Starting phenix.real_space_refine on Thu Feb 22 00:19:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cuf_7622/02_2024/6cuf_7622_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cuf_7622/02_2024/6cuf_7622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cuf_7622/02_2024/6cuf_7622.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cuf_7622/02_2024/6cuf_7622.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cuf_7622/02_2024/6cuf_7622_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cuf_7622/02_2024/6cuf_7622_neut.pdb" } resolution = 4.0 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= 0.014 sd= 0.127 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 162 5.16 5 C 20319 2.51 5 N 5319 2.21 5 O 6525 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "4 ARG 113": "NH1" <-> "NH2" Residue "5 TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 53": "NH1" <-> "NH2" Residue "8 ARG 61": "NH1" <-> "NH2" Residue "C PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 113": "NH1" <-> "NH2" Residue "M TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 61": "NH1" <-> "NH2" Residue "R ARG 53": "NH1" <-> "NH2" Residue "l ARG 113": "NH1" <-> "NH2" Residue "m TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 61": "NH1" <-> "NH2" Residue "r ARG 53": "NH1" <-> "NH2" Residue "2 PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 288": "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: 32325 Number of models: 1 Model: "" Number of chains: 72 Chain: "3" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 930 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "4" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 882 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "5" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "6" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "7" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "8" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "C" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3565 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 930 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "L" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 882 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "M" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "Q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "R" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "h" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 930 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "l" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 882 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "m" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "n" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "r" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "2" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3565 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "A" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "c" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "d" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3565 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 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: "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: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 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: "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: "o" 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: "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: "s" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "t" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "u" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "v" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "z" Number of atoms: 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: "0" 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: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "9" 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: "AA" 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: "BA" 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: "CA" 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: "DA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" 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: "D" 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: "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: "A" 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: "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: "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 Time building chain proxies: 17.01, per 1000 atoms: 0.53 Number of scatterers: 32325 At special positions: 0 Unit cell: (155.82, 162.18, 154.76, 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 162 16.00 O 6525 8.00 N 5319 7.00 C 20319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS 3 22 " - pdb=" SG CYS 3 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 23 " - pdb=" SG CYS 4 93 " distance=2.04 Simple disulfide: pdb=" SG CYS 5 22 " - pdb=" SG CYS 5 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 23 " - pdb=" SG CYS 6 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 22 " - pdb=" SG CYS 8 92 " distance=2.04 Simple disulfide: pdb=" SG CYS 8 98 " - pdb=" SG CYS 8 100A" distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 98 " - pdb=" SG CYS Q 100A" distance=2.03 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 93 " 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 q 22 " - pdb=" SG CYS q 92 " distance=2.04 Simple disulfide: pdb=" SG CYS q 98 " - pdb=" SG CYS q 100A" distance=2.03 Simple disulfide: pdb=" SG CYS 2 119 " - pdb=" SG CYS 2 205 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 126 " - pdb=" SG CYS 2 196 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 131 " - pdb=" SG CYS 2 157 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 218 " - pdb=" SG CYS 2 247 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 228 " - pdb=" SG CYS 2 239 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 296 " - pdb=" SG CYS 2 331 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 378 " - pdb=" SG CYS 2 445 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 385 " - pdb=" SG CYS 2 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS c 598 " - pdb=" SG CYS c 604 " distance=2.02 Simple disulfide: pdb=" SG CYS d 119 " - pdb=" SG CYS d 205 " distance=2.02 Simple disulfide: pdb=" SG CYS d 126 " - pdb=" SG CYS d 196 " distance=2.03 Simple disulfide: pdb=" SG CYS d 131 " - pdb=" SG CYS d 157 " distance=2.04 Simple disulfide: pdb=" SG CYS d 218 " - pdb=" SG CYS d 247 " distance=2.03 Simple disulfide: pdb=" SG CYS d 228 " - pdb=" SG CYS d 239 " distance=2.04 Simple disulfide: pdb=" SG CYS d 296 " - pdb=" SG CYS d 331 " distance=2.02 Simple disulfide: pdb=" SG CYS d 378 " - pdb=" SG CYS d 445 " distance=2.03 Simple disulfide: pdb=" SG CYS d 385 " - pdb=" SG CYS d 418 " 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 Atom "HETATM31616 O5 NAG u 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30971 O5 NAG Y 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31733 O5 NAG x 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30443 O5 NAG I 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31088 O5 NAG b 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31021 O5 NAG Z 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30376 O5 NAG F 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31666 O5 NAG v 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32000 O5 NAGAA 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30710 O5 NAG T 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31355 O5 NAG k 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30326 O5 NAG E 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31872 O5 NAG 0 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30582 O5 NAG O 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31227 O5 NAG g 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32225 O5 NAG C 628 .*. O " rejected from bonding due to valence issues. Atom "HETATM32323 O5 NAG d 628 .*. O " rejected from bonding due to valence issues. Atom "HETATM32267 O5 NAG 2 628 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " " MAN e 4 " - " MAN e 5 " " MAN o 4 " - " MAN o 5 " " MAN o 5 " - " MAN o 6 " " MAN y 4 " - " MAN y 5 " " MANBA 4 " - " MANBA 5 " " MANBA 5 " - " MANBA 6 " ALPHA1-3 " BMA 9 3 " - " MAN 9 4 " " BMA B 3 " - " MAN B 4 " " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " MAN U 7 " - " MAN U 8 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " BMA e 3 " - " MAN e 4 " " BMA j 3 " - " MAN j 4 " " BMA o 3 " - " MAN o 4 " " MAN o 7 " - " MAN o 8 " " BMA s 3 " - " MAN s 4 " " BMA t 3 " - " MAN t 4 " " BMA u 3 " - " MAN u 4 " " BMA y 3 " - " MAN y 4 " " BMABA 3 " - " MANBA 4 " " MANBA 7 " - " MANBA 8 " " BMADA 3 " - " MANDA 4 " ALPHA1-6 " BMA 9 3 " - " MAN 9 5 " " BMA J 3 " - " MAN J 6 " " BMA S 3 " - " MAN S 5 " " BMA U 3 " - " MAN U 7 " " MAN U 7 " - " MAN U 9 " " BMA e 3 " - " MAN e 6 " " BMA j 3 " - " MAN j 5 " " BMA o 3 " - " MAN o 7 " " MAN o 7 " - " MAN o 9 " " BMA y 3 " - " MAN y 6 " " BMABA 3 " - " MANBA 7 " " MANBA 7 " - " MANBA 9 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " NAG-ASN " NAG 0 1 " - " ASN d 301 " " NAG 1 1 " - " ASN d 363 " " NAG 2 601 " - " ASN 2 133 " " NAG 2 628 " - " ASN 2 355 " " NAG 9 1 " - " ASN d 386 " " NAG A 701 " - " ASN A 637 " " NAG B 1 " - " ASN C 137 " " NAG C 601 " - " ASN C 133 " " NAG C 628 " - " ASN C 355 " " NAG D 701 " - " ASN D 637 " " NAG E 1 " - " ASN C 156 " " NAG F 1 " - " ASN C 160 " " NAG G 1 " - " ASN C 197 " " NAG I 1 " - " ASN C 234 " " NAG J 1 " - " ASN C 262 " " NAG K 1 " - " ASN C 295 " " NAG O 1 " - " ASN C 301 " " NAG P 1 " - " ASN C 363 " " NAG S 1 " - " ASN C 386 " " NAG T 1 " - " ASN C 392 " " NAG U 1 " - " ASN C 332 " " NAG V 1 " - " ASN C 448 " " NAG W 1 " - " ASN C 276 " " NAG X 1 " - " ASN 2 137 " " NAG Y 1 " - " ASN 2 156 " " NAG Z 1 " - " ASN 2 160 " " NAG a 1 " - " ASN 2 197 " " NAG b 1 " - " ASN 2 234 " " NAG c 701 " - " ASN c 637 " " NAG d 601 " - " ASN d 133 " " NAG d 628 " - " ASN d 355 " " NAG e 1 " - " ASN 2 262 " " NAG f 1 " - " ASN 2 295 " " NAG g 1 " - " ASN 2 301 " " NAG i 1 " - " ASN 2 363 " " NAG j 1 " - " ASN 2 386 " " NAG k 1 " - " ASN 2 392 " " NAG o 1 " - " ASN 2 332 " " NAG p 1 " - " ASN 2 448 " " NAG s 1 " - " ASN 2 276 " " NAG t 1 " - " ASN d 137 " " NAG u 1 " - " ASN d 156 " " NAG v 1 " - " ASN d 160 " " NAG w 1 " - " ASN d 197 " " NAG x 1 " - " ASN d 234 " " NAG y 1 " - " ASN d 262 " " NAG z 1 " - " ASN d 295 " " NAGAA 1 " - " ASN d 392 " " NAGBA 1 " - " ASN d 332 " " NAGCA 1 " - " ASN d 448 " " NAGDA 1 " - " ASN d 276 " Time building additional restraints: 16.02 Conformation dependent library (CDL) restraints added in 6.0 seconds 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7050 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 82 sheets defined 15.9% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain '3' and resid 28 through 32 removed outlier: 4.191A pdb=" N ASP 3 31 " --> pdb=" O THR 3 28 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR 3 32 " --> pdb=" O PHE 3 29 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 28 through 32' Processing helix chain '3' and resid 83 through 87 Processing helix chain '5' and resid 83 through 87 removed outlier: 3.592A pdb=" N SER 5 87 " --> pdb=" O ALA 5 84 " (cutoff:3.500A) Processing helix chain '5' and resid 100D through 100H Processing helix chain '6' and resid 79 through 83 Processing helix chain '7' and resid 79 through 83 Processing helix chain '8' and resid 61 through 64 Processing helix chain '8' and resid 83 through 87 Processing helix chain 'C' and resid 58 through 63 removed outlier: 3.527A pdb=" N THR C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 115 removed outlier: 3.733A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 removed outlier: 4.017A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 126' Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.720A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'D' and resid 514 through 520 removed outlier: 4.394A pdb=" N VAL D 518 " --> pdb=" O GLY D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.629A pdb=" N ALA D 526 " --> pdb=" O LEU D 523 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 523 through 527' Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 546 removed outlier: 3.662A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER D 546 " --> pdb=" O ARG D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 595 removed outlier: 4.016A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 616 removed outlier: 4.048A pdb=" N SER D 615 " --> pdb=" O ASN D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.538A pdb=" N ILE D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TRP D 623 " --> pdb=" O LEU D 619 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 640 through 664 removed outlier: 3.709A pdb=" N GLY D 644 " --> pdb=" O GLN D 640 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.168A pdb=" N ASP H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'Q' and resid 61 through 64 Processing helix chain 'Q' and resid 83 through 87 removed outlier: 3.551A pdb=" N THR Q 87 " --> pdb=" O PRO Q 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'h' and resid 28 through 32 removed outlier: 4.135A pdb=" N ASP h 31 " --> pdb=" O THR h 28 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR h 32 " --> pdb=" O PHE h 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 28 through 32' Processing helix chain 'h' and resid 83 through 87 Processing helix chain 'm' and resid 83 through 87 removed outlier: 3.671A pdb=" N SER m 87 " --> pdb=" O ALA m 84 " (cutoff:3.500A) Processing helix chain 'n' and resid 79 through 83 Processing helix chain 'q' and resid 61 through 64 Processing helix chain 'q' and resid 83 through 87 Processing helix chain 'r' and resid 79 through 83 Processing helix chain '2' and resid 58 through 63 removed outlier: 3.526A pdb=" N THR 2 63 " --> pdb=" O LYS 2 59 " (cutoff:3.500A) Processing helix chain '2' and resid 101 through 115 removed outlier: 3.733A pdb=" N ILE 2 109 " --> pdb=" O HIS 2 105 " (cutoff:3.500A) Processing helix chain '2' and resid 123 through 126 removed outlier: 4.017A pdb=" N CYS 2 126 " --> pdb=" O THR 2 123 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 123 through 126' Processing helix chain '2' and resid 177 through 179 No H-bonds generated for 'chain '2' and resid 177 through 179' Processing helix chain '2' and resid 195 through 198 Processing helix chain '2' and resid 335 through 350 Processing helix chain '2' and resid 368 through 373 removed outlier: 3.719A pdb=" N THR 2 373 " --> pdb=" O LEU 2 369 " (cutoff:3.500A) Processing helix chain '2' and resid 475 through 481 Processing helix chain '2' and resid 482 through 484 No H-bonds generated for 'chain '2' and resid 482 through 484' Processing helix chain 'A' and resid 514 through 520 removed outlier: 4.395A pdb=" N VAL A 518 " --> pdb=" O GLY A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 527 removed outlier: 3.629A pdb=" N ALA A 526 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 523 through 527' Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 537 through 546 removed outlier: 3.662A pdb=" N LEU A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER A 546 " --> pdb=" O ARG A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 595 removed outlier: 4.017A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 616 removed outlier: 4.047A pdb=" N SER A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 626 removed outlier: 3.538A pdb=" N ILE A 622 " --> pdb=" O ASN A 618 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TRP A 623 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 640 through 664 removed outlier: 3.709A pdb=" N GLY A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) Processing helix chain 'c' and resid 514 through 520 removed outlier: 4.394A pdb=" N VAL c 518 " --> pdb=" O GLY c 514 " (cutoff:3.500A) Processing helix chain 'c' and resid 523 through 527 removed outlier: 3.630A pdb=" N ALA c 526 " --> pdb=" O LEU c 523 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY c 527 " --> pdb=" O GLY c 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 523 through 527' Processing helix chain 'c' and resid 529 through 534 Processing helix chain 'c' and resid 537 through 546 removed outlier: 3.662A pdb=" N LEU c 545 " --> pdb=" O ALA c 541 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER c 546 " --> pdb=" O ARG c 542 " (cutoff:3.500A) Processing helix chain 'c' and resid 570 through 595 removed outlier: 4.016A pdb=" N LYS c 574 " --> pdb=" O VAL c 570 " (cutoff:3.500A) Processing helix chain 'c' and resid 611 through 616 removed outlier: 4.048A pdb=" N SER c 615 " --> pdb=" O ASN c 611 " (cutoff:3.500A) Processing helix chain 'c' and resid 618 through 626 removed outlier: 3.538A pdb=" N ILE c 622 " --> pdb=" O ASN c 618 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TRP c 623 " --> pdb=" O LEU c 619 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP c 624 " --> pdb=" O SER c 620 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET c 626 " --> pdb=" O ILE c 622 " (cutoff:3.500A) Processing helix chain 'c' and resid 627 through 636 Processing helix chain 'c' and resid 640 through 664 removed outlier: 3.709A pdb=" N GLY c 644 " --> pdb=" O GLN c 640 " (cutoff:3.500A) Processing helix chain 'd' and resid 58 through 63 removed outlier: 3.526A pdb=" N THR d 63 " --> pdb=" O LYS d 59 " (cutoff:3.500A) Processing helix chain 'd' and resid 101 through 115 removed outlier: 3.734A pdb=" N ILE d 109 " --> pdb=" O HIS d 105 " (cutoff:3.500A) Processing helix chain 'd' and resid 123 through 126 removed outlier: 4.018A pdb=" N CYS d 126 " --> pdb=" O THR d 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 123 through 126' Processing helix chain 'd' and resid 177 through 179 No H-bonds generated for 'chain 'd' and resid 177 through 179' Processing helix chain 'd' and resid 195 through 198 Processing helix chain 'd' and resid 335 through 350 Processing helix chain 'd' and resid 368 through 373 removed outlier: 3.720A pdb=" N THR d 373 " --> pdb=" O LEU d 369 " (cutoff:3.500A) Processing helix chain 'd' and resid 475 through 481 Processing helix chain 'd' and resid 482 through 484 No H-bonds generated for 'chain 'd' and resid 482 through 484' Processing sheet with id=AA1, first strand: chain '3' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain '3' and resid 10 through 11 removed outlier: 6.663A pdb=" N GLU 3 10 " --> pdb=" O THR 3 110 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE 3 34 " --> pdb=" O ALA 3 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ALA 3 50 " --> pdb=" O ILE 3 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP 3 36 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '4' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain '4' and resid 10 through 12 removed outlier: 6.405A pdb=" N LEU 4 11 " --> pdb=" O GLU 4 110 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY 4 89 " --> pdb=" O LEU 4 109 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU 4 42 " --> pdb=" O LEU 4 51 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU 4 51 " --> pdb=" O LEU 4 42 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '4' and resid 10 through 12 removed outlier: 6.405A pdb=" N LEU 4 11 " --> pdb=" O