205 (m-80) REVERT: L 377 MET cc_start: 0.8813 (tmm) cc_final: 0.8378 (tmm) REVERT: L 425 MET cc_start: 0.8591 (mmp) cc_final: 0.8337 (tpp) REVERT: F 36 TYR cc_start: 0.8123 (t80) cc_final: 0.7685 (t80) REVERT: F 50 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.7938 (m-80) REVERT: F 121 ARG cc_start: 0.8815 (ttm110) cc_final: 0.8604 (mtm-85) REVERT: F 282 ARG cc_start: 0.8017 (ptm160) cc_final: 0.7717 (ttp-110) REVERT: F 364 SER cc_start: 0.9129 (p) cc_final: 0.8897 (m) REVERT: F 379 LYS cc_start: 0.9161 (ttpt) cc_final: 0.8833 (ptpt) REVERT: F 423 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8669 (pp30) REVERT: D 22 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7359 (tm-30) REVERT: D 26 ASP cc_start: 0.8080 (m-30) cc_final: 0.7419 (m-30) REVERT: D 122 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8765 (ttpt) REVERT: D 257 MET cc_start: 0.8317 (mmm) cc_final: 0.7723 (mmm) REVERT: D 359 ARG cc_start: 0.7682 (tmm160) cc_final: 0.7399 (tmt170) REVERT: D 406 MET cc_start: 0.7840 (mmm) cc_final: 0.7510 (mmm) REVERT: G 31 ASP cc_start: 0.8979 (OUTLIER) cc_final: 0.8627 (t0) REVERT: G 95 SER cc_start: 0.9366 (m) cc_final: 0.9151 (p) REVERT: G 121 ARG cc_start: 0.8704 (ttm110) cc_final: 0.7921 (mtm-85) REVERT: G 158 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7944 (tt0) REVERT: G 180 VAL cc_start: 0.9088 (m) cc_final: 0.8761 (p) REVERT: G 257 MET cc_start: 0.7954 (mmp) cc_final: 0.7286 (mmp) REVERT: G 375 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8098 (pp30) REVERT: G 403 MET cc_start: 0.8024 (mmp) cc_final: 0.7590 (mmt) REVERT: G 407 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8545 (mp0) REVERT: H 31 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8376 (t0) REVERT: H 108 GLU cc_start: 0.8312 (tp30) cc_final: 0.8105 (tm-30) REVERT: H 129 CYS cc_start: 0.8261 (t) cc_final: 0.7843 (t) REVERT: H 167 PHE cc_start: 0.7910 (m-80) cc_final: 0.7690 (m-10) REVERT: H 291 GLN cc_start: 0.8830 (pt0) cc_final: 0.8491 (pm20) REVERT: H 322 SER cc_start: 0.8000 (m) cc_final: 0.7727 (p) REVERT: H 388 MET cc_start: 0.8106 (mtp) cc_final: 0.7361 (mmt) REVERT: H 407 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8310 (mp0) REVERT: I 31 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8307 (t0) REVERT: I 69 GLU cc_start: 0.7728 (pt0) cc_final: 0.7421 (mp0) REVERT: I 73 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8205 (mpp) REVERT: I 180 VAL cc_start: 0.9111 (m) cc_final: 0.8595 (p) REVERT: I 198 GLU cc_start: 0.7932 (pt0) cc_final: 0.7732 (pt0) REVERT: I 257 MET cc_start: 0.8660 (mmm) cc_final: 0.8165 (mmm) REVERT: I 267 MET cc_start: 0.8738 (mtp) cc_final: 0.8475 (mtt) REVERT: B 147 MET cc_start: 0.8106 (ttp) cc_final: 0.7856 (ttt) REVERT: B 255 VAL cc_start: 0.9097 (p) cc_final: 0.8822 (p) REVERT: B 320 ARG cc_start: 0.7391 (tpp-160) cc_final: 0.6867 (mmm160) REVERT: B 359 ARG cc_start: 0.6912 (ttp-170) cc_final: 0.6628 (tmm160) outliers start: 138 outliers final: 100 residues processed: 1288 average time/residue: 0.5302 time to fit residues: 1110.2283 Evaluate side-chains 1291 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1168 time to evaluate : 4.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 352 LYS Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 352 LYS Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 392 ASP Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain G residue 14 ASN Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 334 GLN Chi-restraints excluded: chain G residue 375 GLN Chi-restraints excluded: chain G residue 407 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 407 GLU Chi-restraints excluded: chain H residue 423 GLN Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 293 MET Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 321 optimal weight: 8.9990 chunk 430 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 373 optimal weight: 2.9990 chunk 59 optimal weight: 0.0270 chunk 112 optimal weight: 0.7980 chunk 405 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 416 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 ASN F 298 ASN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 ASN H 307 HIS H 375 GLN ** H 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 ASN I 298 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.123450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.102818 restraints weight = 65293.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.106480 restraints weight = 34807.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.109041 restraints weight = 22267.767| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 41998 Z= 0.190 Angle : 0.654 14.620 57035 Z= 0.322 Chirality : 0.044 0.186 6240 Planarity : 0.004 0.076 7411 Dihedral : 10.090 174.274 5827 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.88 % Allowed : 28.59 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.12), residues: 5136 helix: 1.40 (0.11), residues: 2412 sheet: -0.68 (0.19), residues: 768 loop : -0.99 (0.15), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D 397 HIS 0.014 0.001 HIS D 6 PHE 0.040 0.002 PHE F 167 TYR 0.022 0.001 TYR J 210 ARG 0.013 0.000 ARG G 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16227.99 seconds wall clock time: 288 minutes 18.42 seconds (17298.42 seconds total)