Starting phenix.real_space_refine on Wed Feb 21 17:09:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttw_41613/02_2024/8ttw_41613_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttw_41613/02_2024/8ttw_41613.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttw_41613/02_2024/8ttw_41613_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttw_41613/02_2024/8ttw_41613_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttw_41613/02_2024/8ttw_41613_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttw_41613/02_2024/8ttw_41613.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttw_41613/02_2024/8ttw_41613.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttw_41613/02_2024/8ttw_41613_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttw_41613/02_2024/8ttw_41613_updated.pdb" } resolution = 2.96 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= 0.043 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 153 5.16 5 C 19545 2.51 5 N 5199 2.21 5 O 6378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 49": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 621": "OE1" <-> "OE2" Residue "B ASP 624": "OD1" <-> "OD2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "C TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 49": "OE1" <-> "OE2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 368": "OD1" <-> "OD2" Residue "E GLU 370": "OE1" <-> "OE2" Residue "F TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 621": "OE1" <-> "OE2" Residue "F ASP 624": "OD1" <-> "OD2" Residue "F GLU 634": "OE1" <-> "OE2" Residue "F TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 648": "OE1" <-> "OE2" Residue "G TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 49": "OE1" <-> "OE2" Residue "I GLU 102": "OE1" <-> "OE2" Residue "I TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 190": "OE1" <-> "OE2" Residue "I GLU 275": "OE1" <-> "OE2" Residue "I TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 654": "OE1" <-> "OE2" Residue "K TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 86": "OD1" <-> "OD2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 170": "OD1" <-> "OD2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31275 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3554 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "B" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "C" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1710 Classifications: {'peptide': 227} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 213} Chain breaks: 1 Chain: "D" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1626 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Chain: "E" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3554 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "F" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "G" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1710 Classifications: {'peptide': 227} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 213} Chain breaks: 1 Chain: "H" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1626 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Chain: "I" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3554 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "J" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "K" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1710 Classifications: {'peptide': 227} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 213} Chain breaks: 1 Chain: "L" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1626 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Chain: "M" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1021 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "N" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 812 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "O" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1021 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "P" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 812 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "Q" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1021 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "R" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 812 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "o" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "0" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 91 Unusual residues: {'83J': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 91 Unusual residues: {'83J': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 91 Unusual residues: {'83J': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" C1 MAN b 4 " occ=0.93 ... (9 atoms not shown) pdb=" O6 MAN b 4 " occ=0.93 residue: pdb=" C1 MAN b 8 " occ=0.80 ... (9 atoms not shown) pdb=" O6 MAN b 8 " occ=0.80 residue: pdb=" C1 MAN b 9 " occ=0.85 ... (9 atoms not shown) pdb=" O6 MAN b 9 " occ=0.85 residue: pdb=" C1 MAN n 4 " occ=0.77 ... (9 atoms not shown) pdb=" O6 MAN n 4 " occ=0.77 residue: pdb=" C1 MAN n 8 " occ=0.74 ... (9 atoms not shown) pdb=" O6 MAN n 8 " occ=0.74 residue: pdb=" C1 MAN n 9 " occ=0.82 ... (9 atoms not shown) pdb=" O6 MAN n 9 " occ=0.82 residue: pdb=" C1 MAN z 4 " occ=0.90 ... (9 atoms not shown) pdb=" O6 MAN z 4 " occ=0.90 residue: pdb=" C1 MAN z 8 " occ=0.87 ... (9 atoms not shown) pdb=" O6 MAN z 8 " occ=0.87 residue: pdb=" C1 MAN z 9 " occ=0.79 ... (9 atoms not shown) pdb=" O6 MAN z 9 " occ=0.79 Time building chain proxies: 16.59, per 1000 atoms: 0.53 Number of scatterers: 31275 At special positions: 0 Unit cell: (196.248, 190.032, 149.184, 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 153 16.00 O 6378 8.00 N 5199 7.00 C 19545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 140 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.02 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.05 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.04 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.04 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 140 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 3 4 " - " MAN 3 5 " " MAN 3 5 " - " MAN 3 6 " " MAN b 4 " - " MAN b 5 " " MAN b 5 " - " MAN b 6 " " MAN b 8 " - " MAN b 9 " " MAN f 4 " - " MAN f 5 " " MAN f 5 " - " MAN f 6 " " MAN n 4 " - " MAN n 5 " " MAN n 5 " - " MAN n 6 " " MAN n 8 " - " MAN n 9 " " MAN r 4 " - " MAN r 5 " " MAN r 5 " - " MAN r 6 " " MAN z 4 " - " MAN z 5 " " MAN z 5 " - " MAN z 6 " " MAN z 8 " - " MAN z 9 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA 3 3 " - " MAN 3 4 " " MAN 3 7 " - " MAN 3 8 " " BMA b 3 " - " MAN b 4 " " MAN b 7 " - " MAN b 10 " " BMA c 3 " - " MAN c 4 " " BMA f 3 " - " MAN f 4 " " MAN f 7 " - " MAN f 8 " " BMA n 3 " - " MAN n 4 " " MAN n 7 " - " MAN n 10 " " BMA o 3 " - " MAN o 4 " " BMA r 3 " - " MAN r 4 " " MAN r 7 " - " MAN r 8 " " BMA z 3 " - " MAN z 4 " " MAN z 7 " - " MAN z 10 " ALPHA1-6 " BMA 0 3 " - " MAN 0 5 " " BMA 3 3 " - " MAN 3 7 " " MAN 3 7 " - " MAN 3 9 " " BMA b 3 " - " MAN b 7 " " MAN b 7 " - " MAN b 8 " " BMA c 3 " - " MAN c 5 " " BMA f 3 " - " MAN f 7 " " MAN f 7 " - " MAN f 9 " " BMA n 3 " - " MAN n 7 " " MAN n 7 " - " MAN n 8 " " BMA o 3 " - " MAN o 5 " " BMA r 3 " - " MAN r 7 " " MAN r 7 " - " MAN r 9 " " BMA z 3 " - " MAN z 7 " " MAN z 7 " - " MAN z 8 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " NAG-ASN " NAG 0 1 " - " ASN I 262 " " NAG 1 1 " - " ASN I 295 " " NAG 2 1 " - " ASN I 301 " " NAG 3 1 " - " ASN I 332 " " NAG 4 1 " - " ASN I 363 " " NAG 5 1 " - " ASN I 386 " " NAG 6 1 " - " ASN I 392 " " NAG 7 1 " - " ASN I 448 " " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 355 " " NAG A 603 " - " ASN A 339 " " NAG A 604 " - " ASN A 88 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG C 301 " - " ASN C 82B" " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 355 " " NAG E 603 " - " ASN E 339 " " NAG E 604 " - " ASN E 88 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG G 301 " - " ASN G 82B" " NAG I 601 " - " ASN I 133 " " NAG I 602 " - " ASN I 355 " " NAG I 603 " - " ASN I 339 " " NAG I 604 " - " ASN I 88 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 618 " " NAG K 301 " - " ASN K 82B" " NAG S 1 " - " ASN A 276 " " NAG T 1 " - " ASN B 637 " " NAG U 1 " - " ASN E 276 " " NAG V 1 " - " ASN F 637 " " NAG W 1 " - " ASN I 276 " " NAG X 1 " - " ASN J 637 " " NAG Y 1 " - " ASN A 156 " " NAG Z 1 " - " ASN A 160 " " NAG a 1 " - " ASN A 197 " " NAG b 1 " - " ASN A 234 " " NAG c 1 " - " ASN A 262 " " NAG d 1 " - " ASN A 295 " " NAG e 1 " - " ASN A 301 " " NAG f 1 " - " ASN A 332 " " NAG g 1 " - " ASN A 363 " " NAG h 1 " - " ASN A 386 " " NAG i 1 " - " ASN A 392 " " NAG j 1 " - " ASN A 448 " " NAG k 1 " - " ASN E 156 " " NAG l 1 " - " ASN E 160 " " NAG m 1 " - " ASN E 197 " " NAG n 1 " - " ASN E 234 " " NAG o 1 " - " ASN E 262 " " NAG p 1 " - " ASN E 295 " " NAG q 1 " - " ASN E 301 " " NAG r 1 " - " ASN E 332 " " NAG s 1 " - " ASN E 363 " " NAG t 1 " - " ASN E 386 " " NAG u 1 " - " ASN E 392 " " NAG v 1 " - " ASN E 448 " " NAG w 1 " - " ASN I 156 " " NAG x 1 " - " ASN I 160 " " NAG y 1 " - " ASN I 197 " " NAG z 1 " - " ASN I 234 " Time building additional restraints: 14.52 Conformation dependent library (CDL) restraints added in 5.1 seconds 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6924 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 71 sheets defined 10.3% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.51 Creating SS restraints... Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 101 through 116 removed outlier: 4.171A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 125 removed outlier: 3.612A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 125' Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.781A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 479 No H-bonds generated for 'chain 'A' and resid 476 through 479' Processing helix chain 'B' and resid 524 through 526 No H-bonds generated for 'chain 'B' and resid 524 through 526' Processing helix chain 'B' and resid 537 through 543 removed outlier: 4.061A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 584 removed outlier: 3.681A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 595 Processing helix chain 'B' and resid 628 through 635 Processing helix chain 'B' and resid 639 through 648 removed outlier: 3.643A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 662 removed outlier: 4.903A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.746A pdb=" N SER D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 188 removed outlier: 3.550A pdb=" N GLU D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 99 through 116 removed outlier: 4.132A pdb=" N THR E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 125 removed outlier: 3.601A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 125' Processing helix chain 'E' and resid 335 through 352 removed outlier: 3.575A pdb=" N VAL E 345 " --> pdb=" O THR E 341 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 526 No H-bonds generated for 'chain 'F' and resid 524 through 526' Processing helix chain 'F' and resid 530 through 533 No H-bonds generated for 'chain 'F' and resid 530 through 533' Processing helix chain 'F' and resid 537 through 543 removed outlier: 4.061A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 595 removed outlier: 3.673A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR F 586 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 628 through 635 Processing helix chain 'F' and resid 639 through 648 removed outlier: 3.660A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 662 removed outlier: 5.014A pdb=" N LYS F 655 " --> pdb=" O ASN F 651 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA F 662 " --> pdb=" O GLN F 658 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 188 No H-bonds generated for 'chain 'G' and resid 186 through 188' Processing helix chain 'H' and resid 122 through 127 removed outlier: 3.764A pdb=" N SER H 127 " --> pdb=" O GLU H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 188 removed outlier: 3.546A pdb=" N GLU H 187 " --> pdb=" O LYS H 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 73 No H-bonds generated for 'chain 'I' and resid 71 through 73' Processing helix chain 'I' and resid 101 through 116 removed outlier: 4.177A pdb=" N THR I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER I 115 " --> pdb=" O LEU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 125 removed outlier: 3.603A pdb=" N LEU I 125 " --> pdb=" O LEU I 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 122 through 125' Processing helix chain 'I' and resid 335 through 352 removed outlier: 3.557A pdb=" N VAL I 345 " --> pdb=" O THR I 341 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 479 No H-bonds generated for 'chain 'I' and resid 476 through 479' Processing helix chain 'J' and resid 524 through 526 No H-bonds generated for 'chain 'J' and resid 524 through 526' Processing helix chain 'J' and resid 530 through 533 No H-bonds generated for 'chain 'J' and resid 530 through 533' Processing helix chain 'J' and resid 537 through 543 removed outlier: 4.019A pdb=" N ASN J 543 " --> pdb=" O VAL J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 570 through 584 removed outlier: 3.610A pdb=" N ALA J 578 " --> pdb=" O LYS J 574 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG J 579 " --> pdb=" O GLN J 575 " (cutoff:3.500A) Processing helix chain 'J' and resid 586 through 595 removed outlier: 3.506A pdb=" N GLN J 590 " --> pdb=" O TYR J 586 " (cutoff:3.500A) Processing helix chain 'J' and resid 628 through 635 Processing helix chain 'J' and resid 639 through 648 removed outlier: 3.633A pdb=" N GLY J 644 " --> pdb=" O GLN J 640 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU J 647 " --> pdb=" O TYR J 643 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU J 648 " --> pdb=" O GLY J 644 " (cutoff:3.500A) Processing helix chain 'J' and resid 650 through 662 removed outlier: 4.945A pdb=" N LYS J 655 " --> pdb=" O ASN J 651 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA J 662 " --> pdb=" O GLN J 658 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 188 No H-bonds generated for 'chain 'K' and resid 186 through 188' Processing helix chain 'L' and resid 122 through 127 removed outlier: 3.784A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.545A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 36 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= E, first strand: chain 'A' and resid 130 through 133 removed outlier: 3.701A pdb=" N SER A 158 " --> pdb=" O GLN A 130 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 200 through 203 removed outlier: 3.683A pdb=" N TYR A 435 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.775A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ALA A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 443 through 449 removed outlier: 7.612A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 374 through 377 Processing sheet with id= J, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.942A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 3 through 6 Processing sheet with id= L, first strand: chain 'C' and resid 10 through 12 Processing sheet with id= M, first strand: chain 'C' and resid 88 through 96 removed outlier: 6.354A pdb=" N ARG C 38 " --> pdb=" O TYR C 47 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N TYR C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ALA C 40 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU C 45 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 121 through 124 removed outlier: 3.636A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 136 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 181 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 152 through 154 removed outlier: 4.615A pdb=" N TYR C 194 " --> pdb=" O VAL C 211 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 4 through 7 Processing sheet with id= Q, first strand: chain 'D' and resid 33 through 38 Processing sheet with id= R, first strand: chain 'D' and resid 116 through 118 removed outlier: 3.837A pdb=" N PHE D 118 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU D 175 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 153 through 155 removed outlier: 4.597A pdb=" N TRP D 148 " --> pdb=" O GLN D 155 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS D 145 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 205 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 36 through 40 Processing sheet with id= U, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.473A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU E 86 " --> pdb=" O VAL E 242 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= W, first strand: chain 'E' and resid 91 through 94 Processing sheet with id= X, first strand: chain 'E' and resid 130 through 133 removed outlier: 3.705A pdb=" N SER E 158 " --> pdb=" O GLN E 130 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 200 through 203 removed outlier: 3.643A pdb=" N TYR E 435 " --> pdb=" O THR E 202 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.785A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N ALA E 362 " --> pdb=" O PRO E 470 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 443 through 449 removed outlier: 7.627A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 374 through 378 Processing sheet with id= AC, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.925A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 3 through 6 Processing sheet with id= AE, first strand: chain 'G' and resid 10 through 12 Processing sheet with id= AF, first strand: chain 'G' and resid 88 through 96 removed outlier: 6.405A pdb=" N ARG G 38 " --> pdb=" O TYR G 47 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TYR G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ALA G 40 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU G 45 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 121 through 124 removed outlier: 3.796A pdb=" N GLY G 139 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA G 136 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TYR G 176 " --> pdb=" O ASP G 144 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL G 181 " --> pdb=" O HIS G 164 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 152 through 154 removed outlier: 4.604A pdb=" N TYR G 194 " --> pdb=" O VAL G 211 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 5 through 7 Processing sheet with id= AJ, first strand: chain 'H' and resid 33 through 38 Processing sheet with id= AK, first strand: chain 'H' and resid 116 through 118 removed outlier: 3.815A