GLU 4 110 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY 4 89 " --> pdb=" O LEU 4 109 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR 4 102 " --> pdb=" O GLN 4 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '5' and resid 5 through 7 Processing sheet with id=AA7, first strand: chain '5' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain '5' and resid 46 through 51 removed outlier: 5.074A pdb=" N TRP 5 47 " --> pdb=" O ARG 5 38 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG 5 38 " --> pdb=" O TRP 5 47 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR 5 90 " --> pdb=" O THR 5 105 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR 5 105 " --> pdb=" O TYR 5 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '5' and resid 96 through 100A removed outlier: 3.754A pdb=" N GLY 5 98 " --> pdb=" O TYR 5 100M" (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '6' and resid 9 through 13 removed outlier: 5.786A pdb=" N VAL 6 11 " --> pdb=" O ILE 6 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR 6 102 " --> pdb=" O TYR 6 86 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLN 6 37 " --> pdb=" O LEU 6 46 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LEU 6 46 " --> pdb=" O GLN 6 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '6' and resid 19 through 26 removed outlier: 3.621A pdb=" N ALA 6 71 " --> pdb=" O CYS 6 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '7' and resid 4 through 6 Processing sheet with id=AB4, first strand: chain '7' and resid 10 through 13 removed outlier: 6.012A pdb=" N GLN 7 37 " --> pdb=" O LEU 7 46 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU 7 46 " --> pdb=" O GLN 7 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '8' and resid 3 through 6 Processing sheet with id=AB6, first strand: chain '8' and resid 3 through 6 Processing sheet with id=AB7, first strand: chain '8' and resid 10 through 11 removed outlier: 6.779A pdb=" N VAL 8 10 " --> pdb=" O VAL 8 110 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ARG 8 38 " --> pdb=" O TRP 8 47 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TRP 8 47 " --> pdb=" O ARG 8 38 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE 8 40 " --> pdb=" O PHE 8 45 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N PHE 8 45 " --> pdb=" O ILE 8 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '8' and resid 10 through 11 removed outlier: 6.779A pdb=" N VAL 8 10 " --> pdb=" O VAL 8 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 35 through 39 Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.515A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AC3, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.620A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.836A pdb=" N VAL C 120 " --> pdb=" O GLN C 203 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AC6, first strand: chain 'C' and resid 181 through 184 removed outlier: 4.589A pdb=" N GLU C 190 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.299A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS C 374 " --> pdb=" O CYS C 385 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.570A pdb=" N PHE C 288 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.402A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.257A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 10.582A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.196A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 304 through 306 Processing sheet with id=AD1, first strand: chain 'C' and resid 359 through 360 Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.727A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ALA H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.391A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY L 89 " --> pdb=" O LEU L 109 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU L 42 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU L 51 " --> pdb=" O LEU L 42 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.391A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY L 89 " --> pdb=" O LEU L 109 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR L 102 " --> pdb=" O GLN L 95 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 5 through 7 Processing sheet with id=AD8, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AD9, first strand: chain 'M' and resid 46 through 51 removed outlier: 5.062A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR M 33 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR M 95 " --> pdb=" O TYR M 33 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY M 98 " --> pdb=" O TYR M 100M" (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 9 through 13 removed outlier: 5.877A pdb=" N VAL N 11 " --> pdb=" O ILE N 105 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR N 102 " --> pdb=" O TYR N 86 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 19 through 26 removed outlier: 3.614A pdb=" N ALA N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AE4, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'Q' and resid 10 through 11 removed outlier: 6.730A pdb=" N VAL Q 10 " --> pdb=" O VAL Q 110 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE Q 40 " --> pdb=" O PHE Q 45 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE Q 45 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 10 through 11 removed outlier: 6.730A pdb=" N VAL Q 10 " --> pdb=" O VAL Q 110 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 4 through 6 Processing sheet with id=AE8, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.495A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'h' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'h' and resid 10 through 11 removed outlier: 6.989A pdb=" N ILE h 34 " --> pdb=" O ALA h 50 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA h 50 " --> pdb=" O ILE h 34 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TRP h 36 " --> pdb=" O ILE h 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'l' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'l' and resid 10 through 12 removed outlier: 6.397A pdb=" N LEU l 11 " --> pdb=" O GLU l 110 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY l 89 " --> pdb=" O LEU l 109 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU l 42 " --> pdb=" O LEU l 51 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU l 51 " --> pdb=" O LEU l 42 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'l' and resid 10 through 12 removed outlier: 6.397A pdb=" N LEU l 11 " --> pdb=" O GLU l 110 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY l 89 " --> pdb=" O LEU l 109 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR l 102 " --> pdb=" O GLN l 95 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'm' and resid 5 through 7 Processing sheet with id=AF6, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.695A pdb=" N THR m 95 " --> pdb=" O TYR m 33 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR m 33 " --> pdb=" O THR m 95 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY m 49 " --> pdb=" O TRP m 36 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG m 38 " --> pdb=" O TRP m 47 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N TRP m 47 " --> pdb=" O ARG m 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.799A pdb=" N GLY m 98 " --> pdb=" O TYR m 100M" (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'n' and resid 9 through 13 removed outlier: 5.922A pdb=" N VAL n 11 " --> pdb=" O ILE n 105 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLN n 37 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU n 46 " --> pdb=" O GLN n 37 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'n' and resid 19 through 26 removed outlier: 3.694A pdb=" N ALA n 71 " --> pdb=" O CYS n 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'q' and resid 3 through 5 Processing sheet with id=AG2, first strand: chain 'q' and resid 3 through 5 Processing sheet with id=AG3, first strand: chain 'q' and resid 10 through 11 removed outlier: 6.621A pdb=" N VAL q 10 " --> pdb=" O VAL q 110 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY q 49 " --> pdb=" O TRP q 36 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ARG q 38 " --> pdb=" O TRP q 47 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N TRP q 47 " --> pdb=" O ARG q 38 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE q 40 " --> pdb=" O PHE q 45 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE q 45 " --> pdb=" O ILE q 40 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'q' and resid 10 through 11 removed outlier: 6.621A pdb=" N VAL q 10 " --> pdb=" O VAL q 110 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'r' and resid 5 through 6 Processing sheet with id=AG6, first strand: chain 'r' and resid 10 through 13 removed outlier: 6.534A pdb=" N TRP r 35 " --> pdb=" O LEU r 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain '2' and resid 35 through 39 Processing sheet with id=AG8, first strand: chain '2' and resid 45 through 47 removed outlier: 3.515A pdb=" N LYS 2 487 " --> pdb=" O LEU 2 226 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE 2 225 " --> pdb=" O VAL 2 245 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain '2' and resid 75 through 76 Processing sheet with id=AH1, first strand: chain '2' and resid 91 through 94 removed outlier: 3.620A pdb=" N GLU 2 91 " --> pdb=" O CYS 2 239 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain '2' and resid 120 through 121 removed outlier: 3.837A pdb=" N VAL 2 120 " --> pdb=" O GLN 2 203 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '2' and resid 130 through 133 Processing sheet with id=AH4, first strand: chain '2' and resid 181 through 184 removed outlier: 