Starting phenix.real_space_refine on Fri Feb 16 15:25:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pnb_13546/02_2024/7pnb_13546_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pnb_13546/02_2024/7pnb_13546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pnb_13546/02_2024/7pnb_13546.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pnb_13546/02_2024/7pnb_13546.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pnb_13546/02_2024/7pnb_13546_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pnb_13546/02_2024/7pnb_13546_updated.pdb" } resolution = 3.46 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= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 9819 2.51 5 N 2061 2.21 5 O 3753 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15714 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "M" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "N" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "S" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "U" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "W" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "X" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Y" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "b" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "c" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "e" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "f" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "g" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "h" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "i" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "j" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "k" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "l" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "m" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "n" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "o" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "p" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "q" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "r" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "s" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "t" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "u" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "v" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "w" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "x" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "y" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "z" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "0" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "1" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 8.61, per 1000 atoms: 0.55 Number of scatterers: 15714 At special positions: 0 Unit cell: (75.384, 74.337, 343.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 3753 8.00 N 2061 7.00 C 9819 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 Links applied ?1-3 " NAG 0 2 " - " YZT 0 3 " " NAG 1 2 " - " YZT 1 3 " " NAG J 2 " - " YZT J 3 " " NAG K 2 " - " YZT K 3 " " NAG L 2 " - " YZT L 3 " " NAG M 2 " - " YZT M 3 " " NAG N 2 " - " YZT N 3 " " NAG O 2 " - " YZT O 3 " " NAG P 2 " - " YZT P 3 " " NAG Q 2 " - " YZT Q 3 " " NAG R 2 " - " YZT R 3 " " NAG S 2 " - " YZT S 3 " " NAG T 2 " - " YZT T 3 " " NAG U 2 " - " YZT U 3 " " NAG V 2 " - " YZT V 3 " " NAG W 2 " - " YZT W 3 " " NAG X 2 " - " YZT X 3 " " NAG Y 2 " - " YZT Y 3 " " NAG Z 2 " - " YZT Z 3 " " NAG a 2 " - " YZT a 3 " " NAG b 2 " - " YZT b 3 " " NAG c 2 " - " YZT c 3 " " NAG d 2 " - " YZT d 3 " " NAG e 2 " - " YZT e 3 " " NAG f 2 " - " YZT f 3 " " NAG g 2 " - " YZT g 3 " " NAG h 2 " - " YZT h 3 " " NAG i 2 " - " YZT i 3 " " NAG j 2 " - " YZT j 3 " " NAG k 2 " - " YZT k 3 " " NAG l 2 " - " YZT l 3 " " NAG m 2 " - " YZT m 3 " " NAG n 2 " - " YZT n 3 " " NAG o 2 " - " YZT o 3 " " NAG p 2 " - " YZT p 3 " " NAG q 2 " - " YZT q 3 " " NAG r 2 " - " YZT r 3 " " NAG s 2 " - " YZT s 3 " " NAG t 2 " - " YZT t 3 " " NAG u 2 " - " YZT u 3 " " NAG v 2 " - " YZT v 3 " " NAG w 2 " - " YZT w 3 " " NAG x 2 " - " YZT x 3 " " NAG y 2 " - " YZT y 3 " " NAG z 2 " - " YZT z 3 " ALPHA1-4 " NAG 0 2 " - " MAN 0 5 " " NAG 1 2 " - " MAN 1 5 " " NAG J 2 " - " MAN J 5 " " NAG K 2 " - " MAN K 4 " " NAG L 2 " - " MAN L 5 " " NAG M 2 " - " MAN M 5 " " NAG N 2 " - " MAN N 5 " " NAG O 2 " - " MAN O 5 " " NAG P 2 " - " MAN P 4 " " NAG Q 2 " - " MAN Q 5 " " NAG R 2 " - " MAN R 5 " " NAG S 2 " - " MAN S 5 " " NAG T 2 " - " MAN T 5 " " NAG U 2 " - " MAN U 4 " " NAG V 2 " - " MAN V 5 " " NAG W 2 " - " MAN W 5 " " NAG X 2 " - " MAN X 5 " " NAG Y 2 " - " MAN Y 5 " " NAG Z 2 " - " MAN Z 4 " " NAG a 2 " - " MAN a 5 " " NAG b 2 " - " MAN b 5 " " NAG c 2 " - " MAN c 5 " " NAG d 2 " - " MAN d 5 " " NAG e 2 " - " MAN e 4 " " NAG f 2 " - " MAN f 5 " " NAG g 2 " - " MAN g 5 " " NAG h 2 " - " MAN h 5 " " NAG i 2 " - " MAN i 5 " " NAG j 2 " - " MAN j 4 " " NAG k 2 " - " MAN k 5 " " NAG l 2 " - " MAN l 5 " " NAG m 2 " - " MAN m 5 " " NAG n 2 " - " MAN n 5 " " NAG o 2 " - " MAN o 4 " " NAG p 2 " - " MAN p 5 " " NAG q 2 " - " MAN q 5 " " NAG r 2 " - " MAN r 5 " " NAG s 2 " - " MAN s 5 " " NAG t 2 " - " MAN t 4 " " NAG u 2 " - " MAN u 5 " " NAG v 2 " - " MAN v 5 " " NAG w 2 " - " MAN w 5 " " NAG x 2 " - " MAN x 5 " " NAG y 2 " - " MAN y 4 " " NAG z 2 " - " MAN z 5 " ALPHA1-6 " NAG 0 2 " - " MAN 0 6 " " NAG 1 2 " - " MAN 1 6 " " NAG J 2 " - " MAN J 6 " " NAG L 2 " - " MAN L 6 " " NAG M 2 " - " MAN M 6 " " NAG N 2 " - " MAN N 6 " " NAG O 2 " - " MAN O 6 " " NAG Q 2 " - " MAN Q 6 " " NAG R 2 " - " MAN R 6 " " NAG S 2 " - " MAN S 6 " " NAG T 2 " - " MAN T 6 " " NAG V 2 " - " MAN V 6 " " NAG W 2 " - " MAN W 6 " " NAG X 2 " - " MAN X 6 " " NAG Y 2 " - " MAN Y 6 " " NAG a 2 " - " MAN a 6 " " NAG b 2 " - " MAN b 6 " " NAG c 2 " - " MAN c 6 " " NAG d 2 " - " MAN d 6 " " NAG f 2 " - " MAN f 6 " " NAG g 2 " - " MAN g 6 " " NAG h 2 " - " MAN h 6 " " NAG i 2 " - " MAN i 6 " " NAG k 2 " - " MAN k 6 " " NAG l 2 " - " MAN l 6 " " NAG m 2 " - " MAN m 6 " " NAG n 2 " - " MAN n 6 " " NAG p 2 " - " MAN p 6 " " NAG q 2 " - " MAN q 6 " " NAG r 2 " - " MAN r 6 " " NAG s 2 " - " MAN s 6 " " NAG u 2 " - " MAN u 6 " " NAG v 2 " - " MAN v 6 " " NAG w 2 " - " MAN w 6 " " NAG x 2 " - " MAN x 6 " " NAG z 2 " - " MAN z 6 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " YZT 0 3 " - " BGC 0 4 " " NAG 1 1 " - " NAG 1 2 " " YZT 1 3 " - " BGC 1 4 " " NAG J 1 " - " NAG J 2 " " YZT J 3 " - " BGC J 4 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " YZT L 3 " - " BGC L 4 " " NAG M 1 " - " NAG M 2 " " YZT M 3 " - " BGC M 4 " " NAG N 1 " - " NAG N 2 " " YZT N 3 " - " BGC N 4 " " NAG O 1 " - " NAG O 2 " " YZT O 3 " - " BGC O 4 