pdb=" N PHE H 118 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL H 133 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU H 175 " --> pdb=" O LEU H 136 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.608A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS H 145 " --> pdb=" O THR H 197 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'I' and resid 36 through 40 Processing sheet with id= AN, first strand: chain 'I' and resid 45 through 47 Processing sheet with id= AO, first strand: chain 'I' and resid 53 through 55 Processing sheet with id= AP, first strand: chain 'I' and resid 91 through 94 Processing sheet with id= AQ, first strand: chain 'I' and resid 130 through 133 removed outlier: 3.684A pdb=" N SER I 158 " --> pdb=" O GLN I 130 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'I' and resid 200 through 203 removed outlier: 3.607A pdb=" N TYR I 435 " --> pdb=" O THR I 202 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'I' and resid 271 through 274 removed outlier: 6.760A pdb=" N ILE I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N PHE I 468 " --> pdb=" O ILE I 358 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ALA I 362 " --> pdb=" O PRO I 470 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'I' and resid 443 through 449 removed outlier: 7.595A pdb=" N GLN I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER I 334 " --> pdb=" O GLN I 293 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'I' and resid 374 through 378 Processing sheet with id= AV, first strand: chain 'I' and resid 304 through 312 removed outlier: 6.941A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'K' and resid 3 through 6 Processing sheet with id= AX, first strand: chain 'K' and resid 10 through 12 Processing sheet with id= AY, first strand: chain 'K' and resid 88 through 96 removed outlier: 6.328A pdb=" N ARG K 38 " --> pdb=" O TYR K 47 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TYR K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ALA K 40 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU K 45 " --> pdb=" O ALA K 40 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'K' and resid 121 through 124 removed outlier: 3.658A pdb=" N GLY K 139 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA K 136 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR K 176 " --> pdb=" O ASP K 144 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL K 181 " --> pdb=" O HIS K 164 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'K' and resid 152 through 154 removed outlier: 4.619A pdb=" N TYR K 194 " --> pdb=" O VAL K 211 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= BC, first strand: chain 'L' and resid 33 through 38 Processing sheet with id= BD, first strand: chain 'L' and resid 116 through 118 removed outlier: 3.506A pdb=" N PHE L 118 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU L 175 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.599A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'M' and resid 18 through 20 removed outlier: 3.504A pdb=" N VAL M 20 " --> pdb=" O LEU M 80 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER M 79 " --> pdb=" O SER M 70 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER M 70 " --> pdb=" O SER M 79 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'M' and resid 107 through 109 removed outlier: 3.894A pdb=" N VAL M 109 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA M 93 " --> pdb=" O THR M 35 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER M 40 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU M 45 " --> pdb=" O SER M 40 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'M' and resid 93 through 100A removed outlier: 3.869A pdb=" N VAL M 102 " --> pdb=" O THR M 94 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ARG M 96 " --> pdb=" O MET M 100P" (cutoff:3.500A) removed outlier: 5.778A pdb=" N MET M 100P" --> pdb=" O ARG M 96 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLY M 98 " --> pdb=" O TYR M 100N" (cutoff:3.500A) removed outlier: 5.334A pdb=" N TYR M 100N" --> pdb=" O GLY M 98 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG M 100 " --> pdb=" O TYR M 100L" (cutoff:3.500A) removed outlier: 5.431A pdb=" N TYR M 100L" --> pdb=" O ARG M 100 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'N' and resid 20 through 22 Processing sheet with id= BJ, first strand: chain 'N' and resid 101 through 103 removed outlier: 3.870A pdb=" N ILE N 48 " --> pdb=" O TRP N 35 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'O' and resid 107 through 109 removed outlier: 3.920A pdb=" N VAL O 109 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA O 93 " --> pdb=" O THR O 35 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N SER O 40 " --> pdb=" O LEU O 45 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU O 45 " --> pdb=" O SER O 40 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'O' and resid 67 through 71 removed outlier: 3.863A pdb=" N SER O 70 " --> pdb=" O SER O 79 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER O 79 " --> pdb=" O SER O 70 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'O' and resid 93 through 100A removed outlier: 3.876A pdb=" N VAL O 102 " --> pdb=" O THR O 94 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG O 96 " --> pdb=" O MET O 100P" (cutoff:3.500A) removed outlier: 5.720A pdb=" N MET O 100P" --> pdb=" O ARG O 96 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLY O 98 " --> pdb=" O TYR O 100N" (cutoff:3.500A) removed outlier: 5.269A pdb=" N TYR O 100N" --> pdb=" O GLY O 98 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG O 100 " --> pdb=" O TYR O 100L" (cutoff:3.500A) removed outlier: 5.410A pdb=" N TYR O 100L" --> pdb=" O ARG O 100 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'P' and resid 20 through 22 Processing sheet with id= BO, first strand: chain 'P' and resid 101 through 103 removed outlier: 3.921A pdb=" N ILE P 48 " --> pdb=" O TRP P 35 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLN P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU P 46 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'Q' and resid 107 through 109 removed outlier: 3.888A pdb=" N VAL Q 109 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA Q 93 " --> pdb=" O THR Q 35 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER Q 40 " --> pdb=" O LEU Q 45 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU Q 45 " --> pdb=" O SER Q 40 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'Q' and resid 93 through 100A removed outlier: 3.890A pdb=" N VAL Q 102 " --> pdb=" O THR Q 94 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ARG Q 96 " --> pdb=" O MET Q 100P" (cutoff:3.500A) removed outlier: 5.792A pdb=" N MET Q 100P" --> pdb=" O ARG Q 96 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY Q 98 " --> pdb=" O TYR Q 100N" (cutoff:3.500A) removed outlier: 5.253A pdb=" N TYR Q 100N" --> pdb=" O GLY Q 98 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG Q 100 " --> pdb=" O TYR Q 100L" (cutoff:3.500A) removed outlier: 5.430A pdb=" N TYR Q 100L" --> pdb=" O ARG Q 100 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'R' and resid 20 through 22 Processing sheet with id= BS, first strand: chain 'R' and resid 101 through 103 removed outlier: 3.558A pdb=" N THR R 102 " --> pdb=" O TYR R 86 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE R 48 " --> pdb=" O TRP R 35 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLN R 37 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU R 46 " --> pdb=" O GLN R 37 " (cutoff:3.500A) 760 hydrogen bonds defined for protein. 2058 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: 12.22 Time building geometry restraints manager: 15.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4866 1.31 - 1.45: 9602 1.45 - 1.59: 17266 1.59 - 1.72: 0 1.72 - 1.86: 204 Bond restraints: 31938 Sorted by residual: bond pdb=" C PRO A 206 " pdb=" O PRO A 206 " ideal model delta sigma weight residual 1.236 1.187 0.049 1.36e-02 5.41e+03 1.31e+01 bond pdb=" C PRO I 206 " pdb=" O PRO I 206 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.30e-02 5.92e+03 1.17e+01 bond pdb=" N TYR H 140 " pdb=" CA TYR H 140 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.41e-02 5.03e+03 5.45e+00 bond pdb=" C PRO P 44 " pdb=" O PRO P 44 " ideal model delta sigma weight residual 1.233 1.209 0.024 1.10e-02 8.26e+03 4.78e+00 bond pdb=" C PRO R 44 " pdb=" O PRO R 44 " ideal model delta sigma weight residual 1.234 1.209 0.024 1.14e-02 7.69e+03 4.44e+00 ... (remaining 31933 not shown) Histogram of bond angle deviations from ideal: 97.89 - 106.56: 946 106.56 - 115.22: 20455 115.22 - 123.89: 21099 123.89 - 132.56: 820 132.56 - 141.22: 108 Bond angle restraints: 43428 Sorted by residual: angle pdb=" C13 83J E 605 " pdb=" C15 83J E 605 " pdb=" C21 83J E 605 " ideal model delta sigma weight residual 82.04 139.18 -57.14 3.00e+00 1.11e-01 3.63e+02 angle pdb=" C13 83J A 605 " pdb=" C15 83J A 605 " pdb=" C21 83J A 605 " ideal model delta sigma weight residual 82.04 139.16 -57.12 3.00e+00 1.11e-01 3.62e+02 angle pdb=" C13 83J I 605 " pdb=" C15 83J I 605 " pdb=" C21 83J I 605 " ideal model delta sigma weight residual 82.04 139.10 -57.06 3.00e+00 1.11e-01 3.62e+02 angle pdb=" C13 83J A 605 " pdb=" C15 83J A 605 " pdb=" C20 