4.590A pdb=" N GLU 2 190 " --> pdb=" O ILE 2 184 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain '2' and resid 271 through 273 removed outlier: 7.299A pdb=" N GLN 2 293 " --> pdb=" O SER 2 334 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER 2 334 " --> pdb=" O GLN 2 293 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS 2 374 " --> pdb=" O CYS 2 385 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain '2' and resid 271 through 273 removed outlier: 3.570A pdb=" N PHE 2 288 " --> pdb=" O THR 2 450 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR 2 450 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N THR 2 290 " --> pdb=" O ASN 2 448 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N ASN 2 448 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 10.402A pdb=" N VAL 2 292 " --> pdb=" O VAL 2 446 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N VAL 2 446 " --> pdb=" O VAL 2 292 " (cutoff:3.500A) removed outlier: 11.257A pdb=" N ILE 2 294 " --> pdb=" O ARG 2 444 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N ARG 2 444 " --> pdb=" O ILE 2 294 " (cutoff:3.500A) removed outlier: 10.582A pdb=" N CYS 2 296 " --> pdb=" O VAL 2 442 " (cutoff:3.500A) removed outlier: 10.196A pdb=" N VAL 2 442 " --> pdb=" O CYS 2 296 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain '2' and resid 304 through 306 Processing sheet with id=AH8, first strand: chain '2' and resid 359 through 360 Processing sheet with id=AH9, first strand: chain 'd' and resid 35 through 39 Processing sheet with id=AI1, first strand: chain 'd' and resid 45 through 47 removed outlier: 3.515A pdb=" N LYS d 487 " --> pdb=" O LEU d 226 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE d 225 " --> pdb=" O VAL d 245 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'd' and resid 75 through 76 Processing sheet with id=AI3, first strand: chain 'd' and resid 91 through 94 removed outlier: 3.620A pdb=" N GLU d 91 " --> pdb=" O CYS d 239 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'd' and resid 120 through 121 removed outlier: 3.837A pdb=" N VAL d 120 " --> pdb=" O GLN d 203 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'd' and resid 130 through 133 Processing sheet with id=AI6, first strand: chain 'd' and resid 181 through 184 removed outlier: 4.590A pdb=" N GLU d 190 " --> pdb=" O ILE d 184 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'd' and resid 271 through 273 removed outlier: 7.299A pdb=" N GLN d 293 " --> pdb=" O SER d 334 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER d 334 " --> pdb=" O GLN d 293 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N HIS d 374 " --> pdb=" O CYS d 385 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'd' and resid 271 through 273 removed outlier: 3.570A pdb=" N PHE d 288 " --> pdb=" O THR d 450 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR d 450 " --> pdb=" O PHE d 288 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N THR d 290 " --> pdb=" O ASN d 448 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N ASN d 448 " --> pdb=" O THR d 290 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N VAL d 292 " --> pdb=" O VAL d 446 " (cutoff:3.500A) removed outlier: 9.724A pdb=" N VAL d 446 " --> pdb=" O VAL d 292 " (cutoff:3.500A) removed outlier: 11.257A pdb=" N ILE d 294 " --> pdb=" O ARG d 444 " (cutoff:3.500A) removed outlier: 9.857A pdb=" N ARG d 444 " --> pdb=" O ILE d 294 " (cutoff:3.500A) removed outlier: 10.582A pdb=" N CYS d 296 " --> pdb=" O VAL d 442 " (cutoff:3.500A) removed outlier: 10.196A pdb=" N VAL d 442 " --> pdb=" O CYS d 296 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'd' and resid 304 through 306 Processing sheet with id=AJ1, first strand: chain 'd' and resid 359 through 360 1078 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.45 Time building geometry restraints manager: 16.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9612 1.33 - 1.46: 8154 1.46 - 1.58: 15060 1.58 - 1.70: 3 1.70 - 1.82: 216 Bond restraints: 33045 Sorted by residual: bond pdb=" C1 BMA 1 3 " pdb=" C2 BMA 1 3 " ideal model delta sigma weight residual 1.519 1.580 -0.061 2.00e-02 2.50e+03 9.43e+00 bond pdb=" C1 BMA P 3 " pdb=" C2 BMA P 3 " ideal model delta sigma weight residual 1.519 1.580 -0.061 2.00e-02 2.50e+03 9.34e+00 bond pdb=" C1 BMA i 3 " pdb=" C2 BMA i 3 " ideal model delta sigma weight residual 1.519 1.580 -0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" C5 MAN J 4 " pdb=" O5 MAN J 4 " ideal model delta sigma weight residual 1.418 1.471 -0.053 2.00e-02 2.50e+03 7.13e+00 bond pdb=" C5 MAN y 4 " pdb=" O5 MAN y 4 " ideal model delta sigma weight residual 1.418 1.471 -0.053 2.00e-02 2.50e+03 7.11e+00 ... (remaining 33040 not shown) Histogram of bond angle deviations from ideal: 97.87 - 105.21: 590 105.21 - 112.55: 18068 112.55 - 119.88: 10991 119.88 - 127.22: 14817 127.22 - 134.56: 441 Bond angle restraints: 44907 Sorted by residual: angle pdb=" CA LEU 2 494 " pdb=" CB LEU 2 494 " pdb=" CG LEU 2 494 " ideal model delta sigma weight residual 116.30 134.56 -18.26 3.50e+00 8.16e-02 2.72e+01 angle pdb=" CA LEU d 494 " pdb=" CB LEU d 494 " pdb=" CG LEU d 494 " ideal model delta sigma weight residual 116.30 134.54 -18.24 3.50e+00 8.16e-02 2.72e+01 angle pdb=" CA LEU C 494 " pdb=" CB LEU C 494 " pdb=" CG LEU C 494 " ideal model delta sigma weight residual 116.30 134.53 -18.23 3.50e+00 8.16e-02 2.71e+01 angle pdb=" C ASN 2 99 " pdb=" N MET 2 100 " pdb=" CA MET 2 100 " ideal model delta sigma weight residual 121.54 130.84 -9.30 1.91e+00 2.74e-01 2.37e+01 angle pdb=" C ASN C 99 " pdb=" N MET C 100 " pdb=" CA MET C 100 " ideal model delta sigma weight residual 121.54 130.83 -9.29 1.91e+00 2.74e-01 2.37e+01 ... (remaining 44902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.16: 20486 22.16 - 44.32: 704 44.32 - 66.48: 137 66.48 - 88.65: 144 88.65 - 110.81: 102 Dihedral angle restraints: 21573 sinusoidal: 10551 harmonic: 11022 Sorted by residual: dihedral pdb=" CA LYS 4 55 " pdb=" C LYS 4 55 " pdb=" N VAL 4 56 " pdb=" CA VAL 4 56 " ideal model delta harmonic sigma weight residual -180.00 -140.73 -39.27 0 5.00e+00 4.00e-02 6.17e+01 dihedral pdb=" CA LYS l 55 " pdb=" C LYS l 55 " pdb=" N VAL l 56 " pdb=" CA VAL l 56 " ideal model delta harmonic sigma weight residual 180.00 -140.87 -39.13 0 5.00e+00 4.00e-02 6.13e+01 dihedral pdb=" CA LYS L 55 " pdb=" C LYS L 55 " pdb=" N VAL L 56 " pdb=" CA VAL L 56 " ideal model delta harmonic sigma weight residual 180.00 -141.25 -38.75 0 5.00e+00 4.00e-02 6.01e+01 ... (remaining 21570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.292: 5392 0.292 - 0.584: 27 0.584 - 0.876: 11 0.876 - 1.168: 9 1.168 - 1.460: 3 Chirality restraints: 5442 Sorted by residual: chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN 2 234 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.94 -1.46 2.00e-01 2.50e+01 5.33e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.94 -1.46 2.00e-01 2.50e+01 5.32e+01 chirality pdb=" C1 NAG x 1 " pdb=" ND2 ASN d 234 " pdb=" C2 NAG x 1 " pdb=" O5 NAG x 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.94 -1.46 2.00e-01 2.50e+01 5.31e+01 ... (remaining 5439 not shown) Planarity restraints: 5523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN 2 276 " -0.103 2.00e-02 2.50e+03 3.92e-01 1.92e+03 pdb=" CG ASN 2 276 " 0.134 2.00e-02 2.50e+03 pdb=" OD1 ASN 2 276 " -0.190 2.00e-02 2.50e+03 pdb=" ND2 ASN 2 276 " 0.667 2.00e-02 2.50e+03 pdb=" C1 NAG s 1 " -0.508 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 276 " -0.103 2.00e-02 2.50e+03 3.92e-01 1.92e+03 pdb=" CG ASN C 276 " 0.134 2.00e-02 2.50e+03 pdb=" OD1 ASN C 276 " -0.190 2.00e-02 2.50e+03 pdb=" ND2 ASN C 276 " 0.667 2.00e-02 2.50e+03 pdb=" C1 NAG W 1 " -0.508 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN d 276 " -0.103 2.00e-02 2.50e+03 3.92e-01 1.92e+03 pdb=" CG ASN d 276 " 0.134 2.00e-02 2.50e+03 pdb=" OD1 ASN d 276 " -0.190 2.00e-02 2.50e+03 pdb=" ND2 ASN d 276 " 0.667 2.00e-02 2.50e+03 pdb=" C1 NAGDA 1 " -0.507 2.00e-02 2.50e+03 ... (remaining 5520 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 408 2.57 - 3.15: 25415 3.15 - 3.73: 48915 3.73 - 4.32: 67968 4.32 - 4.90: 110520 Nonbonded interactions: 253226 Sorted by model distance: nonbonded pdb=" O ASN 2 197 " pdb=" OD1 ASN 2 197 " model vdw 1.984 3.040 nonbonded pdb=" O ASN d 197 " pdb=" OD1 ASN d 197 " model vdw 1.984 3.040 nonbonded pdb=" O ASN C 197 " pdb=" OD1 ASN C 197 " model vdw 1.985 3.040 nonbonded pdb=" OE2 GLU 2 164 " pdb=" NH1 ARG 2 308 " model vdw 2.021 2.520 nonbonded pdb=" OE2 GLU C 164 " pdb=" NH1 ARG C 308 " model vdw 2.021 2.520 ... (remaining 253221 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 'AA' selection = chain 'CA' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'T' selection = chain 'V' selection = chain 'a' selection = chain 'f' selection = chain 'g' selection = chain 'k' selection = chain 'p' selection = chain 'w' selection = chain 'z' } ncs_group { reference = chain '1' selection = chain 'F' selection = chain 'I' selection = chain 'P' selection = chain 'Z' selection = chain 'b' selection = chain 'i' selection = chain 'v' selection = chain 'x' } ncs_group { reference = chain '2' selection = chain 'C' selection = chain 'd' } ncs_group { reference = chain '3' selection = chain 'H' selection = chain 'h' } ncs_group { reference = chain '4' selection = chain 'L' selection = chain 'l' } ncs_group { reference = chain '5' selection = chain 'M' selection = chain 'm' } ncs_group { reference = chain '6' selection = chain 'N' selection = chain 'n' } ncs_group { reference = chain '7' selection = chain 'R' selection = chain 'r' } ncs_group { reference = chain '8' selection = chain 'Q' selection = chain 'q' } ncs_group { reference = chain '9' selection = chain 'S' selection = chain 'j' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'c' } ncs_group { reference = chain 'B' selection = chain 'DA' selection = chain 'E' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 's' selection = chain 't' selection = chain 'u' } ncs_group { reference = chain 'BA' selection = chain 'U' selection = chain 'o' } ncs_group { reference = chain 'J' selection = chain 'e' selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.340 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 88.900 Find NCS groups from input model: 2.440 Set up NCS constraints: 0.840 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 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 : 0.008 0.076 33045 Z= 0.504 Angle : 1.059 18.258 44907 Z= 0.529 Chirality : 0.094 1.460 5442 Planarity : 0.007 0.070 5472 Dihedral : 15.872 110.807 14388 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.33 % Favored : 92.59 % Rotamer: Outliers : 0.81 % Allowed : 2.97 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.25 (0.12), residues: 3777 helix: -2.52 (0.19), residues: 480 sheet: -1.42 (0.14), residues: 1203 loop : -2.58 (0.11), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP Q 103 HIS 0.010 0.003 HIS Q 35 PHE 0.025 0.003 PHE r 97 TYR 0.026 0.003 TYR c 638 ARG 0.010 0.001 ARG 2 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 587 time to evaluate : 3.