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " YZT Q 3 " - " BGC Q 4 " " NAG R 1 " - " NAG R 2 " " YZT R 3 " - " BGC R 4 " " NAG S 1 " - " NAG S 2 " " YZT S 3 " - " BGC S 4 " " NAG T 1 " - " NAG T 2 " " YZT T 3 " - " BGC T 4 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " YZT V 3 " - " BGC V 4 " " NAG W 1 " - " NAG W 2 " " YZT W 3 " - " BGC W 4 " " NAG X 1 " - " NAG X 2 " " YZT X 3 " - " BGC X 4 " " NAG Y 1 " - " NAG Y 2 " " YZT Y 3 " - " BGC Y 4 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " YZT a 3 " - " BGC a 4 " " NAG b 1 " - " NAG b 2 " " YZT b 3 " - " BGC b 4 " " NAG c 1 " - " NAG c 2 " " YZT c 3 " - " BGC c 4 " " NAG d 1 " - " NAG d 2 " " YZT d 3 " - " BGC d 4 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " YZT f 3 " - " BGC f 4 " " NAG g 1 " - " NAG g 2 " " YZT g 3 " - " BGC g 4 " " NAG h 1 " - " NAG h 2 " " YZT h 3 " - " BGC h 4 " " NAG i 1 " - " NAG i 2 " " YZT i 3 " - " BGC i 4 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " YZT k 3 " - " BGC k 4 " " NAG l 1 " - " NAG l 2 " " YZT l 3 " - " BGC l 4 " " NAG m 1 " - " NAG m 2 " " YZT m 3 " - " BGC m 4 " " NAG n 1 " - " NAG n 2 " " YZT n 3 " - " BGC n 4 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " YZT p 3 " - " BGC p 4 " " NAG q 1 " - " NAG q 2 " " YZT q 3 " - " BGC q 4 " " NAG r 1 " - " NAG r 2 " " YZT r 3 " - " BGC r 4 " " NAG s 1 " - " NAG s 2 " " YZT s 3 " - " BGC s 4 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " YZT u 3 " - " BGC u 4 " " NAG v 1 " - " NAG v 2 " " YZT v 3 " - " BGC v 4 " " NAG w 1 " - " NAG w 2 " " YZT w 3 " - " BGC w 4 " " NAG x 1 " - " NAG x 2 " " YZT x 3 " - " BGC x 4 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " YZT z 3 " - " BGC z 4 " NAG-ASN " NAG 0 1 " - " ASN I 146 " " NAG 1 1 " - " ASN I 121 " " NAG J 1 " - " ASN A 56 " " NAG K 1 " - " ASN A 80 " " NAG L 1 " - " ASN A 83 " " NAG M 1 " - " ASN A 146 " " NAG N 1 " - " ASN A 121 " " NAG O 1 " - " ASN B 56 " " NAG P 1 " - " ASN B 80 " " NAG Q 1 " - " ASN B 83 " " NAG R 1 " - " ASN B 146 " " NAG S 1 " - " ASN B 121 " " NAG T 1 " - " ASN C 56 " " NAG U 1 " - " ASN C 80 " " NAG V 1 " - " ASN C 83 " " NAG W 1 " - " ASN C 146 " " NAG X 1 " - " ASN C 121 " " NAG Y 1 " - " ASN D 56 " " NAG Z 1 " - " ASN D 80 " " NAG a 1 " - " ASN D 83 " " NAG b 1 " - " ASN D 146 " " NAG c 1 " - " ASN D 121 " " NAG d 1 " - " ASN E 56 " " NAG e 1 " - " ASN E 80 " " NAG f 1 " - " ASN E 83 " " NAG g 1 " - " ASN E 146 " " NAG h 1 " - " ASN E 121 " " NAG i 1 " - " ASN F 56 " " NAG j 1 " - " ASN F 80 " " NAG k 1 " - " ASN F 83 " " NAG l 1 " - " ASN F 146 " " NAG m 1 " - " ASN F 121 " " NAG n 1 " - " ASN G 56 " " NAG o 1 " - " ASN G 80 " " NAG p 1 " - " ASN G 83 " " NAG q 1 " - " ASN G 146 " " NAG r 1 " - " ASN G 121 " " NAG s 1 " - " ASN H 56 " " NAG t 1 " - " ASN H 80 " " NAG u 1 " - " ASN H 83 " " NAG v 1 " - " ASN H 146 " " NAG w 1 " - " ASN H 121 " " NAG x 1 " - " ASN I 56 " " NAG y 1 " - " ASN I 80 " " NAG z 1 " - " ASN I 83 " Time building additional restraints: 12.07 Conformation dependent library (CDL) restraints added in 2.2 seconds 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3042 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 36 sheets defined 3.3% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'E' and resid 48 through 50 No H-bonds generated for 'chain 'E' and resid 48 through 50' Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'F' and resid 48 through 50 No H-bonds generated for 'chain 'F' and resid 48 through 50' Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'G' and resid 48 through 50 No H-bonds generated for 'chain 'G' and resid 48 through 50' Processing helix chain 'G' and resid 70 through 72 No H-bonds generated for 'chain 'G' and resid 70 through 72' Processing helix chain 'H' and resid 48 through 50 No H-bonds generated for 'chain 'H' and resid 48 through 50' Processing helix chain 'H' and resid 70 through 72 No H-bonds generated for 'chain 'H' and resid 70 through 72' Processing helix chain 'I' and resid 48 through 50 No H-bonds generated for 'chain 'I' and resid 48 through 50' Processing helix chain 'I' and resid 70 through 72 No H-bonds generated for 'chain 'I' and resid 70 through 72' Processing sheet with id= A, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.861A pdb=" N MET A 93 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU A 124 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LYS A 138 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE A 126 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LYS A 136 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 64 through 68 Processing sheet with id= C, first strand: chain 'A' and resid 87 through 89 Processing sheet with id= D, first strand: chain 'A' and resid 154 through 156 removed outlier: 6.707A pdb=" N ASN A 188 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL A 108 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR A 186 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR A 110 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR A 184 " --> pdb=" O TYR A 110 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 42 through 45 removed outlier: 3.860A pdb=" N MET B 93 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU B 124 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LYS B 138 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE B 126 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LYS B 136 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 64 through 68 Processing sheet with id= G, first strand: chain 'B' and resid 87 through 89 Processing sheet with id= H, first strand: chain 'B' and resid 154 through 156 removed outlier: 6.702A pdb=" N ASN B 188 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 108 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR B 186 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR B 110 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR B 184 " --> pdb=" O TYR B 110 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.861A pdb=" N MET C 93 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU C 124 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LYS C 138 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE C 126 " --> pdb=" O LYS C 136 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LYS C 136 " --> pdb=" O ILE C 126 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 64 through 68 Processing sheet with id= K, first strand: chain 'C' and resid 87 through 89 Processing sheet with id= L, first strand: chain 'C' and resid 154 through 156 removed outlier: 6.700A pdb=" N ASN C 188 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL C 108 