83J A 605 " ideal model delta sigma weight residual 155.13 100.12 55.01 3.00e+00 1.11e-01 3.36e+02 angle pdb=" C13 83J E 605 " pdb=" C15 83J E 605 " pdb=" C20 83J E 605 " ideal model delta sigma weight residual 155.13 100.18 54.95 3.00e+00 1.11e-01 3.35e+02 ... (remaining 43423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.72: 18454 22.72 - 45.44: 1916 45.44 - 68.16: 514 68.16 - 90.88: 128 90.88 - 113.60: 36 Dihedral angle restraints: 21048 sinusoidal: 10272 harmonic: 10776 Sorted by residual: dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual -86.00 1.69 -87.69 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 179.17 -86.17 1 1.00e+01 1.00e-02 8.96e+01 dihedral pdb=" CB CYS P 23 " pdb=" SG CYS P 23 " pdb=" SG CYS P 88 " pdb=" CB CYS P 88 " ideal model delta sinusoidal sigma weight residual 93.00 6.97 86.03 1 1.00e+01 1.00e-02 8.94e+01 ... (remaining 21045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 5074 0.104 - 0.207: 235 0.207 - 0.311: 17 0.311 - 0.415: 6 0.415 - 0.518: 2 Chirality restraints: 5334 Sorted by residual: chirality pdb=" CA CYS E 196 " pdb=" N CYS E 196 " pdb=" C CYS E 196 " pdb=" CB CYS E 196 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" C1 NAG A 604 " pdb=" ND2 ASN A 88 " pdb=" C2 NAG A 604 " pdb=" O5 NAG A 604 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.31e+00 chirality pdb=" C1 NAG 4 1 " pdb=" ND2 ASN I 363 " pdb=" C2 NAG 4 1 " pdb=" O5 NAG 4 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 5331 not shown) Planarity restraints: 5364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR L 140 " -0.019 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C TYR L 140 " 0.068 2.00e-02 2.50e+03 pdb=" O TYR L 140 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO L 141 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS I 205 " -0.020 2.00e-02 2.50e+03 3.80e-02 1.45e+01 pdb=" C CYS I 205 " 0.066 2.00e-02 2.50e+03 pdb=" O CYS I 205 " -0.024 2.00e-02 2.50e+03 pdb=" N PRO I 206 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 205 " 0.019 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C CYS A 205 " -0.062 2.00e-02 2.50e+03 pdb=" O CYS A 205 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO A 206 " 0.021 2.00e-02 2.50e+03 ... (remaining 5361 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 381 2.54 - 3.13: 24549 3.13 - 3.72: 45243 3.72 - 4.31: 68983 4.31 - 4.90: 116520 Nonbonded interactions: 255676 Sorted by model distance: nonbonded pdb=" O3 NAG I 604 " pdb=" O7 NAG I 604 " model vdw 1.953 2.440 nonbonded pdb=" O3 NAG E 604 " pdb=" O7 NAG E 604 " model vdw 1.960 2.440 nonbonded pdb=" O3 NAG X 2 " pdb=" O7 NAG X 2 " model vdw 1.963 2.440 nonbonded pdb=" O3 NAG V 2 " pdb=" O7 NAG V 2 " model vdw 1.966 2.440 nonbonded pdb=" O3 NAG T 2 " pdb=" O7 NAG T 2 " model vdw 1.976 2.440 ... (remaining 255671 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 'c' selection = chain 'o' } ncs_group { reference = chain '1' selection = chain '2' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' } ncs_group { reference = (chain '3' and (resid 1 or resid 4 through 9)) selection = (chain 'b' and (resid 2 or resid 5 through 10)) selection = (chain 'f' and (resid 1 or resid 4 through 9)) selection = (chain 'n' and (resid 2 or resid 5 through 10)) selection = (chain 'r' and (resid 1 or resid 4 through 9)) selection = (chain 'z' and (resid 2 or resid 5 through 10)) } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.74 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 11.200 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 82.770 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.720 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: 0.000 Load rotamer database and sin/cos tables:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 : 0.005 0.091 31938 Z= 0.292 Angle : 1.029 57.139 43428 Z= 0.433 Chirality : 0.050 0.518 5334 Planarity : 0.004 0.084 5301 Dihedral : 19.412 113.598 13971 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 31.63 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.52 % Favored : 91.80 % Rotamer: Outliers : 10.42 % Allowed : 30.06 % Favored : 59.51 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 7.02 % 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: -2.50 (0.13), residues: 3684 helix: -3.64 (0.18), residues: 426 sheet: -0.95 (0.16), residues: 1152 loop : -1.63 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 69 HIS 0.003 0.001 HIS I 66 PHE 0.009 0.001 PHE E 391 TYR 0.017 0.001 TYR H 91 ARG 0.006 0.000 ARG F 588 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 322 time to evaluate : 3.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 100 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8086 (mpt) REVERT: E 189 LYS cc_start: 0.7253 (tptt) cc_final: 0.6962 (tmtt) REVERT: E 360 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7813 (ptt-90) REVERT: F 616 ASN cc_start: 0.8235 (p0) cc_final: 0.7988 (p0) REVERT: G 105 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7846 (pt0) REVERT: H 61 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7159 (ptp-170) REVERT: K 100 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.7726 (mtp) REVERT: L 79 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6475 (mp10) REVERT: L 107 LYS cc_start: 0.6585 (OUTLIER) cc_final: 0.6198 (mmtt) outliers start: 338 outliers final: 307 residues processed: 644 average time/residue: 1.0703 time to fit residues: 850.7204 Evaluate side-chains 635 residues out of total 3243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 321 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 248 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 368 ASP Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain J residue 520 LEU Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 23 SER Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 40 SER Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain P residue 97 SER Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 40 SER Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 25 ARG Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 311 optimal weight: 8.9990 chunk 279 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 95 optimal weight: 30.0000 chunk 188 optimal weight: 0.3980 chunk 149 optimal weight: 0.9990 chunk 289 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 335 optimal weight: 20.0000 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN B 630 GLN C 105 GLN D 3 GLN D 124 GLN D 166 GLN E 195 ASN F 630 GLN H 3 GLN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 GLN J 577 GLN J 630 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN N 37 GLN ** N 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 GLN P 51 ASN Q 77 GLN Q 99 GLN R 37 GLN R 51 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 31938 Z= 0.423 Angle : 0.794 13.406 43428 Z= 0.392 Chirality : 0.052 0.297 5334 Planarity : 0.006 0.149 5301 Dihedral : 14.809 90.435 7805 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.60 % Favored : 91.88 % Rotamer: Outliers : 13.85 % Allowed : 25.96 % Favored : 60.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.13), residues: 3684 helix: -2.71 (0.21), residues: 429 sheet: -0.89 (0.14), residues: 1257 loop : -1.66 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 610 HIS 0.006 0.001 HIS I 105 PHE 0.013 0.002 PHE E 159 TYR 0.036 0.002 TYR H 140 ARG 0.005 0.001 ARG I 476 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 3243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 449 poor density : 321 time to evaluate : 3.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8341 (mt) REVERT: A 149 ASP cc_start: 0.3312 (OUTLIER) cc_final: 0.3078 (p0) REVERT: A 456 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7663 (mtp180) REVERT: B 658 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: C 30 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8525 (m-10) REVERT: E 102 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7872 (mm-30) REVERT: E 153 GLU cc_start: 0.6867 (tt0) cc_final: 0.6552 (pt0) REVERT: F 535 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7484 (mmt) REVERT: F 616 ASN cc_start: 0.8223 (p0) cc_final: 0.7921 (p0) REVERT: F 624 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7943 (p0) REVERT: F 658 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: G 30 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8457 (m-10) REVERT: H 61 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.6996 (ptt-90) REVERT: H 79 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.6347 (mp10) REVERT: I 149 ASP cc_start: 0.3087 (OUTLIER) cc_final: 0.2805 (p0) REVERT: I 189 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.6352 (tmtt) REVERT: I 360 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8115 (ptt-90) REVERT: J 575 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8096 (tp-100) REVERT: J 640 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8275 (mp10) REVERT: J 654 GLU cc_start: 0.6382 (OUTLIER) cc_final: 0.5827 (tt0) REVERT: K 30 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8424 (m-10) REVERT: L 61 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6930 (ptp-170) REVERT: L 79 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.6355 (mp10) REVERT: N 50 ASN cc_start: 0.8359 (t0) cc_final: 