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 5 GLN cc_start: 0.9454 (tp40) cc_final: 0.9160 (tm-30) REVERT: 3 33 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7935 (mt-10) REVERT: 4 51 LEU cc_start: 0.2959 (tp) cc_final: 0.0375 (tt) REVERT: 4 77 THR cc_start: 0.7447 (m) cc_final: 0.7172 (m) REVERT: 7 1 GLU cc_start: 0.8680 (pt0) cc_final: 0.8298 (mt-10) REVERT: 7 54 ARG cc_start: 0.8417 (mtm110) cc_final: 0.7923 (ptp90) REVERT: 8 28 ASN cc_start: 0.8866 (t0) cc_final: 0.8446 (t0) REVERT: 8 39 LEU cc_start: 0.8669 (tp) cc_final: 0.8132 (tt) REVERT: C 52 LEU cc_start: 0.9194 (mt) cc_final: 0.8987 (mt) REVERT: D 654 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8447 (tp30) REVERT: H 99 TRP cc_start: 0.8292 (m100) cc_final: 0.7845 (m100) REVERT: H 100 PHE cc_start: 0.6267 (m-80) cc_final: 0.5903 (m-80) REVERT: L 67 PHE cc_start: 0.7175 (m-80) cc_final: 0.6715 (m-80) REVERT: N 90 ILE cc_start: 0.9123 (pt) cc_final: 0.8918 (mt) REVERT: Q 73 LEU cc_start: 0.8668 (mt) cc_final: 0.8230 (mt) REVERT: R 1 GLU cc_start: 0.8739 (pt0) cc_final: 0.7994 (mt-10) REVERT: R 70 ASP cc_start: 0.9232 (m-30) cc_final: 0.8650 (m-30) REVERT: R 81 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8934 (tp30) REVERT: h 86 ASP cc_start: 0.7311 (m-30) cc_final: 0.6984 (m-30) REVERT: h 100 PHE cc_start: 0.6291 (m-80) cc_final: 0.5775 (m-80) REVERT: q 28 ASN cc_start: 0.8816 (t0) cc_final: 0.8414 (t0) REVERT: q 100 TYR cc_start: 0.9213 (m-80) cc_final: 0.8692 (m-10) REVERT: r 1 GLU cc_start: 0.8766 (pt0) cc_final: 0.8472 (mt-10) REVERT: 2 100 MET cc_start: 0.8748 (ptp) cc_final: 0.8487 (ptp) REVERT: A 652 GLN cc_start: 0.9374 (tt0) cc_final: 0.8666 (tp-100) REVERT: c 535 MET cc_start: 0.9118 (mmt) cc_final: 0.8557 (mmt) REVERT: c 654 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8516 (tp30) outliers start: 27 outliers final: 10 residues processed: 611 average time/residue: 0.5350 time to fit residues: 486.5442 Evaluate side-chains 274 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 264 time to evaluate : 3.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain 2 residue 197 ASN Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 332 ASN Chi-restraints excluded: chain 2 residue 392 ASN Chi-restraints excluded: chain d residue 197 ASN Chi-restraints excluded: chain d residue 332 ASN Chi-restraints excluded: chain d residue 392 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 9.9990 chunk 284 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 293 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 218 optimal weight: 10.0000 chunk 340 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 35 HIS 3 39 GLN 3 43 HIS ** 3 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 97 ASN ** 4 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 58 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS C 293 GLN C 374 HIS D 611 ASN D 630 GLN H 35 HIS H 39 GLN ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 GLN h 35 HIS h 39 GLN ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 97 ASN l 27 GLN ** l 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 249 HIS 2 293 GLN 2 374 HIS A 611 ASN A 630 GLN c 577 GLN c 611 ASN c 630 GLN ** d 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 249 HIS d 293 GLN d 374 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 33045 Z= 0.305 Angle : 0.759 15.205 44907 Z= 0.369 Chirality : 0.048 0.297 5442 Planarity : 0.005 0.058 5472 Dihedral : 14.700 79.545 7453 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.01 % Allowed : 9.13 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.56 (0.13), residues: 3777 helix: -1.28 (0.23), residues: 450 sheet: -1.33 (0.14), residues: 1251 loop : -2.05 (0.12), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP q 100F HIS 0.005 0.001 HIS d 330 PHE 0.016 0.002 PHE d 288 TYR 0.017 0.002 TYR d 318 ARG 0.009 0.001 ARG 7 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 302 time to evaluate : 3.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 5 GLN cc_start: 0.9420 (tp40) cc_final: 0.9188 (tm-30) REVERT: 3 62 LYS cc_start: 0.9273 (tppt) cc_final: 0.8804 (ttpp) REVERT: 4 51 LEU cc_start: 0.1042 (tp) cc_final: 0.0390 (tt) REVERT: 5 100 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8783 (mmm) REVERT: 7 1 GLU cc_start: 0.8796 (pt0) cc_final: 0.8333 (mt-10) REVERT: 8 28 ASN cc_start: 0.8995 (t0) cc_final: 0.8032 (t0) REVERT: 8 31 ASP cc_start: 0.8222 (m-30) cc_final: 0.7462 (m-30) REVERT: C 425 ASN cc_start: 0.8544 (t0) cc_final: 0.8125 (t0) REVERT: H 66 LYS cc_start: 0.7165 (ptmt) cc_final: 0.6516 (tptp) REVERT: H 99 TRP cc_start: 0.8388 (m100) cc_final: 0.7772 (m100) REVERT: H 100 PHE cc_start: 0.6686 (m-80) cc_final: 0.6236 (m-80) REVERT: M 100 MET cc_start: 0.8943 (mmm) cc_final: 0.8537 (mmm) REVERT: N 31 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8665 (ptp-110) REVERT: R 1 GLU cc_start: 0.8885 (pt0) cc_final: 0.8095 (mt-10) REVERT: R 81 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8924 (tp30) REVERT: h 86 ASP cc_start: 0.7290 (m-30) cc_final: 0.6982 (m-30) REVERT: h 98 TYR cc_start: 0.8878 (m-80) cc_final: 0.8224 (m-80) REVERT: h 100 PHE cc_start: 0.6463 (m-80) cc_final: 0.5783 (m-80) REVERT: q 28 ASN cc_start: 0.8973 (t0) cc_final: 0.7939 (t0) REVERT: q 31 ASP cc_start: 0.8262 (m-30) cc_final: 0.7387 (m-30) REVERT: q 99 ASP cc_start: 0.8457 (p0) cc_final: 0.8087 (p0) REVERT: q 100 TYR cc_start: 0.9072 (m-80) cc_final: 0.8743 (m-80) REVERT: q 100 ASP cc_start: 0.7857 (p0) cc_final: 0.7596 (p0) REVERT: r 1 GLU cc_start: 0.8893 (pt0) cc_final: 0.8490 (mt-10) REVERT: r 81 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8921 (tp30) REVERT: 2 100 MET cc_start: 0.8951 (ptp) cc_final: 0.8638 (ptp) REVERT: 2 161 MET cc_start: 0.9552 (tpp) cc_final: 0.9335 (tpp) REVERT: 2 265 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8604 (pp) REVERT: A 530 MET cc_start: 0.7878 (ptp) cc_final: 0.7624 (ptp) REVERT: A 652 GLN cc_start: 0.9302 (tt0) cc_final: 0.8687 (tp-100) REVERT: A 654 GLU cc_start: 0.8555 (tp30) cc_final: 0.7634 (tm-30) REVERT: c 654 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8930 (tm-30) REVERT: d 100 MET cc_start: 0.9022 (ptm) cc_final: 0.8638 (ppp) outliers start: 67 outliers final: 37 residues processed: 345 average time/residue: 0.4553 time to fit residues: 247.9817 Evaluate side-chains 277 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 237 time to evaluate : 3.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 98 TYR Chi-restraints excluded: chain 4 residue 52 LEU Chi-restraints excluded: chain 4 residue 65 ASP Chi-restraints excluded: chain 4 residue 102 THR Chi-restraints excluded: chain 5 residue 100 MET Chi-restraints excluded: chain 6 residue 90 ILE Chi-restraints excluded: chain 7 residue 56 SER Chi-restraints excluded: chain 7 residue 78 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain m residue 100 MET Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain r residue 78 LEU Chi-restraints excluded: chain r residue 100 LEU Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 265 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 494 LEU Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain c residue 587 LEU Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 373 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 283 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 341 optimal weight: 2.9990 chunk 368 optimal weight: 4.9990 chunk 303 optimal weight: 3.9990 chunk 338 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 273 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 ASN ** 4 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 ASN ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN N 95CASN Q 6 GLN ** l 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 95CASN ** 2 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 33045 Z= 0.413 Angle : 0.793 14.789 44907 Z= 0.383 Chirality : 0.048 0.240 5442 Planarity : 0.005 0.053 5472 Dihedral : 12.021 72.839 7435 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.33 % Allowed : 9.76 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.29 (0.13), residues: 3777 helix: -0.86 (0.24), residues: 429 sheet: -1.32 (0.14), residues: 1269 loop : -1.79 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP q 100F HIS 0.007 0.002 HIS 3 35 PHE 0.021 0.002 PHE L 67 TYR 0.016 0.002 TYR c 638 ARG 0.012 0.001 ARG Q 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 260 time to evaluate : 3.