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR C 186 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR C 110 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR C 184 " --> pdb=" O TYR C 110 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 42 through 45 removed outlier: 3.862A pdb=" N MET D 93 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU D 124 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LYS D 138 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE D 126 " --> pdb=" O LYS D 136 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS D 136 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 64 through 68 Processing sheet with id= O, first strand: chain 'D' and resid 87 through 89 Processing sheet with id= P, first strand: chain 'D' and resid 154 through 156 removed outlier: 6.701A pdb=" N ASN D 188 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL D 108 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR D 186 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR D 110 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR D 184 " --> pdb=" O TYR D 110 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 42 through 45 removed outlier: 3.863A pdb=" N MET E 93 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU E 124 " --> pdb=" O LYS E 138 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LYS E 138 " --> pdb=" O LEU E 124 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE E 126 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LYS E 136 " --> pdb=" O ILE E 126 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 64 through 68 Processing sheet with id= S, first strand: chain 'E' and resid 87 through 89 Processing sheet with id= T, first strand: chain 'E' and resid 154 through 156 removed outlier: 6.708A pdb=" N ASN E 188 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL E 108 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR E 186 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR E 110 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR E 184 " --> pdb=" O TYR E 110 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 42 through 45 removed outlier: 3.860A pdb=" N MET F 93 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU F 124 " --> pdb=" O LYS F 138 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LYS F 138 " --> pdb=" O LEU F 124 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE F 126 " --> pdb=" O LYS F 136 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LYS F 136 " --> pdb=" O ILE F 126 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 64 through 68 Processing sheet with id= W, first strand: chain 'F' and resid 87 through 89 Processing sheet with id= X, first strand: chain 'F' and resid 154 through 156 removed outlier: 6.702A pdb=" N ASN F 188 " --> pdb=" O ALA F 106 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL F 108 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR F 186 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR F 110 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR F 184 " --> pdb=" O TYR F 110 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 42 through 45 removed outlier: 3.860A pdb=" N MET G 93 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU G 124 " --> pdb=" O LYS G 138 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LYS G 138 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE G 126 " --> pdb=" O LYS G 136 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LYS G 136 " --> pdb=" O ILE G 126 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 64 through 68 Processing sheet with id= AA, first strand: chain 'G' and resid 87 through 89 Processing sheet with id= AB, first strand: chain 'G' and resid 154 through 156 removed outlier: 6.702A pdb=" N ASN G 188 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL G 108 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR G 186 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR G 110 " --> pdb=" O THR G 184 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR G 184 " --> pdb=" O TYR G 110 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 42 through 45 removed outlier: 3.860A pdb=" N MET H 93 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU H 124 " --> pdb=" O LYS H 138 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LYS H 138 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE H 126 " --> pdb=" O LYS H 136 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LYS H 136 " --> pdb=" O ILE H 126 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 64 through 68 Processing sheet with id= AE, first strand: chain 'H' and resid 87 through 89 Processing sheet with id= AF, first strand: chain 'H' and resid 154 through 156 removed outlier: 6.699A pdb=" N ASN H 188 " --> pdb=" O ALA H 106 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL H 108 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR H 186 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR H 110 " --> pdb=" O THR H 184 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR H 184 " --> pdb=" O TYR H 110 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 42 through 45 removed outlier: 3.861A pdb=" N MET I 93 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU I 124 " --> pdb=" O LYS I 138 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LYS I 138 " --> pdb=" O LEU I 124 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE I 126 " --> pdb=" O LYS I 136 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LYS I 136 " --> pdb=" O ILE I 126 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 64 through 68 Processing sheet with id= AI, first strand: chain 'I' and resid 87 through 89 Processing sheet with id= AJ, first strand: chain 'I' and resid 154 through 156 removed outlier: 6.705A pdb=" N ASN I 188 " --> pdb=" O ALA I 106 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL I 108 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR I 186 " --> pdb=" O VAL I 108 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR I 110 " --> pdb=" O THR I 184 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR I 184 " --> pdb=" O TYR I 110 " (cutoff:3.500A) 324 hydrogen bonds defined for protein. 837 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: 4.15 Time building geometry restraints manager: 12.