0.7773 (t0) REVERT: P 28 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6969 (mp) outliers start: 449 outliers final: 278 residues processed: 699 average time/residue: 1.0736 time to fit residues: 924.4443 Evaluate side-chains 594 residues out of total 3243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 294 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 456 ARG Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 248 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain J residue 536 THR Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 25 ARG Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 186 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 278 optimal weight: 30.0000 chunk 228 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 335 optimal weight: 10.0000 chunk 362 optimal weight: 6.9990 chunk 298 optimal weight: 7.9990 chunk 332 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN F 577 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 3 GLN K 3 HIS ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN N 37 GLN O 99 GLN P 51 ASN Q 99 GLN R 51 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.114 31938 Z= 0.642 Angle : 0.905 11.746 43428 Z= 0.442 Chirality : 0.058 0.311 5334 Planarity : 0.006 0.133 5301 Dihedral : 14.023 91.866 7632 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.33 % Favored : 91.15 % Rotamer: Outliers : 14.12 % Allowed : 26.67 % Favored : 59.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.13), residues: 3684 helix: -2.73 (0.21), residues: 429 sheet: -1.10 (0.14), residues: 1320 loop : -1.74 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP J 610 HIS 0.008 0.001 HIS E 72 PHE 0.016 0.003 PHE G 91 TYR 0.029 0.003 TYR H 140 ARG 0.006 0.001 ARG A 476 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 3243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 458 poor density : 305 time to evaluate : 3.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8361 (mt) REVERT: A 153 GLU cc_start: 0.6987 (tt0) cc_final: 0.6746 (pt0) REVERT: B 658 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7937 (tm-30) REVERT: C 30 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.8536 (m-10) REVERT: C 46 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: E 153 GLU cc_start: 0.6896 (tt0) cc_final: 0.6598 (pt0) REVERT: F 624 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.8035 (p0) REVERT: G 30 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8571 (m-10) REVERT: G 80 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8584 (tp) REVERT: G 105 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8066 (pt0) REVERT: H 79 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.6422 (mp10) REVERT: H 91 TYR cc_start: 0.9260 (OUTLIER) cc_final: 0.8988 (p90) REVERT: I 84 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8577 (mp) REVERT: I 149 ASP cc_start: 0.3081 (OUTLIER) cc_final: 0.2789 (p0) REVERT: I 155 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8258 (mttp) REVERT: I 198 THR cc_start: 0.8763 (p) cc_final: 0.8490 (t) REVERT: I 205 CYS cc_start: 0.6513 (OUTLIER) cc_final: 0.6121 (m) REVERT: I 360 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8179 (ptt-90) REVERT: J 575 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8060 (tp-100) REVERT: J 640 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8161 (mp10) REVERT: J 654 GLU cc_start: 0.6413 (OUTLIER) cc_final: 0.5791 (tt0) REVERT: K 30 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8465 (m-10) REVERT: L 79 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.6845 (mp10) REVERT: L 107 LYS cc_start: 0.6853 (OUTLIER) cc_final: 0.6219 (mptt) REVERT: M 75 LYS cc_start: 0.5179 (OUTLIER) cc_final: 0.4549 (pttp) REVERT: O 75 LYS cc_start: 0.5536 (OUTLIER) cc_final: 0.4976 (pptt) REVERT: P 75 ILE cc_start: 0.5747 (OUTLIER) cc_final: 0.5359 (pt) REVERT: Q 75 LYS cc_start: 0.5437 (OUTLIER) cc_final: 0.4639 (pttp) outliers start: 458 outliers final: 297 residues processed: 697 average time/residue: 1.0507 time to fit residues: 906.3283 Evaluate side-chains 619 residues out of total 3243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 297 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 432 GLN Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 607 ASN Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 248 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 356 ASN Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain J residue 536 THR Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain J residue 663 LEU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 25 ARG Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 331 optimal weight: 5.9990 chunk 252 optimal weight: 0.8980 chunk 174 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 225 optimal weight: 0.7980 chunk 336 optimal weight: 6.9990 chunk 356 optimal weight: 0.0030 chunk 176 optimal weight: 40.0000 chunk 319 optimal weight: 9.9990 chunk 96 optimal weight: 40.0000 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 3 GLN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN F 616 ASN G 6 GLN G 105 GLN H 3 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN N 37 GLN ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 99 GLN P 51 ASN Q 3 GLN R 37 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 31938 Z= 0.227 Angle : 0.699 10.691 43428 Z= 0.340 Chirality : 0.048 0.300 5334 Planarity : 0.005 0.129 5301 Dihedral : 12.544 89.618 7599 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.32 % Favored : 93.27 % Rotamer: Outliers : 11.38 % Allowed : 29.39 % Favored : 59.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.13), residues: 3684 helix: -2.16 (0.23), residues: 429 sheet: -0.86 (0.14), residues: 1293 loop : -1.57 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 610 HIS 0.003 0.001 HIS A 105 PHE 0.012 0.001 PHE L 118 TYR 0.022 0.001 TYR H 140 ARG 0.006 0.000 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 369 poor density : 317 time to evaluate : 3.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8281 (mt) REVERT: A 325 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8298 (p0) REVERT: B 658 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: C 100 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8517 (mmt) REVERT: C 179 SER cc_start: 0.8078 (OUTLIER) cc_final: 0.7506 (p) REVERT: D 79 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.6669 (mp10) REVERT: E 75 VAL cc_start: 0.8905 (p) cc_final: 0.8697 (m) REVERT: E 153 GLU cc_start: 0.6794 (tt0) cc_final: 0.6415 (pt0) REVERT: F 535 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7817 (mpp) REVERT: F 616 ASN cc_start: 0.8104 (p0) cc_final: 0.7814 (p0) REVERT: G 30 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8497 (m-10) REVERT: G 80 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8597 (tp) REVERT: G 179 SER cc_start: 0.8105 (OUTLIER) cc_final: 0.7544 (p) REVERT: H 20 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6896 (mtm180) REVERT: H 61 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6951 (ptt-90) REVERT: H 79 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.6250 (mp10) REVERT: I 75 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8615 (m) REVERT: I 360 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8045 (ptt-90) REVERT: J 568 LEU cc_start: 0.7490 (tp) cc_final: 0.7270 (tp) REVERT: J 575 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7962 (tp-100) REVERT: J 616 ASN cc_start: 0.8091 (p0) cc_final: 0.7831 (p0) REVERT: J 640 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8223 (mp10) REVERT: J 654 GLU cc_start: 0.6068 (OUTLIER) cc_final: 0.5371 (tt0) REVERT: K 179 SER cc_start: 0.8121 (OUTLIER) cc_final: 0.7517 (p) REVERT: L 79 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.6686 (mp10) REVERT: M 75 LYS cc_start: 0.5440 (OUTLIER) cc_final: 0.4713 (pttp) REVERT: N 50 ASN cc_start: 0.8172 (t0) cc_final: 0.7762 (t0) REVERT: O 75 LYS cc_start: 0.5378 (OUTLIER) cc_final: 0.4724 (pttp) REVERT: P 28 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6999 (mp) REVERT: P 50 ASN cc_start: 0.8319 (t0) cc_final: 0.7917 (t0) REVERT: Q 75 LYS cc_start: 0.5514 (OUTLIER) cc_final: 0.4715 (pttp) outliers start: 369 outliers final: 227 residues processed: 623 average time/residue: 1.1970 time to fit residues: 938.8046 Evaluate side-chains 542 residues out of total 3243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 291 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 640 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain J residue 536 THR Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 25 ARG Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 297 optimal weight: 20.0000 chunk 202 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 265 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 304 optimal weight: 20.0000 chunk 246 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 320 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 3 GLN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 3 GLN H 100 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN L 166 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN N 37 GLN O 3 GLN O 99 GLN P 37 GLN ** P 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 GLN Q 99 GLN R 37 GLN R 51 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 31938 Z= 0.470 Angle : 0.803 13.291 43428 Z= 0.389 Chirality : 0.053 0.314 5334 Planarity : 0.006 0.136 5301 Dihedral : 12.304 86.368 7537 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.12 % Favored : 91.50 % Rotamer: Outliers : 12.24 % Allowed : 28.09 % Favored : 59.