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 62 LYS cc_start: 0.9293 (tppt) cc_final: 0.8961 (ttpp) REVERT: 5 100 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8832 (mmm) REVERT: 7 1 GLU cc_start: 0.8886 (pt0) cc_final: 0.8218 (mt-10) REVERT: 7 33 MET cc_start: 0.8803 (tpp) cc_final: 0.8529 (tpp) REVERT: 7 60 ASP cc_start: 0.8678 (m-30) cc_final: 0.8278 (t0) REVERT: 7 81 GLU cc_start: 0.8540 (tp30) cc_final: 0.8330 (tp30) REVERT: 8 28 ASN cc_start: 0.8968 (t0) cc_final: 0.7998 (t0) REVERT: 8 31 ASP cc_start: 0.8314 (m-30) cc_final: 0.7461 (m-30) REVERT: 8 80 MET cc_start: 0.8653 (tmm) cc_final: 0.8424 (tmm) REVERT: 8 100 ASP cc_start: 0.7983 (p0) cc_final: 0.7774 (p0) REVERT: H 66 LYS cc_start: 0.7363 (ptmt) cc_final: 0.6901 (tptp) REVERT: H 85 GLU cc_start: 0.9415 (mt-10) cc_final: 0.9175 (tp30) REVERT: H 99 TRP cc_start: 0.8232 (m100) cc_final: 0.7710 (m100) REVERT: H 100 PHE cc_start: 0.7208 (m-80) cc_final: 0.6519 (m-80) REVERT: L 59 ARG cc_start: 0.7777 (mpt-90) cc_final: 0.7520 (mpt-90) REVERT: L 107 THR cc_start: 0.4710 (p) cc_final: 0.4290 (p) REVERT: M 100 MET cc_start: 0.9146 (mmm) cc_final: 0.8644 (mmm) REVERT: N 31 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8738 (ttm110) REVERT: R 81 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8870 (tp30) REVERT: h 62 LYS cc_start: 0.9242 (tppt) cc_final: 0.8884 (ttpp) REVERT: h 86 ASP cc_start: 0.7261 (m-30) cc_final: 0.7054 (m-30) REVERT: h 98 TYR cc_start: 0.8678 (m-80) cc_final: 0.7963 (m-80) REVERT: h 100 PHE cc_start: 0.7191 (m-80) cc_final: 0.6480 (m-80) REVERT: q 28 ASN cc_start: 0.9033 (t0) cc_final: 0.8087 (t0) REVERT: q 31 ASP cc_start: 0.8203 (m-30) cc_final: 0.7344 (m-30) REVERT: q 73 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8579 (tp) REVERT: q 76 ASP cc_start: 0.9090 (t0) cc_final: 0.8830 (t0) REVERT: q 80 MET cc_start: 0.8740 (tmm) cc_final: 0.8414 (tmm) REVERT: q 99 ASP cc_start: 0.8430 (p0) cc_final: 0.8198 (p0) REVERT: q 100 TYR cc_start: 0.9116 (m-80) cc_final: 0.8763 (m-10) REVERT: q 100 ASP cc_start: 0.8106 (p0) cc_final: 0.7672 (p0) REVERT: r 1 GLU cc_start: 0.8979 (pt0) cc_final: 0.8452 (mt-10) REVERT: 2 100 MET cc_start: 0.9033 (ptp) cc_final: 0.8733 (ptp) REVERT: 2 265 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8561 (pp) REVERT: A 530 MET cc_start: 0.8066 (ptp) cc_final: 0.7808 (ptp) REVERT: A 652 GLN cc_start: 0.9329 (tt0) cc_final: 0.8751 (tp-100) REVERT: d 104 MET cc_start: 0.8710 (tmm) cc_final: 0.8353 (tmm) outliers start: 111 outliers final: 60 residues processed: 338 average time/residue: 0.4316 time to fit residues: 236.0136 Evaluate side-chains 289 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 225 time to evaluate : 3.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 98 TYR Chi-restraints excluded: chain 4 residue 52 LEU Chi-restraints excluded: chain 4 residue 58 ASN Chi-restraints excluded: chain 4 residue 77 THR Chi-restraints excluded: chain 4 residue 102 THR Chi-restraints excluded: chain 4 residue 108 LYS Chi-restraints excluded: chain 5 residue 100 GLU Chi-restraints excluded: chain 5 residue 100 MET Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 6 residue 25 GLU Chi-restraints excluded: chain 6 residue 90 ILE Chi-restraints excluded: chain 7 residue 56 SER Chi-restraints excluded: chain 7 residue 78 LEU Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain 8 residue 42 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 43 HIS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 99 ASP Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain m residue 100 MET Chi-restraints excluded: chain n residue 90 ILE Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 73 LEU Chi-restraints excluded: chain r residue 56 SER Chi-restraints excluded: chain r residue 78 LEU Chi-restraints excluded: chain r residue 100 LEU Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 265 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 494 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain c residue 536 THR Chi-restraints excluded: chain c residue 595 ILE Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 265 LEU Chi-restraints excluded: chain d residue 373 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 0.8980 chunk 256 optimal weight: 9.9990 chunk 177 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 229 optimal weight: 0.9990 chunk 342 optimal weight: 3.9990 chunk 362 optimal weight: 0.9990 chunk 178 optimal weight: 0.6980 chunk 324 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 ASN ** 4 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 3 GLN 8 6 GLN 8 101 GLN C 302 ASN ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 6 GLN q 101 GLN ** r 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 302 ASN c 577 GLN d 302 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33045 Z= 0.176 Angle : 0.660 16.241 44907 Z= 0.316 Chirality : 0.046 0.238 5442 Planarity : 0.004 0.054 5472 Dihedral : 10.268 70.073 7435 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.55 % Allowed : 11.08 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.87 (0.13), residues: 3777 helix: -0.42 (0.24), residues: 429 sheet: -0.94 (0.14), residues: 1260 loop : -1.61 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP d 427 HIS 0.004 0.001 HIS 2 374 PHE 0.021 0.001 PHE 3 100A TYR 0.018 0.001 TYR 3 79 ARG 0.003 0.000 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 286 time to evaluate : 3.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 62 LYS cc_start: 0.9291 (tppt) cc_final: 0.8992 (ttpp) REVERT: 3 64 ARG cc_start: 0.8653 (tpp-160) cc_final: 0.8218 (mtp85) REVERT: 3 85 GLU cc_start: 0.8393 (tp30) cc_final: 0.8075 (mp0) REVERT: 5 100 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8867 (mmm) REVERT: 7 1 GLU cc_start: 0.8864 (pt0) cc_final: 0.8213 (mt-10) REVERT: 7 33 MET cc_start: 0.8764 (tpp) cc_final: 0.8518 (tpp) REVERT: 7 60 ASP cc_start: 0.8686 (m-30) cc_final: 0.8345 (t0) REVERT: 7 81 GLU cc_start: 0.8448 (tp30) cc_final: 0.8174 (tp30) REVERT: 8 28 ASN cc_start: 0.8907 (t0) cc_final: 0.7915 (t0) REVERT: 8 31 ASP cc_start: 0.8272 (m-30) cc_final: 0.7459 (m-30) REVERT: 8 80 MET cc_start: 0.8549 (tmm) cc_final: 0.8292 (tmm) REVERT: C 95 MET cc_start: 0.8829 (ppp) cc_final: 0.8346 (ppp) REVERT: C 104 MET cc_start: 0.8574 (tmm) cc_final: 0.8359 (tmm) REVERT: D 601 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7481 (ttpt) REVERT: D 622 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.8851 (mm) REVERT: H 33 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7311 (tp30) REVERT: H 62 LYS cc_start: 0.9262 (tppt) cc_final: 0.9006 (ttpp) REVERT: H 66 LYS cc_start: 0.7352 (ptmt) cc_final: 0.6795 (tptp) REVERT: H 100 PHE cc_start: 0.7155 (m-80) cc_final: 0.6175 (m-80) REVERT: L 107 THR cc_start: 0.3839 (p) cc_final: 0.3440 (p) REVERT: M 100 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8698 (mmm) REVERT: N 90 ILE cc_start: 0.9174 (pt) cc_final: 0.8971 (mt) REVERT: Q 69 MET cc_start: 0.8855 (mtt) cc_final: 0.8559 (mtm) REVERT: Q 76 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8124 (t0) REVERT: Q 100 TYR cc_start: 0.9038 (m-80) cc_final: 0.8630 (m-10) REVERT: R 81 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8847 (tp30) REVERT: h 62 LYS cc_start: 0.9276 (tppt) cc_final: 0.8820 (tmtt) REVERT: h 86 ASP cc_start: 0.7317 (m-30) cc_final: 0.7107 (m-30) REVERT: h 94 ARG cc_start: 0.6279 (OUTLIER) cc_final: 0.5965 (tmm160) REVERT: h 98 TYR cc_start: 0.8681 (m-80) cc_final: 0.7935 (m-80) REVERT: h 100 PHE cc_start: 0.6864 (m-80) cc_final: 0.6652 (m-80) REVERT: q 28 ASN cc_start: 0.8962 (t0) cc_final: 0.7986 (t0) REVERT: q 31 ASP cc_start: 0.8190 (m-30) cc_final: 0.7332 (m-30) REVERT: q 76 ASP cc_start: 0.9001 (t0) cc_final: 0.8786 (t0) REVERT: q 80 MET cc_start: 0.8661 (tmm) cc_final: 0.8419 (tmm) REVERT: q 100 TYR cc_start: 0.9070 (m-80) cc_final: 0.8777 (m-10) REVERT: q 100 ASP cc_start: 0.7964 (p0) cc_final: 0.7503 (p0) REVERT: r 1 GLU cc_start: 0.8988 (pt0) cc_final: 0.8465 (mt-10) REVERT: 2 95 MET cc_start: 0.8753 (ptm) cc_final: 0.8245 (ppp) REVERT: 2 104 MET cc_start: 0.8451 (tmm) cc_final: 0.7992 (tmm) REVERT: A 530 MET cc_start: 0.7845 (ptp) cc_final: 0.7561 (ptp) REVERT: A 601 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7685 (ttpt) REVERT: A 652 GLN cc_start: 0.9285 (tt0) cc_final: 0.8686 (tp-100) REVERT: A 654 GLU cc_start: 0.8861 (tp30) cc_final: 0.8655 (tp30) REVERT: c 601 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7715 (ttpt) REVERT: c 652 GLN cc_start: 0.9296 (tt0) cc_final: 0.8772 (tp-100) REVERT: d 95 MET cc_start: 0.8805 (ppp) cc_final: 0.8331 (ppp) REVERT: d 100 MET cc_start: 0.9100 (ppp) cc_final: 0.8833 (ppp) outliers start: 85 outliers final: 55 residues processed: 349 average time/residue: 0.4411 time to fit residues: 247.5291 Evaluate side-chains 297 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 233 time to evaluate : 3.