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2834 1.33 - 1.46: 5681 1.46 - 1.58: 7441 1.58 - 1.71: 1 1.71 - 1.83: 117 Bond restraints: 16074 Sorted by residual: bond pdb=" S6 YZT d 3 " pdb="O2S6 YZT d 3 " ideal model delta sigma weight residual 1.477 1.585 -0.108 2.00e-02 2.50e+03 2.89e+01 bond pdb=" S6 YZT Y 3 " pdb="O2S6 YZT Y 3 " ideal model delta sigma weight residual 1.477 1.572 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" S6 YZT W 3 " pdb="O2S6 YZT W 3 " ideal model delta sigma weight residual 1.477 1.570 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" S6 YZT i 3 " pdb="O2S6 YZT i 3 " ideal model delta sigma weight residual 1.477 1.569 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" S6 YZT q 3 " pdb="O2S6 YZT q 3 " ideal model delta sigma weight residual 1.477 1.569 -0.092 2.00e-02 2.50e+03 2.10e+01 ... (remaining 16069 not shown) Histogram of bond angle deviations from ideal: 95.42 - 101.84: 146 101.84 - 108.25: 2116 108.25 - 114.67: 9415 114.67 - 121.08: 6373 121.08 - 127.50: 4099 Bond angle restraints: 22149 Sorted by residual: angle pdb=" C ASN B 57 " pdb=" CA ASN B 57 " pdb=" CB ASN B 57 " ideal model delta sigma weight residual 112.44 100.26 12.18 1.72e+00 3.38e-01 5.01e+01 angle pdb=" C ASN A 57 " pdb=" CA ASN A 57 " pdb=" CB ASN A 57 " ideal model delta sigma weight residual 112.44 100.26 12.18 1.72e+00 3.38e-01 5.01e+01 angle pdb=" CA ASN G 146 " pdb=" CB ASN G 146 " pdb=" CG ASN G 146 " ideal model delta sigma weight residual 112.60 119.65 -7.05 1.00e+00 1.00e+00 4.97e+01 angle pdb=" C ASN C 57 " pdb=" CA ASN C 57 " pdb=" CB ASN C 57 " ideal model delta sigma weight residual 112.44 100.32 12.12 1.72e+00 3.38e-01 4.96e+01 angle pdb=" CA ASN E 146 " pdb=" CB ASN E 146 " pdb=" CG ASN E 146 " ideal model delta sigma weight residual 112.60 119.62 -7.02 1.00e+00 1.00e+00 4.92e+01 ... (remaining 22144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.32: 11891 23.32 - 46.64: 458 46.64 - 69.96: 170 69.96 - 93.28: 189 93.28 - 116.60: 45 Dihedral angle restraints: 12753 sinusoidal: 7920 harmonic: 4833 Sorted by residual: dihedral pdb=" C ASN A 57 " pdb=" N ASN A 57 " pdb=" CA ASN A 57 " pdb=" CB ASN A 57 " ideal model delta harmonic sigma weight residual -122.60 -108.46 -14.14 0 2.50e+00 1.60e-01 3.20e+01 dihedral pdb=" C ASN B 57 " pdb=" N ASN B 57 " pdb=" CA ASN B 57 " pdb=" CB ASN B 57 " ideal model delta harmonic sigma weight residual -122.60 -108.53 -14.07 0 2.50e+00 1.60e-01 3.17e+01 dihedral pdb=" C ASN C 57 " pdb=" N ASN C 57 " pdb=" CA ASN C 57 " pdb=" CB ASN C 57 " ideal model delta harmonic sigma weight residual -122.60 -108.64 -13.96 0 2.50e+00 1.60e-01 3.12e+01 ... (remaining 12750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.184: 2936 0.184 - 0.368: 279 0.368 - 0.552: 16 0.552 - 0.736: 0 0.736 - 0.920: 9 Chirality restraints: 3240 Sorted by residual: chirality pdb=" C1 MAN e 4 " pdb=" O4 NAG e 2 " pdb=" C2 MAN e 4 " pdb=" O5 MAN e 4 " both_signs ideal model delta sigma weight residual False 2.40 1.48 0.92 2.00e-02 2.50e+03 2.12e+03 chirality pdb=" C1 MAN U 4 " pdb=" O4 NAG U 2 " pdb=" C2 MAN U 4 " pdb=" O5 MAN U 4 " both_signs ideal model delta sigma weight residual False 2.40 1.48 0.92 2.00e-02 2.50e+03 2.11e+03 chirality pdb=" C1 MAN Z 4 " pdb=" O4 NAG Z 2 " pdb=" C2 MAN Z 4 " pdb=" O5 MAN Z 4 " both_signs ideal model delta sigma weight residual False 2.40 1.48 0.92 2.00e-02 2.50e+03 2.11e+03 ... (remaining 3237 not shown) Planarity restraints: 2439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG U 1 " -0.364 2.00e-02 2.50e+03 3.08e-01 1.18e+03 pdb=" C7 NAG U 1 " 0.093 2.00e-02 2.50e+03 pdb=" C8 NAG U 1 " -0.152 2.00e-02 2.50e+03 pdb=" N2 NAG U 1 " 0.542 2.00e-02 2.50e+03 pdb=" O7 NAG U 1 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 1 " -0.359 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG j 1 " 0.090 2.00e-02 2.50e+03 pdb=" C8 NAG j 1 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG j 1 " 0.538 2.00e-02 2.50e+03 pdb=" O7 NAG j 1 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG y 1 " -0.357 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG y 1 " 0.089 2.00e-02 2.50e+03 pdb=" C8 NAG y 1 " -0.152 2.00e-02 2.50e+03 pdb=" N2 NAG y 1 " 0.538 2.00e-02 2.50e+03 pdb=" O7 NAG y 1 " -0.118 2.00e-02 2.50e+03 ... (remaining 2436 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.03: 7 2.03 - 2.75: 1699 2.75 - 3.47: 21480 3.47 - 4.18: 40357 4.18 - 4.90: 65723 Nonbonded interactions: 129266 Sorted by model distance: nonbonded pdb=" CG ASN G 57 " pdb=" N ASP I 24 " model vdw 1.317 3.350 nonbonded pdb=" CG ASN F 57 " pdb=" N ASP H 24 " model vdw 1.321 3.350 nonbonded pdb=" CG ASN A 57 " pdb=" N ASP C 24 " model vdw 1.325 3.350 nonbonded pdb=" CG ASN B 57 " pdb=" N ASP D 24 " model vdw 1.326 3.350 nonbonded pdb=" CG ASN E 57 " pdb=" N ASP G 24 " model vdw 1.326 3.350 ... (remaining 129261 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 '0' selection = chain '1' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'K' selection = chain 'P' selection = chain 'U' selection = chain 'Z' selection = chain 'e' selection = chain 'j' selection = chain 'o' selection = chain 't' selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.870 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 47.630 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 : 0.013 0.108 16074 Z= 0.755 Angle : 1.746 12.180 22149 Z= 0.901 Chirality : 0.122 0.920 3240 Planarity : 0.028 0.308 2394 Dihedral : 18.905 116.601 9711 Min Nonbonded Distance : 1.317 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.56 % Allowed : 3.21 % Favored : 94.23 % Cbeta Deviations : 1.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.58 (0.19), residues: 639 loop : -0.24 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.041 0.011 PHE D 44 TYR 0.044 0.010 TYR F 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 379 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 PHE cc_start: 0.8640 (m-80) cc_final: 0.8295 (m-80) REVERT: A 87 ASN cc_start: 0.8783 (m-40) cc_final: 0.8581 (m110) REVERT: A 129 GLN cc_start: 0.8412 (tt0) cc_final: 0.8156 (tt0) REVERT: A 152 THR cc_start: 0.8561 (m) cc_final: 0.8249 (p) REVERT: B 102 TYR cc_start: 0.8575 (m-80) cc_final: 0.8176 (m-80) REVERT: B 125 TYR cc_start: 0.8443 (m-80) cc_final: 0.7776 (m-80) REVERT: B 128 ASN cc_start: 0.8471 (t0) cc_final: 0.8243 (t0) REVERT: B 165 LEU cc_start: 0.8658 (tp) cc_final: 0.8437 (tt) REVERT: B 194 MET cc_start: 0.8270 (mtm) cc_final: 0.8044 (mtp) REVERT: B 201 ILE cc_start: 0.8496 (mm) cc_final: 0.8268 (mm) REVERT: C 76 THR cc_start: 0.8824 (m) cc_final: 0.8492 (p) REVERT: C 93 MET cc_start: 0.8618 (mmp) cc_final: 0.8139 (tpp) REVERT: C 102 TYR cc_start: 0.8729 (m-80) cc_final: 0.8112 (m-80) REVERT: C 104 TYR cc_start: 0.8709 (p90) cc_final: 0.8356 (p90) REVERT: C 177 THR cc_start: 0.8481 (m) cc_final: 0.8277 (p) REVERT: C 194 MET cc_start: 0.8186 (mtm) cc_final: 0.7928 (mtp) REVERT: E 69 SER cc_start: 0.8483 (t) cc_final: 0.8263 (m) REVERT: E 80 ASN cc_start: 