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.13), residues: 3684 helix: -2.27 (0.23), residues: 429 sheet: -0.87 (0.14), residues: 1296 loop : -1.68 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 610 HIS 0.006 0.001 HIS E 72 PHE 0.029 0.002 PHE L 118 TYR 0.023 0.002 TYR L 140 ARG 0.010 0.000 ARG E 500 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 397 poor density : 299 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8312 (mt) REVERT: A 153 GLU cc_start: 0.6914 (tt0) cc_final: 0.6425 (tt0) REVERT: A 325 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8316 (p0) REVERT: B 658 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: C 30 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8548 (m-10) REVERT: C 69 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8239 (mm) REVERT: C 100 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8624 (mmt) REVERT: C 179 SER cc_start: 0.8159 (OUTLIER) cc_final: 0.7620 (p) REVERT: D 79 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.6647 (mp10) REVERT: E 153 GLU cc_start: 0.6887 (tt0) cc_final: 0.6513 (pt0) REVERT: F 535 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7856 (mpp) REVERT: G 30 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8598 (m-10) REVERT: G 37 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8267 (m) REVERT: G 80 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8600 (tp) REVERT: G 105 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7849 (pt0) REVERT: G 179 SER cc_start: 0.8085 (OUTLIER) cc_final: 0.7548 (p) REVERT: H 20 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6912 (mtm180) REVERT: H 47 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8536 (mt) REVERT: H 79 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.6341 (mp10) REVERT: I 84 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8513 (mp) REVERT: I 205 CYS cc_start: 0.6422 (OUTLIER) cc_final: 0.6019 (m) REVERT: I 360 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8137 (ptt-90) REVERT: J 542 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7704 (ptt90) REVERT: J 568 LEU cc_start: 0.7588 (tp) cc_final: 0.7351 (tp) REVERT: J 575 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8027 (tp-100) REVERT: J 616 ASN cc_start: 0.8219 (p0) cc_final: 0.7902 (p0) REVERT: J 640 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8180 (mp10) REVERT: J 654 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5494 (tt0) REVERT: L 79 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.6686 (mp10) REVERT: M 75 LYS cc_start: 0.5481 (OUTLIER) cc_final: 0.4736 (pttp) REVERT: M 100 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.6712 (mmm) REVERT: O 75 LYS cc_start: 0.5450 (OUTLIER) cc_final: 0.4708 (pttp) REVERT: P 50 ASN cc_start: 0.8463 (t0) cc_final: 0.8026 (t0) REVERT: Q 75 LYS cc_start: 0.5375 (OUTLIER) cc_final: 0.4605 (pttp) outliers start: 397 outliers final: 267 residues processed: 634 average time/residue: 1.1285 time to fit residues: 887.1916 Evaluate side-chains 589 residues out of total 3243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 293 time to evaluate : 4.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 356 ASN Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain J residue 536 THR Chi-restraints excluded: chain J residue 542 ARG Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 66 ARG Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 25 ARG Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 120 optimal weight: 0.8980 chunk 321 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 209 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 357 optimal weight: 4.9990 chunk 296 optimal weight: 20.0000 chunk 165 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 3 GLN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 3 GLN H 100 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN N 37 GLN ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 99 GLN ** P 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 GLN R 37 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 31938 Z= 0.225 Angle : 0.682 13.125 43428 Z= 0.331 Chirality : 0.048 0.324 5334 Planarity : 0.005 0.136 5301 Dihedral : 11.281 89.981 7528 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.32 % Favored : 93.35 % Rotamer: Outliers : 10.33 % Allowed : 30.31 % Favored : 59.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.13), residues: 3684 helix: -1.62 (0.25), residues: 408 sheet: -0.83 (0.14), residues: 1269 loop : -1.52 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 610 HIS 0.003 0.001 HIS A 105 PHE 0.015 0.001 PHE L 118 TYR 0.017 0.001 TYR H 140 ARG 0.008 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 313 time to evaluate : 3.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7112 (mmmm) cc_final: 0.6714 (pptt) REVERT: A 325 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8335 (p0) REVERT: A 428 GLN cc_start: 0.5731 (OUTLIER) cc_final: 0.5244 (mp-120) REVERT: B 658 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7598 (tt0) REVERT: C 69 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.7867 (mm) REVERT: C 100 MET cc_start: 0.8792 (mpp) cc_final: 0.8533 (mmt) REVERT: C 105 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7901 (pm20) REVERT: D 79 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.6696 (mp10) REVERT: E 153 GLU cc_start: 0.6768 (tt0) cc_final: 0.6358 (pt0) REVERT: F 535 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7788 (mpp) REVERT: G 30 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8502 (m-10) REVERT: H 20 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6917 (mtm180) REVERT: H 47 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8582 (mt) REVERT: H 79 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.6359 (mp10) REVERT: I 84 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8361 (mp) REVERT: I 360 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.8042 (ptt-90) REVERT: J 568 LEU cc_start: 0.7540 (tp) cc_final: 0.7306 (tp) REVERT: J 575 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: J 616 ASN cc_start: 0.8123 (p0) cc_final: 0.7843 (p0) REVERT: J 640 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8249 (mp10) REVERT: J 654 GLU cc_start: 0.6054 (OUTLIER) cc_final: 0.5392 (tt0) REVERT: K 38 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.6894 (ttm-80) REVERT: L 78 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7542 (tt) REVERT: L 79 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.6657 (mp10) REVERT: L 143 GLU cc_start: 0.5739 (OUTLIER) cc_final: 0.5297 (pp20) REVERT: M 75 LYS cc_start: 0.5475 (OUTLIER) cc_final: 0.4759 (pttp) REVERT: N 50 ASN cc_start: 0.8060 (t0) cc_final: 0.7792 (t0) REVERT: O 75 LYS cc_start: 0.5632 (OUTLIER) cc_final: 0.4772 (pttp) REVERT: O 100 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.7880 (mt-10) REVERT: P 28 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6774 (mp) REVERT: P 50 ASN cc_start: 0.8365 (t0) cc_final: 0.7923 (t0) REVERT: Q 75 LYS cc_start: 0.5382 (OUTLIER) cc_final: 0.4600 (pttp) outliers start: 335 outliers final: 225 residues processed: 582 average time/residue: 1.0630 time to fit residues: 766.3804 Evaluate side-chains 550 residues out of total 3243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 300 time to evaluate : 3.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 356 ASN Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 598 CYS Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 344 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 203 optimal weight: 0.9990 chunk 260 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 300 optimal weight: 50.0000 chunk 199 optimal weight: 20.0000 chunk 355 optimal weight: 10.0000 chunk 222 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 577 GLN B 651 ASN C 6 GLN D 3 GLN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN F 616 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 3 GLN H 100 GLN I 246 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 99 GLN N 37 GLN O 3 GLN O 99 GLN P 37 GLN P 51 ASN Q 3 GLN Q 99 GLN R 37 GLN R 51 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 31938 Z= 0.252 Angle : 0.680 14.029 43428 Z= 0.331 Chirality : 0.047 0.306 5334 Planarity : 0.005 0.135 5301 Dihedral : 10.745 89.184 7503 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.62 % Favored : 93.05 % Rotamer: Outliers : 9.68 % Allowed : 31.17 % Favored : 59.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.13), residues: 3684 helix: -1.39 (0.25), residues: 408 sheet: -0.76 (0.14), residues: 1269 loop : -1.48 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 610 HIS 0.003 0.001 HIS A 105 PHE 0.012 0.001 PHE L 118 TYR 0.020 0.001 TYR H 140 ARG 0.007 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 300 time to evaluate : 3.