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 33 GLU Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 98 TYR Chi-restraints excluded: chain 4 residue 35 ASN Chi-restraints excluded: chain 4 residue 51 LEU Chi-restraints excluded: chain 4 residue 52 LEU Chi-restraints excluded: chain 4 residue 58 ASN Chi-restraints excluded: chain 4 residue 102 THR Chi-restraints excluded: chain 5 residue 100 MET Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 6 residue 90 ILE Chi-restraints excluded: chain 7 residue 78 LEU Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain 8 residue 99 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 43 HIS Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 99 ASP Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 94 ARG Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain m residue 100 MET Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain r residue 56 SER Chi-restraints excluded: chain r residue 78 LEU Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain 2 residue 494 LEU Chi-restraints excluded: chain 2 residue 496 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain c residue 536 THR Chi-restraints excluded: chain c residue 601 LYS Chi-restraints excluded: chain c residue 608 VAL Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 373 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 269 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 309 optimal weight: 4.9990 chunk 250 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 185 optimal weight: 10.0000 chunk 325 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 ASN ** q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 33045 Z= 0.440 Angle : 0.797 17.469 44907 Z= 0.382 Chirality : 0.048 0.254 5442 Planarity : 0.004 0.047 5472 Dihedral : 9.938 68.300 7435 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 3.75 % Allowed : 11.56 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.97 (0.13), residues: 3777 helix: -0.49 (0.25), residues: 432 sheet: -1.17 (0.14), residues: 1254 loop : -1.56 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 5 34 HIS 0.008 0.002 HIS C 330 PHE 0.017 0.002 PHE C 53 TYR 0.019 0.002 TYR 3 100 ARG 0.008 0.001 ARG 8 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 241 time to evaluate : 4.096 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: 3 62 LYS cc_start: 0.9253 (tppt) cc_final: 0.8924 (ttpp) REVERT: 3 85 GLU cc_start: 0.8370 (tp30) cc_final: 0.8125 (tp30) REVERT: 5 100 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8895 (mmm) REVERT: 7 1 GLU cc_start: 0.8999 (pt0) cc_final: 0.8294 (mt-10) REVERT: 7 81 GLU cc_start: 0.8518 (tp30) cc_final: 0.8255 (tp30) REVERT: 8 28 ASN cc_start: 0.8935 (t0) cc_final: 0.8515 (t0) REVERT: C 49 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7734 (mm-30) REVERT: C 95 MET cc_start: 0.9060 (ppp) cc_final: 0.8511 (ppp) REVERT: C 104 MET cc_start: 0.8710 (tmm) cc_final: 0.8179 (tmm) REVERT: D 601 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7560 (ttpt) REVERT: D 622 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.8951 (mm) REVERT: H 63 PHE cc_start: 0.7426 (m-80) cc_final: 0.6414 (m-80) REVERT: H 66 LYS cc_start: 0.7712 (ptmt) cc_final: 0.7186 (tptp) REVERT: H 85 GLU cc_start: 0.9419 (mt-10) cc_final: 0.9175 (tp30) REVERT: H 99 TRP cc_start: 0.8285 (m100) cc_final: 0.7787 (m100) REVERT: H 100 PHE cc_start: 0.7287 (m-80) cc_final: 0.6593 (m-80) REVERT: L 107 THR cc_start: 0.3869 (p) cc_final: 0.3496 (p) REVERT: M 100 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8722 (mmm) REVERT: Q 76 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.7994 (t0) REVERT: R 81 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8820 (tp30) REVERT: h 62 LYS cc_start: 0.9277 (tppt) cc_final: 0.8945 (ttpp) REVERT: h 86 ASP cc_start: 0.7467 (m-30) cc_final: 0.7142 (m-30) REVERT: h 100 PHE cc_start: 0.7068 (m-80) cc_final: 0.6823 (m-80) REVERT: q 28 ASN cc_start: 0.9067 (t0) cc_final: 0.8181 (t0) REVERT: q 31 ASP cc_start: 0.8277 (m-30) cc_final: 0.7491 (m-30) REVERT: q 73 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8487 (tp) REVERT: q 76 ASP cc_start: 0.9062 (t0) cc_final: 0.8750 (t0) REVERT: q 100 ASP cc_start: 0.8183 (p0) cc_final: 0.7733 (p0) REVERT: r 1 GLU cc_start: 0.9030 (pt0) cc_final: 0.8494 (mt-10) REVERT: r 81 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8711 (mp0) REVERT: 2 95 MET cc_start: 0.8988 (ptm) cc_final: 0.8169 (ppp) REVERT: 2 104 MET cc_start: 0.8675 (tmm) cc_final: 0.8242 (tmm) REVERT: 2 271 MET cc_start: 0.8100 (mmt) cc_final: 0.7635 (mmm) REVERT: A 530 MET cc_start: 0.8061 (ptp) cc_final: 0.7832 (ptp) REVERT: A 622 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8926 (mm) REVERT: A 652 GLN cc_start: 0.9331 (tt0) cc_final: 0.8740 (tp-100) REVERT: d 100 MET cc_start: 0.9118 (ppp) cc_final: 0.8897 (ppp) REVERT: d 452 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8737 (mm) outliers start: 125 outliers final: 81 residues processed: 333 average time/residue: 0.4434 time to fit residues: 237.6345 Evaluate side-chains 315 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 225 time to evaluate : 3.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 98 TYR Chi-restraints excluded: chain 4 residue 52 LEU Chi-restraints excluded: chain 4 residue 58 ASN Chi-restraints excluded: chain 4 residue 77 THR Chi-restraints excluded: chain 4 residue 102 THR Chi-restraints excluded: chain 5 residue 100 MET Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 6 residue 25 GLU Chi-restraints excluded: chain 6 residue 90 ILE Chi-restraints excluded: chain 7 residue 56 SER Chi-restraints excluded: chain 7 residue 78 LEU Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 43 HIS Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain m residue 100 MET Chi-restraints excluded: chain n residue 90 ILE Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 73 LEU Chi-restraints excluded: chain r residue 56 SER Chi-restraints excluded: chain r residue 78 LEU Chi-restraints excluded: chain r residue 100 LEU Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 194 ILE Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain 2 residue 494 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 595 ILE Chi-restraints excluded: chain c residue 608 VAL Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 255 VAL Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 285 LEU Chi-restraints excluded: chain d residue 373 THR Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 452 LEU Chi-restraints excluded: chain d residue 496 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 1.9990 chunk 326 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 212 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 362 optimal weight: 5.9990 chunk 301 optimal weight: 0.9990 chunk 167 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 35 ASN 4 43 GLN 5 32 ASN D 577 GLN ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN ** r 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 577 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 33045 Z= 0.270 Angle : 0.692 16.190 44907 Z= 0.333 Chirality : 0.046 0.258 5442 Planarity : 0.004 0.050 5472 Dihedral : 9.263 66.803 7435 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.02 % Favored : 92.96 % Rotamer: Outliers : 3.36 % Allowed : 12.61 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.76 (0.13), residues: 3777 helix: -0.27 (0.25), residues: 432 sheet: -0.98 (0.14), residues: 1236 loop : -1.46 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP Q 100F HIS 0.004 0.001 HIS 3 35 PHE 0.014 0.001 PHE 2 288 TYR 0.017 0.001 TYR l 91 ARG 0.004 0.000 ARG N 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 259 time to evaluate : 3.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 62 LYS cc_start: 0.9265 (tppt) cc_final: 0.8884 (ttpp) REVERT: 3 85 GLU cc_start: 0.8241 (tp30) cc_final: 0.7969 (tp30) REVERT: 5 100 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8898 (mmm) REVERT: 7 1 GLU cc_start: 0.8999 (pt0) cc_final: 0.8296 (mt-10) REVERT: 7 33 MET cc_start: 0.8623 (tpp) cc_final: 0.8328 (tpp) REVERT: 7 60 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8310 (t0) REVERT: 7 77 LYS cc_start: 0.9163 (ttpp) cc_final: 0.8956 (ttpp) REVERT: 7 81 GLU cc_start: 0.8476 (tp30) cc_final: 0.8196 (tp30) REVERT: 8 28 ASN cc_start: 0.8967 (t0) cc_final: 0.8603 (t0) REVERT: C 95 MET cc_start: 0.9122 (ppp) cc_final: 0.8446 (ppp) REVERT: C 104 MET cc_start: 0.8690 (tmm) cc_final: 0.8052 (tmm) REVERT: C 271 MET cc_start: 0.8273 (mmm) cc_final: 0.7908 (mmt) REVERT: C 425 ASN cc_start: 0.8616 (t0) cc_final: 0.8324 (t0) REVERT: D 530 MET cc_start: 0.7733 (ptp) cc_final: 0.7169 (mpp) REVERT: D 601 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7661 (ttpt) REVERT: H 63 PHE cc_start: 0.7294 (m-80) cc_final: 0.7037 (m-80) REVERT: H 99 TRP cc_start: 0.8179 (m100) cc_final: 0.7627 (m100) REVERT: H 100 PHE cc_start: 0.7209 (m-80) cc_final: 0.6467 (m-80) REVERT: M 100 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8765 (mmm) REVERT: Q 69 MET cc_start: 0.8939 (mtt) cc_final: 0.8638 (mtm) REVERT: Q 76 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.7892 (t0) REVERT: Q 100 ASP cc_start: 0.7669 (p0) cc_final: 0.7251 (p0) REVERT: R 81 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8740 (tp30) REVERT: h 62 LYS cc_start: 0.9321 (tppt) cc_final: 0.8999 (ttpp) REVERT: h 86 ASP cc_start: 0.7366 (m-30) cc_final: 0.7078 (m-30) REVERT: h 100 PHE cc_start: 0.6905 (m-80) cc_final: 0.6291 (m-80) REVERT: q 28 ASN cc_start: 0.9034 (t0) cc_final: 0.8652 (t0) REVERT: q 76 ASP cc_start: 0.9076 (t0) cc_final: 0.8761 (t0) REVERT: q 100 ASP cc_start: 0.7993 (p0) cc_final: 0.7507 (p0) REVERT: r 1 GLU cc_start: 0.9085 (pt0) cc_final: 0.8502 (mt-10) REVERT: r 81 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8736 (mp0) REVERT: 2 95 MET cc_start: 0.8914 (ptm) cc_final: 0.8184 (ppp) REVERT: 2 104 MET cc_start: 0.8649 (tmm) cc_final: 0.8249 (tmm) REVERT: 2 125 LEU cc_start: 0.9385 (tt) cc_final: 0.9137 (tt) REVERT: 2 271 MET cc_start: 0.8091 (mmt) cc_final: 0.7612 (mmm) REVERT: A 601 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7835 (ttpt) REVERT: A 622 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8876 (mm) REVERT: A 652 GLN cc_start: 0.9324 (tt0) cc_final: 0.8722 (tp-100) REVERT: A 654 GLU cc_start: 0.9024 (tp30) cc_final: 0.8669 (tp30) REVERT: c 571 TRP cc_start: 0.8413 (m-10) cc_final: 0.8121 (m-10) REVERT: c 630 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8616 (pt0) REVERT: d 95 MET cc_start: 0.9161 (ppp) cc_final: 0.8532 (ppp) REVERT: d 452 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8759 (mm) outliers start: 112 outliers final: 75 residues processed: 337 average time/residue: 0.4491 time to fit residues: 245.4720 Evaluate side-chains 317 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 233 time to evaluate : 3.