0.8514 (m-40) cc_final: 0.8214 (m-40) REVERT: E 125 TYR cc_start: 0.8405 (m-80) cc_final: 0.7551 (m-80) REVERT: E 129 GLN cc_start: 0.8629 (tt0) cc_final: 0.8156 (mt0) REVERT: F 125 TYR cc_start: 0.8699 (m-80) cc_final: 0.8095 (m-80) REVERT: F 151 SER cc_start: 0.8431 (p) cc_final: 0.8226 (t) REVERT: F 164 SER cc_start: 0.8551 (m) cc_final: 0.8163 (p) REVERT: F 177 THR cc_start: 0.8356 (m) cc_final: 0.8154 (t) REVERT: F 178 PRO cc_start: 0.8837 (Cg_exo) cc_final: 0.8602 (Cg_endo) REVERT: G 97 VAL cc_start: 0.8470 (t) cc_final: 0.8252 (m) REVERT: G 102 TYR cc_start: 0.8870 (m-80) cc_final: 0.8406 (m-80) REVERT: G 194 MET cc_start: 0.8422 (mtm) cc_final: 0.8175 (mtp) REVERT: G 195 THR cc_start: 0.8573 (p) cc_final: 0.8031 (t) REVERT: G 201 ILE cc_start: 0.8318 (mm) cc_final: 0.7987 (mt) REVERT: H 86 TYR cc_start: 0.8623 (m-80) cc_final: 0.8411 (m-80) REVERT: H 128 ASN cc_start: 0.8527 (t0) cc_final: 0.8327 (m-40) REVERT: H 161 TYR cc_start: 0.8475 (m-80) cc_final: 0.7856 (m-80) REVERT: I 59 ASN cc_start: 0.7672 (OUTLIER) cc_final: 0.7447 (m-40) REVERT: I 89 TYR cc_start: 0.7652 (m-80) cc_final: 0.7419 (m-80) REVERT: I 102 TYR cc_start: 0.8580 (m-80) cc_final: 0.8144 (m-10) REVERT: I 125 TYR cc_start: 0.8243 (m-80) cc_final: 0.7131 (m-80) REVERT: I 161 TYR cc_start: 0.8249 (m-80) cc_final: 0.8036 (m-80) REVERT: I 186 THR cc_start: 0.8488 (m) cc_final: 0.8254 (p) outliers start: 36 outliers final: 5 residues processed: 396 average time/residue: 0.2109 time to fit residues: 133.9681 Evaluate side-chains 301 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 295 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain I residue 59 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 126 optimal weight: 0.1980 chunk 49 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 147 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 59 ASN A 117 ASN A 129 GLN B 37 ASN B 59 ASN B 87 ASN C 37 ASN D 37 ASN E 37 ASN E 120 GLN E 129 GLN F 37 ASN F 59 ASN F 120 GLN F 132 GLN G 37 ASN G 87 ASN G 171 GLN H 67 GLN H 78 GLN H 120 GLN ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16074 Z= 0.265 Angle : 0.907 8.945 22149 Z= 0.379 Chirality : 0.052 0.237 3240 Planarity : 0.005 0.048 2394 Dihedral : 15.814 106.103 6910 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.06 % Allowed : 9.69 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.57 (0.19), residues: 657 loop : -0.20 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.002 PHE C 92 TYR 0.024 0.002 TYR H 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 329 time to evaluate : 1.393 Fit side-chains REVERT: A 152 THR cc_start: 0.8577 (m) cc_final: 0.8258 (p) REVERT: B 93 MET cc_start: 0.8294 (mmm) cc_final: 0.7885 (mmm) REVERT: B 102 TYR cc_start: 0.8593 (m-80) cc_final: 0.8224 (m-80) REVERT: B 112 TYR cc_start: 0.8522 (p90) cc_final: 0.7891 (p90) REVERT: B 125 TYR cc_start: 0.8436 (m-80) cc_final: 0.7978 (m-80) REVERT: B 194 MET cc_start: 0.8361 (mtm) cc_final: 0.8073 (mtp) REVERT: C 76 THR cc_start: 0.8834 (m) cc_final: 0.8506 (p) REVERT: C 93 MET cc_start: 0.8448 (mmp) cc_final: 0.8094 (mmm) REVERT: C 102 TYR cc_start: 0.8750 (m-80) cc_final: 0.8026 (m-80) REVERT: C 104 TYR cc_start: 0.8728 (p90) cc_final: 0.8519 (p90) REVERT: C 177 THR cc_start: 0.8525 (m) cc_final: 0.8209 (p) REVERT: C 194 MET cc_start: 0.8222 (mtm) cc_final: 0.7898 (mtm) REVERT: C 201 ILE cc_start: 0.8268 (mm) cc_final: 0.8040 (mm) REVERT: E 69 SER cc_start: 0.8391 (t) cc_final: 0.8168 (m) REVERT: E 125 TYR cc_start: 0.8386 (m-80) cc_final: 0.7503 (m-80) REVERT: F 38 VAL cc_start: 0.8117 (OUTLIER) cc_final: 0.7787 (m) REVERT: F 47 GLN cc_start: 0.8665 (mt0) cc_final: 0.8375 (mt0) REVERT: F 59 ASN cc_start: 0.8532 (t0) cc_final: 0.8262 (t0) REVERT: F 125 TYR cc_start: 0.8787 (m-80) cc_final: 0.8158 (m-80) REVERT: F 177 THR cc_start: 0.8369 (m) cc_final: 0.8011 (p) REVERT: F 178 PRO cc_start: 0.8785 (Cg_exo) cc_final: 0.8584 (Cg_endo) REVERT: F 180 ASN cc_start: 0.8489 (p0) cc_final: 0.8265 (p0) REVERT: G 97 VAL cc_start: 0.8435 (t) cc_final: 0.8182 (m) REVERT: G 102 TYR cc_start: 0.8857 (m-80) cc_final: 0.8358 (m-80) REVERT: G 194 MET cc_start: 0.8316 (mtm) cc_final: 0.8058 (mtp) REVERT: G 195 THR cc_start: 0.8609 (p) cc_final: 0.8063 (t) REVERT: H 47 GLN cc_start: 0.8436 (mt0) cc_final: 0.8075 (mt0) REVERT: H 78 GLN cc_start: 0.8125 (tt0) cc_final: 0.7814 (tm-30) REVERT: H 148 THR cc_start: 0.8106 (p) cc_final: 0.7820 (p) REVERT: I 51 ASN cc_start: 0.7834 (t0) cc_final: 0.7529 (t0) REVERT: I 102 TYR cc_start: 0.8544 (m-80) cc_final: 0.8022 (m-10) REVERT: I 125 TYR cc_start: 0.8228 (m-80) cc_final: 0.7685 (m-80) REVERT: I 186 THR cc_start: 0.8511 (m) cc_final: 0.8150 (p) outliers start: 43 outliers final: 27 residues processed: 356 average time/residue: 0.2180 time to fit residues: 125.0306 Evaluate side-chains 338 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 310 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 157 ASN Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 0.0970 chunk 45 optimal weight: 0.0040 chunk 122 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 146 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN B 67 GLN B 78 GLN B 87 ASN B 120 GLN B 129 GLN E 59 ASN E 120 GLN F 120 GLN F 132 GLN G 87 ASN G 171 GLN H 65 ASN H 188 ASN ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16074 Z= 0.238 Angle : 0.834 8.846 22149 Z= 0.344 Chirality : 0.048 0.234 3240 Planarity : 0.005 0.048 2394 Dihedral : 13.134 103.879 6906 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.77 % Allowed : 12.32 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.12 (0.18), residues: 792 loop : 0.49 (0.24), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE C 92 TYR 0.026 0.002 TYR I 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 330 time to evaluate : 1.460 Fit side-chains revert: symmetry clash REVERT: A 130 GLN cc_start: 0.8803 (mp-120) cc_final: 0.8530 (mp10) REVERT: A 152 THR cc_start: 0.8581 (m) cc_final: 0.8269 (p) REVERT: B 102 TYR cc_start: 0.8586 (m-80) cc_final: 0.8227 (m-80) REVERT: B 125 TYR cc_start: 0.8423 (m-80) cc_final: 0.7839 (m-80) REVERT: B 141 VAL cc_start: 0.8776 (t) cc_final: 0.8482 (m) REVERT: B 194 MET cc_start: 0.8378 (mtm) cc_final: 0.8102 (mtp) REVERT: C 76 THR cc_start: 0.8831 (m) cc_final: 0.8494 (p) REVERT: C 93 MET cc_start: 0.8438 (mmp) cc_final: 0.8058 (mmm) REVERT: C 102 TYR cc_start: 0.8734 (m-80) cc_final: 0.8003 (m-80) REVERT: D 93 MET cc_start: 0.8194 (mmm) cc_final: 0.7834 (mmm) REVERT: E 125 TYR cc_start: 0.8394 (m-80) cc_final: 0.7530 (m-80) REVERT: F 38 VAL cc_start: 0.7977 (OUTLIER) cc_final: 0.7723 (m) REVERT: F 59 ASN cc_start: 0.8632 (t0) cc_final: 0.8282 (t0) REVERT: F 125 TYR cc_start: 0.8795 (m-80) cc_final: 0.8166 (m-80) REVERT: F 155 GLN cc_start: 0.8541 (tt0) cc_final: 0.8253 (tt0) REVERT: F 177 THR cc_start: 0.8377 (m) cc_final: 0.8006 (p) REVERT: G 97 VAL cc_start: 0.8414 (t) cc_final: 0.8170 (m) REVERT: G 102 TYR cc_start: 0.8836 (m-80) cc_final: 0.8337 (m-80) REVERT: G 152 THR cc_start: 0.8642 (m) cc_final: 0.8312 (p) REVERT: G 194 MET cc_start: 0.8315 (mtm) cc_final: 0.8042 (mtp) REVERT: H 148 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7750 (p) REVERT: I 102 TYR cc_start: 0.8582 (m-80) cc_final: 0.8154 (m-80) REVERT: I 186 THR cc_start: 0.8476 (m) cc_final: 0.8044 (p) outliers start: 53 outliers final: 36 residues processed: 363 average time/residue: 0.2185 time to fit residues: 128.4832 Evaluate side-chains 359 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 321 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 142 ASN Chi-restraints excluded: chain G residue 157 ASN Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 147 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 129 GLN C 47 GLN E 120 GLN ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN F 32 GLN F 47 GLN F 120 GLN F 132 GLN G 87 ASN ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16074 Z= 0.380 Angle : 0.852 9.850 22149 Z= 0.361 Chirality : 0.049 0.275 3240 Planarity : 0.005 0.050 2394 Dihedral : 12.450 103.593 6905 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.91 % Allowed : 13.25 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.13 (0.18), residues: 774 loop : 0.39 (0.24), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.003 PHE C 92 TYR 0.026 0.002 TYR I 89 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 347 time to evaluate : 1.598 Fit side-chains revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8293 (m-80) cc_final: 0.8000 (m-80) REVERT: A 152 THR cc_start: 0.8604 (m) cc_final: 0.8299 (p) REVERT: B 102 TYR cc_start: 0.8621 (m-80) cc_final: 0.8310 (m-80) REVERT: B 112 TYR cc_start: 0.8530 (p90) cc_final: 0.8182 (p90) REVERT: B 125 TYR cc_start: 0.8433 (m-80) cc_final: 0.7798 (m-80) REVERT: B 141 VAL cc_start: 0.8822 (t) cc_final: 0.8530 (m) REVERT: B 165 LEU cc_start: 0.8631 (tp) cc_final: 0.8401 (tt) REVERT: B 194 MET cc_start: 0.8426 (mtm) cc_final: 0.8182 (mtp) REVERT: C 76 THR cc_start: 0.8853 (m) cc_final: 0.8490 (p) REVERT: C 93 MET cc_start: 0.8394 (mmp) cc_final: 0.7991 (mmm) REVERT: C 102 TYR cc_start: 0.8751 (m-80) cc_final: 0.8002 (m-80) REVERT: C 112 TYR cc_start: 0.8661 (p90) cc_final: 0.8445 (p90) REVERT: C 194 MET cc_start: 0.8265 (mtm) cc_final: 0.7899 (mtp) REVERT: D 59 ASN cc_start: 0.8710 (t0) cc_final: 0.8485 (t0) REVERT: D 93 MET cc_start: 0.8221 (mmm) cc_final: 0.7785 (mmm) REVERT: E 125 TYR cc_start: 0.8432 (m-80) cc_final: 0.7549 (m-80) REVERT: F 38 VAL cc_start: 0.7818 (OUTLIER) cc_final: 0.7540 (m) REVERT: F 59 ASN cc_start: 0.8751 (t0) cc_final: 0.8369 (t0) REVERT: F 155 GLN cc_start: 0.8583 (tt0) cc_final: 0.8286 (tt0) REVERT: F 177 THR cc_start: 0.8389 (m) cc_final: 0.8006 (p) REVERT: G 97 VAL cc_start: 0.8421 (t) cc_final: 0.8179 (m) REVERT: G 102 TYR cc_start: 0.8797 (m-80) cc_final: 0.8292 (m-80) REVERT: G 152 THR cc_start: 0.8629 (m) cc_final: 0.8402 (t) REVERT: G 194 MET cc_start: 0.8334 (mtm) cc_final: 0.8021 (mtp) REVERT: I 102 TYR cc_start: 0.8555 (m-80) cc_final: 0.8103 (m-80) outliers start: 69 outliers final: 58 residues processed: 381 average time/residue: 0.2069 time to fit residues: 127.2472 Evaluate side-chains 388 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 329 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 142 ASN Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 157 ASN Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 108 optimal weight: 0.0770 chunk 0 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 39 optimal weight: 0.0370 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 47 GLN F 120 GLN F 129 GLN F 132 GLN ** G 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16074 Z= 0.255 Angle : 0.779 8.983 22149 Z= 0.328 Chirality : 0.046 0.262 3240 Planarity : 0.005 0.052 2394 Dihedral : 12.250 103.160 6903 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.42 % Allowed : 14.46 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.12 (0.19), residues: 774 loop : 0.45 (0.24), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE D 92 TYR 0.026 0.002 TYR I 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 338 time to evaluate : 1.458 Fit side-chains revert: symmetry clash REVERT: A 152 THR cc_start: 0.8580 (m) cc_final: 0.8280 (p) REVERT: A 184 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8503 (p) REVERT: B 102 TYR cc_start: 0.8593 (m-80) cc_final: 0.8277 (m-80) REVERT: B 125 TYR cc_start: 0.8407 (m-80) cc_final: 0.7774 (m-80) REVERT: B 141 VAL cc_start: 0.8826 (t) cc_final: 0.8547 (m) REVERT: B 165 LEU cc_start: 0.8625 (tp) cc_final: 0.8403 (tt) REVERT: B 194 MET cc_start: 0.8409 (mtm) cc_final: 0.8170 (mtp) REVERT: C 76 THR cc_start: 0.8843 (m) cc_final: 0.8465 (p) REVERT: C 93 MET cc_start: 0.8398 (mmt) cc_final: 0.8002 (mmm) REVERT: C 102 TYR cc_start: 0.8737 (m-80) cc_final: 0.8000 (m-80) REVERT: C 156 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8330 (tt) REVERT: C 194 MET cc_start: 0.8265 (mtm) cc_final: 0.7904 (mtp) REVERT: D 59 ASN cc_start: 0.8688 (t0) cc_final: 0.8460 (t0) REVERT: D 93 MET cc_start: 0.8196 (mmm) cc_final: 0.7752 (mmm) REVERT: E 125 TYR cc_start: 0.8412 (m-80) cc_final: 0.7535 (m-80) REVERT: F 38 VAL cc_start: 0.7770 (OUTLIER) cc_final: 0.7494 (m) REVERT: F 59 ASN cc_start: 0.8728 (t0) cc_final: 0.8340 (t0) REVERT: F 155 GLN cc_start: 0.8584 (tt0) cc_final: 0.8358 (tt0) REVERT: F 177 THR cc_start: 0.8395 (m) cc_final: 0.8010 (p) REVERT: G 97 VAL cc_start: 0.8394 (t) cc_final: 0.8156 (m) REVERT: G 102 TYR cc_start: 0.8813 (m-80) cc_final: 0.8266 (m-80) REVERT: G 152 THR cc_start: 0.8621 (m) cc_final: 0.8402 (t) REVERT: G 194 MET cc_start: 0.8333 (mtm) cc_final: 0.7963 (mtp) REVERT: I 51 ASN cc_start: 0.7869 (t0) cc_final: 0.7524 (t0) REVERT: I 102 TYR cc_start: 0.8559 (m-80) cc_final: 0.8061 (m-80) REVERT: I 125 TYR cc_start: 0.8209 (m-80) cc_final: 0.7119 (m-80) outliers start: 62 outliers final: 47 residues processed: 372 average time/residue: 0.2083 time to fit residues: 125.2487 Evaluate side-chains 380 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 330 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 142 ASN Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 157 ASN Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN D 188 ASN E 30 GLN ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN F 