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7095 (mmmm) cc_final: 0.6784 (pptt) REVERT: A 325 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8325 (p0) REVERT: B 658 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: C 6 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7960 (mt0) REVERT: C 100 MET cc_start: 0.8835 (mpp) cc_final: 0.8539 (mmt) REVERT: D 79 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.6713 (mp10) REVERT: E 153 GLU cc_start: 0.6763 (tt0) cc_final: 0.6464 (tt0) REVERT: E 228 CYS cc_start: 0.8267 (t) cc_final: 0.7983 (t) REVERT: E 325 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8243 (p0) REVERT: E 416 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8291 (mt) REVERT: F 535 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7798 (mpp) REVERT: F 575 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: G 30 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8492 (m-10) REVERT: G 100 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8572 (mmt) REVERT: H 47 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8596 (mt) REVERT: H 79 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.6379 (mp10) REVERT: I 84 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8395 (mp) REVERT: I 168 LYS cc_start: 0.7100 (mmmm) cc_final: 0.6761 (pptt) REVERT: I 205 CYS cc_start: 0.6351 (OUTLIER) cc_final: 0.6028 (m) REVERT: I 360 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.8035 (ptt-90) REVERT: J 568 LEU cc_start: 0.7606 (tp) cc_final: 0.7367 (tp) REVERT: J 575 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8091 (tt0) REVERT: J 608 VAL cc_start: 0.8229 (OUTLIER) cc_final: 0.7848 (t) REVERT: J 616 ASN cc_start: 0.8127 (p0) cc_final: 0.7813 (p0) REVERT: J 640 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8244 (mp10) REVERT: J 654 GLU cc_start: 0.6073 (OUTLIER) cc_final: 0.5438 (tt0) REVERT: K 38 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.6828 (ttm-80) REVERT: L 78 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7495 (tt) REVERT: L 79 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.6581 (mp10) REVERT: L 143 GLU cc_start: 0.5635 (OUTLIER) cc_final: 0.5379 (pp20) REVERT: M 75 LYS cc_start: 0.5464 (OUTLIER) cc_final: 0.4767 (pttp) REVERT: M 100 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8386 (mt-10) REVERT: O 75 LYS cc_start: 0.5595 (OUTLIER) cc_final: 0.4746 (pttp) REVERT: O 100 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.7922 (mt-10) REVERT: P 28 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6810 (mp) REVERT: P 50 ASN cc_start: 0.8365 (t0) cc_final: 0.7949 (t0) REVERT: Q 75 LYS cc_start: 0.5389 (OUTLIER) cc_final: 0.4600 (pttp) outliers start: 314 outliers final: 211 residues processed: 564 average time/residue: 1.0227 time to fit residues: 716.7215 Evaluate side-chains 531 residues out of total 3243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 291 time to evaluate : 3.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 356 ASN Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 598 CYS Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 220 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 226 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 279 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN F 616 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 3 GLN H 100 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN L 166 GLN M 3 GLN M 99 GLN N 37 GLN O 3 GLN O 99 GLN P 51 ASN Q 3 GLN Q 99 GLN R 37 GLN R 51 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 31938 Z= 0.272 Angle : 0.688 14.020 43428 Z= 0.334 Chirality : 0.048 0.306 5334 Planarity : 0.005 0.133 5301 Dihedral : 10.577 89.021 7480 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.73 % Favored : 92.94 % Rotamer: Outliers : 9.34 % Allowed : 31.58 % Favored : 59.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.13), residues: 3684 helix: -1.30 (0.25), residues: 408 sheet: -0.72 (0.14), residues: 1269 loop : -1.45 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 610 HIS 0.003 0.001 HIS A 105 PHE 0.012 0.001 PHE L 139 TYR 0.023 0.001 TYR P 87 ARG 0.006 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 298 time to evaluate : 3.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7110 (mmmm) cc_final: 0.6862 (pptt) REVERT: A 325 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8308 (p0) REVERT: A 502 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7784 (tmtt) REVERT: B 658 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: C 69 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.7870 (mm) REVERT: D 79 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.6594 (mp10) REVERT: E 153 GLU cc_start: 0.6769 (tt0) cc_final: 0.6476 (tt0) REVERT: E 228 CYS cc_start: 0.8270 (t) cc_final: 0.7988 (t) REVERT: E 325 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8270 (p0) REVERT: F 535 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7808 (mpp) REVERT: G 30 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8471 (m-10) REVERT: G 80 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8620 (tp) REVERT: G 100 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8615 (mmt) REVERT: H 47 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8589 (mt) REVERT: H 79 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.6360 (mp10) REVERT: I 84 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8429 (mp) REVERT: I 168 LYS cc_start: 0.7112 (mmmm) cc_final: 0.6777 (pptt) REVERT: I 205 CYS cc_start: 0.6383 (OUTLIER) cc_final: 0.6055 (m) REVERT: I 360 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8077 (ptt-90) REVERT: J 575 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8106 (tt0) REVERT: J 608 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.7911 (t) REVERT: J 616 ASN cc_start: 0.8132 (p0) cc_final: 0.7833 (p0) REVERT: J 640 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8230 (mp10) REVERT: J 654 GLU cc_start: 0.6085 (OUTLIER) cc_final: 0.5411 (tt0) REVERT: K 38 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.6799 (ttm-80) REVERT: L 78 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7466 (tt) REVERT: L 79 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.6595 (mp10) REVERT: L 143 GLU cc_start: 0.5683 (OUTLIER) cc_final: 0.5479 (pp20) REVERT: M 75 LYS cc_start: 0.5497 (OUTLIER) cc_final: 0.4789 (pttp) REVERT: M 100 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8457 (mt-10) REVERT: O 75 LYS cc_start: 0.5543 (OUTLIER) cc_final: 0.4719 (pttp) REVERT: O 100 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.7928 (mt-10) REVERT: P 50 ASN cc_start: 0.8403 (t0) cc_final: 0.7973 (t0) REVERT: Q 75 LYS cc_start: 0.5448 (OUTLIER) cc_final: 0.4642 (pttp) REVERT: Q 100 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8005 (mt-10) outliers start: 303 outliers final: 228 residues processed: 550 average time/residue: 1.0683 time to fit residues: 729.4348 Evaluate side-chains 545 residues out of total 3243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 288 time to evaluate : 3.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 248 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 598 CYS Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 197 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 323 optimal weight: 50.0000 chunk 340 optimal weight: 8.9990 chunk 310 optimal weight: 7.9990 chunk 331 optimal weight: 20.0000 chunk 199 optimal weight: 0.0050 chunk 144 optimal weight: 0.6980 chunk 260 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 299 optimal weight: 9.9990 chunk 313 optimal weight: 7.9990 chunk 330 optimal weight: 50.0000 overall best weight: 2.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN B 651 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN F 616 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 3 GLN H 100 GLN I 246 GLN J 575 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN L 166 GLN M 3 GLN M 30 ASN M 99 GLN ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 99 GLN P 51 ASN Q 99 GLN R 37 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 31938 Z= 0.343 Angle : 0.728 14.660 43428 Z= 0.353 Chirality : 0.050 0.311 5334 Planarity : 0.005 0.131 5301 Dihedral : 10.677 86.851 7474 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.25 % Favored : 92.43 % Rotamer: Outliers : 9.50 % Allowed : 31.45 % Favored : 59.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.13), residues: 3684 helix: -1.38 (0.25), residues: 408 sheet: -0.74 (0.14), residues: 1251 loop : -1.45 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 610 HIS 0.004 0.001 HIS G 100E PHE 0.012 0.002 PHE L 139 TYR 0.019 0.002 TYR H 140 ARG 0.005 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 287 time to evaluate : 3.