120 GLN F 132 GLN G 87 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16074 Z= 0.382 Angle : 0.824 9.346 22149 Z= 0.353 Chirality : 0.048 0.256 3240 Planarity : 0.005 0.045 2394 Dihedral : 12.164 102.875 6903 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.27 % Allowed : 14.81 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.01 (0.18), residues: 774 loop : 0.38 (0.24), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.003 PHE D 92 TYR 0.025 0.002 TYR I 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 335 time to evaluate : 1.477 Fit side-chains REVERT: A 184 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8464 (p) REVERT: B 102 TYR cc_start: 0.8587 (m-80) cc_final: 0.8292 (m-80) REVERT: B 125 TYR cc_start: 0.8408 (m-80) cc_final: 0.7715 (m-80) REVERT: B 141 VAL cc_start: 0.8856 (t) cc_final: 0.8585 (m) REVERT: B 194 MET cc_start: 0.8429 (mtm) cc_final: 0.8189 (mtp) REVERT: C 76 THR cc_start: 0.8859 (m) cc_final: 0.8474 (p) REVERT: C 93 MET cc_start: 0.8425 (mmt) cc_final: 0.8004 (mmm) REVERT: C 102 TYR cc_start: 0.8774 (m-80) cc_final: 0.8072 (m-80) REVERT: C 156 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8350 (tt) REVERT: C 187 VAL cc_start: 0.8643 (t) cc_final: 0.8291 (p) REVERT: C 194 MET cc_start: 0.8286 (mtm) cc_final: 0.7939 (mtp) REVERT: D 59 ASN cc_start: 0.8712 (t0) cc_final: 0.8460 (t0) REVERT: F 38 VAL cc_start: 0.7739 (OUTLIER) cc_final: 0.7385 (m) REVERT: F 59 ASN cc_start: 0.8850 (t0) cc_final: 0.8479 (t0) REVERT: F 177 THR cc_start: 0.8415 (m) cc_final: 0.8030 (p) REVERT: G 97 VAL cc_start: 0.8406 (t) cc_final: 0.8159 (m) REVERT: G 102 TYR cc_start: 0.8761 (m-80) cc_final: 0.8227 (m-80) REVERT: G 194 MET cc_start: 0.8337 (mtm) cc_final: 0.7933 (mtp) REVERT: I 102 TYR cc_start: 0.8528 (m-80) cc_final: 0.7988 (m-80) REVERT: I 125 TYR cc_start: 0.8271 (m-80) cc_final: 0.8031 (m-10) outliers start: 74 outliers final: 58 residues processed: 374 average time/residue: 0.2040 time to fit residues: 123.9064 Evaluate side-chains 394 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 333 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 142 ASN Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 157 ASN Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 170 TYR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 89 optimal weight: 0.0770 chunk 114 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 156 optimal weight: 0.2980 chunk 97 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN D 188 ASN ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16074 Z= 0.251 Angle : 0.765 8.945 22149 Z= 0.324 Chirality : 0.046 0.220 3240 Planarity : 0.004 0.043 2394 Dihedral : 12.024 102.054 6903 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.20 % Allowed : 16.45 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.02 (0.19), residues: 774 loop : 0.44 (0.24), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.002 PHE D 92 TYR 0.025 0.002 TYR I 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 349 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8299 (m-10) cc_final: 0.7888 (m-80) REVERT: A 184 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8462 (p) REVERT: B 102 TYR cc_start: 0.8582 (m-80) cc_final: 0.8293 (m-80) REVERT: B 112 TYR cc_start: 0.8554 (p90) cc_final: 0.7683 (p90) REVERT: B 125 TYR cc_start: 0.8395 (m-80) cc_final: 0.7745 (m-80) REVERT: B 141 VAL cc_start: 0.8843 (t) cc_final: 0.8588 (m) REVERT: B 194 MET cc_start: 0.8420 (mtm) cc_final: 0.8191 (mtp) REVERT: C 76 THR cc_start: 0.8839 (m) cc_final: 0.8443 (p) REVERT: C 93 MET cc_start: 0.8399 (mmt) cc_final: 0.7992 (mmm) REVERT: C 102 TYR cc_start: 0.8748 (m-80) cc_final: 0.8046 (m-80) REVERT: C 156 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8346 (tt) REVERT: C 187 VAL cc_start: 0.8600 (t) cc_final: 0.8249 (p) REVERT: C 194 MET cc_start: 0.8286 (mtm) cc_final: 0.7957 (mtp) REVERT: F 38 VAL cc_start: 0.7693 (OUTLIER) cc_final: 0.7346 (m) REVERT: F 59 ASN cc_start: 0.8824 (t0) cc_final: 0.8438 (t0) REVERT: F 141 VAL cc_start: 0.8801 (t) cc_final: 0.8531 (m) REVERT: F 177 THR cc_start: 0.8420 (m) cc_final: 0.8036 (p) REVERT: G 152 THR cc_start: 0.8581 (m) cc_final: 0.8378 (t) REVERT: I 102 TYR cc_start: 0.8560 (m-80) cc_final: 0.8018 (m-80) REVERT: I 125 TYR cc_start: 0.8257 (m-80) cc_final: 0.7962 (m-10) outliers start: 59 outliers final: 47 residues processed: 379 average time/residue: 0.2025 time to fit residues: 124.5244 Evaluate side-chains 386 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 336 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 142 ASN Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 157 ASN Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 170 TYR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 142 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN C 49 ASN ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 GLN F 120 GLN F 132 GLN ** G 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16074 Z= 0.278 Angle : 0.770 8.943 22149 Z= 0.327 Chirality : 0.047 0.262 3240 Planarity : 0.004 0.046 2394 Dihedral : 11.859 101.336 6903 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.84 % Allowed : 16.95 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: -0.02 (0.19), residues: 774 loop : 0.45 (0.25), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE D 92 TYR 0.024 0.002 TYR I 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 338 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8306 (m-10) cc_final: 0.7911 (m-80) REVERT: A 184 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8461 (p) REVERT: B 102 TYR cc_start: 0.8592 (m-80) cc_final: 0.8298 (m-80) REVERT: B 112 TYR cc_start: 0.8561 (p90) cc_final: 0.7756 (p90) REVERT: B 125 TYR cc_start: 0.8392 (m-80) cc_final: 0.7711 (m-80) REVERT: B 141 VAL cc_start: 0.8862 (t) cc_final: 0.8597 (m) REVERT: B 194 MET cc_start: 0.8427 (mtm) cc_final: 0.8199 (mtp) REVERT: C 93 MET cc_start: 0.8413 (mmt) cc_final: 0.8030 (mmm) REVERT: C 102 TYR cc_start: 0.8748 (m-80) cc_final: 0.8058 (m-80) REVERT: C 156 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8329 (tt) REVERT: C 187 VAL cc_start: 0.8624 (t) cc_final: 0.8321 (p) REVERT: C 194 MET cc_start: 0.8300 (mtm) cc_final: 0.7963 (mtm) REVERT: F 38 VAL cc_start: 0.7688 (OUTLIER) cc_final: 0.7334 (m) REVERT: F 59 ASN cc_start: 0.8834 (t0) cc_final: 0.8442 (t0) REVERT: F 141 VAL cc_start: 0.8809 (t) cc_final: 0.8515 (m) REVERT: F 177 THR cc_start: 0.8420 (m) cc_final: 0.8034 (p) REVERT: H 148 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7682 (p) REVERT: I 102 TYR cc_start: 0.8592 (m-80) cc_final: 0.8035 (m-80) REVERT: I 125 TYR cc_start: 0.8244 (m-80) cc_final: 0.7964 (m-10) outliers start: 68 outliers final: 53 residues processed: 374 average time/residue: 0.2022 time to fit residues: 122.5729 Evaluate side-chains 393 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 336 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 142 ASN Chi-restraints excluded: chain G residue 157 ASN Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 170 TYR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.4980 chunk 136 optimal weight: 0.4980 chunk 145 optimal weight: 0.9980 chunk 87 optimal weight: 0.3980 chunk 63 optimal weight: 0.0980 chunk 114 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN B 87 ASN C 49 ASN ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16074 Z= 0.226 Angle : 0.748 8.755 22149 Z= 0.317 Chirality : 0.046 0.412 3240 Planarity : 0.004 0.045 2394 Dihedral : 11.715 100.573 6903 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.34 % Allowed : 17.45 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.01 (0.19), residues: 774 loop : 0.50 (0.25), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE D 92 TYR 0.022 0.002 TYR I 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 334 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8305 (m-10) cc_final: 0.7897 (m-80) REVERT: A 184 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8476 (p) REVERT: B 102 TYR cc_start: 0.8592 (m-80) cc_final: 0.8257 (m-80) REVERT: B 112 TYR cc_start: 0.8565 (p90) cc_final: 0.7742 (p90) REVERT: B 125 TYR cc_start: 0.8373 (m-80) cc_final: 0.7713 (m-80) REVERT: B 141 VAL cc_start: 0.8857 (t) cc_final: 0.8592 (m) REVERT: B 194 MET cc_start: 0.8415 (mtm) cc_final: 0.8165 (mtp) REVERT: C 93 MET cc_start: 0.8415 (mmt) cc_final: 0.8019 (mmm) REVERT: C 102 TYR cc_start: 0.8748 (m-80) cc_final: 0.8048 (m-80) REVERT: C 156 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8337 (tt) REVERT: C 187 VAL cc_start: 0.8615 (t) cc_final: 0.8316 (p) REVERT: C 194 MET cc_start: 0.8290 (mtm) cc_final: 0.7955 (mtp) REVERT: F 59 ASN cc_start: 0.8821 (t0) cc_final: 0.8430 (t0) REVERT: F 141 VAL cc_start: 0.8802 (t) cc_final: 0.8518 (m) REVERT: F 177 THR cc_start: 0.8427 (m) cc_final: 0.8043 (p) REVERT: I 51 ASN cc_start: 0.7860 (t0) cc_final: 0.7509 (t0) REVERT: I 102 TYR cc_start: 0.8581 (m-80) cc_final: 0.8019 (m-80) REVERT: I 125 TYR cc_start: 0.8251 (m-80) cc_final: 0.7961 (m-10) outliers start: 61 outliers final: 54 residues processed: 367 average time/residue: 0.2117 time to fit residues: 126.0068 Evaluate side-chains 384 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 328 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 142 ASN Chi-restraints excluded: chain G residue 157 ASN Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 170 TYR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 106 optimal weight: 0.8980 chunk 161 optimal weight: 0.0870 chunk 148 optimal weight: 0.8980 chunk 128 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 99 optimal weight: 0.2980 chunk 78 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 GLN B 87 ASN ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN F 47 GLN F 132 GLN ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16074 Z= 0.202 Angle : 0.735 8.664 22149 Z= 0.311 Chirality : 0.046 0.330 3240 Planarity : 0.004 0.043 2394 Dihedral : 11.521 99.701 6903 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.06 % Allowed : 17.52 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.02 (0.19), residues: 774 loop : 0.54 (0.25), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE E 92 TYR 0.018 0.001 TYR I 89 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 326 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8304 (m-10) cc_final: 0.7920 (m-80) REVERT: A 184 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8466 (p) REVERT: B 102 TYR cc_start: 0.8593 (m-80) cc_final: 0.8260 (m-80) REVERT: B 112 TYR cc_start: 0.8557 (p90) cc_final: 0.7744 (p90) REVERT: B 141 VAL cc_start: 0.8855 (t) cc_final: 0.8584 (m) REVERT: B 194 MET cc_start: 0.8392 (mtm) cc_final: 0.8154 (mtp) REVERT: C 93 MET cc_start: 0.8383 (mmt) cc_final: 0.8012 (mmm) REVERT: C 102 TYR cc_start: 0.8747 (m-80) cc_final: 0.8042 (m-80) REVERT: C 156 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8335 (tt) REVERT: C 187 VAL cc_start: 0.8545 (t) cc_final: 0.8267 (p) REVERT: F 38 VAL cc_start: 0.7445 (p) cc_final: 0.6971 (m) REVERT: F 47 GLN cc_start: 0.8520 (mt0) cc_final: 0.8306 (mt0) REVERT: F 59 ASN cc_start: 0.8823 (t0) cc_final: 0.8432 (t0) REVERT: F 102 TYR cc_start: 0.8750 (m-10) cc_final: 0.8470 (m-10) REVERT: F 128 ASN cc_start: 0.8105 (t0) cc_final: 0.7892 (t0) REVERT: F 130 GLN cc_start: 0.8599 (mp10) cc_final: 0.7879 (mp10) REVERT: F 155 GLN cc_start: 0.8609 (tt0) cc_final: 0.8352 (tt0) REVERT: F 177 THR cc_start: 0.8420 (m) cc_final: 0.8034 (p) REVERT: H 148 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7653 (p) REVERT: I 51 ASN cc_start: 0.7849 (t0) cc_final: 0.7350 (t0) REVERT: I 102 TYR cc_start: 0.8585 (m-80) cc_final: 0.8026 (m-80) REVERT: I 125 TYR cc_start: 0.8236 (m-80) cc_final: 0.7937 (m-10) outliers start: 57 outliers final: 48 residues processed: 358 average time/residue: 0.2062 time to fit residues: 119.7469 Evaluate side-chains 371 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 320 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 142 ASN Chi-restraints excluded: chain G residue 157 ASN Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 170 TYR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 184 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.6980 chunk 39 optimal weight: 0.0970 chunk 118 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 132 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN B 87 ASN C 116 ASN E 120 GLN ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.117267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.096349 restraints weight = 23532.699| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.34 r_work: 0.3022 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.218 16074 Z= 0.314 Angle : 0.911 59.198 22149 Z= 0.455 Chirality : 0.051 1.223 3240 Planarity : 0.004 0.054 2394 Dihedral : 11.523 99.702 6903 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.56 % Allowed : 18.09 % Favored : 78.35 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.22), residues: 1629 helix: None (None), residues: 0 sheet: 0.02 (0.19), residues: 774 loop : 0.54 (0.25), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE E 92 TYR 0.017 0.001 TYR H 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3672.93 seconds wall clock time: 67 minutes 58.41 seconds (4078.41 seconds total)