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7175 (mmmm) cc_final: 0.6974 (pptt) REVERT: A 325 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8342 (p0) REVERT: B 658 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7571 (tt0) REVERT: C 46 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7553 (tt0) REVERT: C 69 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.7880 (mm) REVERT: C 100 MET cc_start: 0.8832 (mpp) cc_final: 0.8551 (mmt) REVERT: C 179 SER cc_start: 0.8157 (OUTLIER) cc_final: 0.7612 (p) REVERT: D 79 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.6602 (mp10) REVERT: E 153 GLU cc_start: 0.6828 (tt0) cc_final: 0.6479 (tt0) REVERT: E 228 CYS cc_start: 0.8248 (t) cc_final: 0.7965 (t) REVERT: E 325 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8285 (p0) REVERT: F 535 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7853 (mpp) REVERT: F 542 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7624 (ptt90) REVERT: G 30 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8587 (m-10) REVERT: G 77 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.7894 (mt) REVERT: G 80 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8606 (tp) REVERT: G 94 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7556 (t) REVERT: G 100 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8633 (mmt) REVERT: H 47 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8654 (mt) REVERT: H 79 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.6303 (mp10) REVERT: I 84 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8465 (mp) REVERT: I 168 LYS cc_start: 0.7194 (mmmm) cc_final: 0.6868 (pptt) REVERT: I 205 CYS cc_start: 0.6398 (OUTLIER) cc_final: 0.6041 (m) REVERT: I 325 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8500 (p0) REVERT: I 360 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8088 (ptt-90) REVERT: J 575 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: J 608 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.7853 (t) REVERT: J 616 ASN cc_start: 0.8135 (p0) cc_final: 0.7816 (p0) REVERT: J 640 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8197 (mp10) REVERT: J 654 GLU cc_start: 0.6135 (OUTLIER) cc_final: 0.5465 (tt0) REVERT: K 38 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.6848 (ttm-80) REVERT: K 66 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7980 (ttt90) REVERT: L 78 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7455 (tt) REVERT: L 79 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.6594 (mp10) REVERT: L 143 GLU cc_start: 0.5644 (OUTLIER) cc_final: 0.5429 (pp20) REVERT: M 75 LYS cc_start: 0.5506 (OUTLIER) cc_final: 0.4799 (pttp) REVERT: M 100 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8400 (mt-10) REVERT: O 75 LYS cc_start: 0.5595 (OUTLIER) cc_final: 0.4769 (pttp) REVERT: O 100 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.7956 (mt-10) REVERT: P 50 ASN cc_start: 0.8488 (t0) cc_final: 0.8049 (t0) REVERT: P 73 LEU cc_start: 0.6123 (OUTLIER) cc_final: 0.5911 (tp) REVERT: Q 75 LYS cc_start: 0.5400 (OUTLIER) cc_final: 0.4637 (pttp) REVERT: Q 100 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: R 85 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.6918 (m-30) outliers start: 308 outliers final: 222 residues processed: 544 average time/residue: 1.1407 time to fit residues: 784.2595 Evaluate side-chains 543 residues out of total 3243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 284 time to evaluate : 3.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 598 CYS Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 66 ARG Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 197 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 217 optimal weight: 3.9990 chunk 350 optimal weight: 10.0000 chunk 213 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 243 optimal weight: 0.5980 chunk 367 optimal weight: 0.8980 chunk 338 optimal weight: 5.9990 chunk 292 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 179 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN B 577 GLN B 651 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN F 616 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 3 GLN H 100 GLN J 575 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN L 166 GLN M 3 GLN M 99 GLN O 3 GLN O 99 GLN P 51 ASN Q 99 GLN R 37 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 31938 Z= 0.316 Angle : 0.719 14.468 43428 Z= 0.348 Chirality : 0.049 0.327 5334 Planarity : 0.005 0.129 5301 Dihedral : 10.554 87.455 7469 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.00 % Favored : 92.67 % Rotamer: Outliers : 8.88 % Allowed : 31.91 % Favored : 59.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.13), residues: 3684 helix: -1.31 (0.25), residues: 408 sheet: -0.71 (0.14), residues: 1251 loop : -1.45 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 610 HIS 0.004 0.001 HIS G 100E PHE 0.016 0.002 PHE I 233 TYR 0.020 0.002 TYR R 87 ARG 0.005 0.000 ARG A 500 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 287 time to evaluate : 3.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8343 (p0) REVERT: B 658 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: C 46 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7541 (tt0) REVERT: C 69 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.7890 (mm) REVERT: C 100 MET cc_start: 0.8837 (mpp) cc_final: 0.8559 (mmt) REVERT: C 179 SER cc_start: 0.8153 (OUTLIER) cc_final: 0.7595 (p) REVERT: E 153 GLU cc_start: 0.6795 (tt0) cc_final: 0.6450 (tt0) REVERT: E 228 CYS cc_start: 0.8247 (t) cc_final: 0.7964 (t) REVERT: E 325 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8326 (p0) REVERT: F 535 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7823 (mpp) REVERT: F 542 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7671 (ptt90) REVERT: G 30 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8586 (m-10) REVERT: G 77 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.7900 (mt) REVERT: G 80 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8608 (tp) REVERT: G 94 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7509 (t) REVERT: G 100 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8651 (mmt) REVERT: H 47 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8639 (mt) REVERT: H 79 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.6298 (mp10) REVERT: I 84 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8465 (mp) REVERT: I 168 LYS cc_start: 0.7184 (mmmm) cc_final: 0.6833 (pptt) REVERT: I 205 CYS cc_start: 0.6398 (OUTLIER) cc_final: 0.6044 (m) REVERT: I 325 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8498 (p0) REVERT: I 360 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8088 (ptt-90) REVERT: J 608 VAL cc_start: 0.8309 (OUTLIER) cc_final: 0.7851 (t) REVERT: J 616 ASN cc_start: 0.8095 (p0) cc_final: 0.7791 (p0) REVERT: J 640 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8226 (mp10) REVERT: J 654 GLU cc_start: 0.6131 (OUTLIER) cc_final: 0.5469 (tt0) REVERT: K 38 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.6814 (ttm-80) REVERT: K 66 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7939 (ttt90) REVERT: L 78 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7409 (tt) REVERT: L 79 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.6579 (mp10) REVERT: M 38 ARG cc_start: 0.6948 (OUTLIER) cc_final: 0.6663 (ppt-90) REVERT: M 45 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5700 (pt) REVERT: M 75 LYS cc_start: 0.5544 (OUTLIER) cc_final: 0.4820 (pttp) REVERT: M 100 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8378 (mt-10) REVERT: O 75 LYS cc_start: 0.5615 (OUTLIER) cc_final: 0.4772 (pttp) REVERT: O 100 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.7928 (mt-10) REVERT: P 50 ASN cc_start: 0.8493 (t0) cc_final: 0.8053 (t0) REVERT: P 73 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5952 (tp) REVERT: Q 75 LYS cc_start: 0.5464 (OUTLIER) cc_final: 0.4712 (pttp) REVERT: Q 100 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.7987 (mt-10) REVERT: R 85 ASP cc_start: 0.6993 (OUTLIER) cc_final: 0.6630 (m-30) outliers start: 288 outliers final: 224 residues processed: 526 average time/residue: 1.1017 time to fit residues: 714.9301 Evaluate side-chains 544 residues out of total 3243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 284 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 598 CYS Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 66 ARG Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 197 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 232 optimal weight: 1.9990 chunk 311 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 269 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 293 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 301 optimal weight: 30.0000 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN F 616 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 100 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN M 3 GLN M 99 GLN O 3 GLN O 99 GLN P 51 ASN Q 99 GLN R 37 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.224038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.171175 restraints weight = 32957.909| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 3.46 r_work: 0.3339 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.194 31938 Z= 0.342 Angle : 0.806 59.200 43428 Z= 0.418 Chirality : 0.051 0.997 5334 Planarity : 0.005 0.129 5301 Dihedral : 10.534 87.454 7466 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.98 % Favored : 92.67 % Rotamer: Outliers : 8.60 % Allowed : 32.04 % Favored : 59.36 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.13), residues: 3684 helix: -1.32 (0.25), residues: 408 sheet: -0.71 (0.14), residues: 1251 loop : -1.45 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 610 HIS 0.003 0.001 HIS G 100E PHE 0.015 0.002 PHE I 233 TYR 0.019 0.002 TYR B 586 ARG 0.004 0.000 ARG A 500 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12161.07 seconds wall clock time: 218 minutes 10.37 seconds (13090.37 seconds total)