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 95 LEU Chi-restraints excluded: chain 3 residue 98 TYR Chi-restraints excluded: chain 4 residue 35 ASN Chi-restraints excluded: chain 4 residue 52 LEU Chi-restraints excluded: chain 4 residue 58 ASN Chi-restraints excluded: chain 4 residue 77 THR Chi-restraints excluded: chain 4 residue 102 THR Chi-restraints excluded: chain 5 residue 100 GLU Chi-restraints excluded: chain 5 residue 100 MET Chi-restraints excluded: chain 6 residue 90 ILE Chi-restraints excluded: chain 7 residue 56 SER Chi-restraints excluded: chain 7 residue 60 ASP Chi-restraints excluded: chain 7 residue 78 LEU Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 43 HIS Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 98 TYR Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain m residue 100 MET Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain r residue 56 SER Chi-restraints excluded: chain r residue 78 LEU Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain 2 residue 494 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain c residue 536 THR Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 601 LYS Chi-restraints excluded: chain c residue 608 VAL Chi-restraints excluded: chain c residue 630 GLN Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 122 LEU Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 373 THR Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 452 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 264 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 chunk 305 optimal weight: 0.9980 chunk 202 optimal weight: 9.9990 chunk 361 optimal weight: 7.9990 chunk 226 optimal weight: 20.0000 chunk 220 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 ASN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 293 GLN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 33045 Z= 0.399 Angle : 0.761 14.326 44907 Z= 0.365 Chirality : 0.047 0.265 5442 Planarity : 0.004 0.048 5472 Dihedral : 9.157 65.702 7435 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.87 % Favored : 91.10 % Rotamer: Outliers : 3.84 % Allowed : 12.73 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.83 (0.13), residues: 3777 helix: -0.46 (0.25), residues: 450 sheet: -1.00 (0.14), residues: 1254 loop : -1.50 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP q 100F HIS 0.007 0.001 HIS C 330 PHE 0.015 0.002 PHE d 288 TYR 0.021 0.002 TYR R 49 ARG 0.013 0.001 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 244 time to evaluate : 3.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 62 LYS cc_start: 0.9239 (tppt) cc_final: 0.8868 (ttpp) REVERT: 5 100 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.8880 (mmm) REVERT: 7 1 GLU cc_start: 0.9165 (pt0) cc_final: 0.8286 (mt-10) REVERT: 7 33 MET cc_start: 0.8678 (tpp) cc_final: 0.8408 (tpp) REVERT: 7 60 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8333 (t0) REVERT: 7 81 GLU cc_start: 0.8545 (tp30) cc_final: 0.8266 (tp30) REVERT: 8 28 ASN cc_start: 0.9047 (t0) cc_final: 0.8635 (t0) REVERT: 8 100 ASP cc_start: 0.7839 (p0) cc_final: 0.7565 (p0) REVERT: C 95 MET cc_start: 0.9152 (ppp) cc_final: 0.8527 (ppp) REVERT: C 104 MET cc_start: 0.8668 (tmm) cc_final: 0.8100 (tmm) REVERT: D 530 MET cc_start: 0.7868 (ptp) cc_final: 0.7365 (mpp) REVERT: D 601 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7701 (ttpt) REVERT: H 63 PHE cc_start: 0.7408 (m-80) cc_final: 0.7167 (m-80) REVERT: H 99 TRP cc_start: 0.8142 (m100) cc_final: 0.7580 (m100) REVERT: H 100 PHE cc_start: 0.7303 (m-80) cc_final: 0.6597 (m-80) REVERT: M 100 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.8751 (mmm) REVERT: Q 71 ARG cc_start: 0.9494 (OUTLIER) cc_final: 0.8499 (pmt-80) REVERT: Q 76 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8072 (t0) REVERT: Q 100 ASP cc_start: 0.8037 (p0) cc_final: 0.7615 (p0) REVERT: R 39 ARG cc_start: 0.8305 (mtm-85) cc_final: 0.7797 (mtp85) REVERT: R 81 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8792 (tp30) REVERT: h 62 LYS cc_start: 0.9318 (tppt) cc_final: 0.9009 (ttpp) REVERT: h 86 ASP cc_start: 0.7477 (m-30) cc_final: 0.7144 (m-30) REVERT: h 100 PHE cc_start: 0.7151 (m-80) cc_final: 0.6755 (m-80) REVERT: m 77 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7524 (tt) REVERT: q 28 ASN cc_start: 0.9058 (t0) cc_final: 0.8674 (t0) REVERT: q 71 ARG cc_start: 0.9521 (OUTLIER) cc_final: 0.9002 (pmt-80) REVERT: q 76 ASP cc_start: 0.9096 (t0) cc_final: 0.8784 (t70) REVERT: q 100 ASP cc_start: 0.8189 (p0) cc_final: 0.7751 (p0) REVERT: r 1 GLU cc_start: 0.9145 (pt0) cc_final: 0.8478 (mt-10) REVERT: 2 95 MET cc_start: 0.8974 (ptm) cc_final: 0.7988 (ppp) REVERT: 2 104 MET cc_start: 0.8755 (tmm) cc_final: 0.8319 (tmm) REVERT: 2 125 LEU cc_start: 0.9429 (tt) cc_final: 0.9138 (tt) REVERT: 2 271 MET cc_start: 0.8148 (mmt) cc_final: 0.7883 (mmm) REVERT: A 601 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7959 (ttpt) REVERT: A 622 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8913 (mm) REVERT: A 654 GLU cc_start: 0.9096 (tp30) cc_final: 0.8752 (tp30) REVERT: c 571 TRP cc_start: 0.8480 (m-10) cc_final: 0.8172 (m-10) REVERT: d 95 MET cc_start: 0.9239 (ppp) cc_final: 0.8635 (ppp) REVERT: d 271 MET cc_start: 0.8116 (mmt) cc_final: 0.7780 (mmm) REVERT: d 452 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8759 (mm) outliers start: 128 outliers final: 96 residues processed: 334 average time/residue: 0.4532 time to fit residues: 245.4876 Evaluate side-chains 338 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 231 time to evaluate : 3.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 53 LYS Chi-restraints excluded: chain 3 residue 98 TYR Chi-restraints excluded: chain 4 residue 35 ASN Chi-restraints excluded: chain 4 residue 52 LEU Chi-restraints excluded: chain 4 residue 58 ASN Chi-restraints excluded: chain 4 residue 102 THR Chi-restraints excluded: chain 5 residue 100 MET Chi-restraints excluded: chain 6 residue 25 GLU Chi-restraints excluded: chain 6 residue 90 ILE Chi-restraints excluded: chain 7 residue 56 SER Chi-restraints excluded: chain 7 residue 60 ASP Chi-restraints excluded: chain 7 residue 78 LEU Chi-restraints excluded: chain 7 residue 100 LEU Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain 8 residue 34 ILE Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 100 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 43 HIS Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 53 LYS Chi-restraints excluded: chain h residue 98 TYR Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain m residue 100 MET Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 71 ARG Chi-restraints excluded: chain r residue 51 THR Chi-restraints excluded: chain r residue 56 SER Chi-restraints excluded: chain r residue 78 LEU Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain 2 residue 494 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 595 ILE Chi-restraints excluded: chain c residue 601 LYS Chi-restraints excluded: chain c residue 608 VAL Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 122 LEU Chi-restraints excluded: chain d residue 215 ILE Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 285 LEU Chi-restraints excluded: chain d residue 373 THR Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 452 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 5.9990 chunk 144 optimal weight: 30.0000 chunk 215 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 229 optimal weight: 0.9980 chunk 246 optimal weight: 7.9990 chunk 178 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 284 optimal weight: 4.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 ASN ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 33045 Z= 0.286 Angle : 0.697 16.515 44907 Z= 0.333 Chirality : 0.046 0.266 5442 Planarity : 0.004 0.048 5472 Dihedral : 8.775 64.516 7435 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.54 % Allowed : 13.45 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.67 (0.14), residues: 3777 helix: -0.24 (0.25), residues: 432 sheet: -0.91 (0.14), residues: 1275 loop : -1.39 (0.14), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP d 427 HIS 0.004 0.001 HIS C 330 PHE 0.016 0.001 PHE d 288 TYR 0.019 0.001 TYR q 100 ARG 0.005 0.000 ARG Q 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 241 time to evaluate : 3.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 85 GLU cc_start: 0.8243 (tp30) cc_final: 0.8028 (tp30) REVERT: 5 100 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.8927 (mmm) REVERT: 7 1 GLU cc_start: 0.9168 (pt0) cc_final: 0.8277 (mt-10) REVERT: 7 33 MET cc_start: 0.8678 (tpp) cc_final: 0.7883 (tpp) REVERT: 7 60 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8358 (t0) REVERT: 7 81 GLU cc_start: 0.8475 (tp30) cc_final: 0.8188 (tp30) REVERT: 8 28 ASN cc_start: 0.9010 (t0) cc_final: 0.8583 (t0) REVERT: 8 71 ARG cc_start: 0.9421 (OUTLIER) cc_final: 0.7025 (pmt-80) REVERT: 8 99 ASP cc_start: 0.8743 (p0) cc_final: 0.8542 (p0) REVERT: C 95 MET cc_start: 0.9146 (ppp) cc_final: 0.8501 (ppp) REVERT: C 104 MET cc_start: 0.8646 (tmm) cc_final: 0.8001 (tmm) REVERT: C 271 MET cc_start: 0.8293 (mmm) cc_final: 0.7930 (mmt) REVERT: C 425 ASN cc_start: 0.8617 (t0) cc_final: 0.8318 (t0) REVERT: D 530 MET cc_start: 0.7730 (ptp) cc_final: 0.7344 (mpp) REVERT: D 601 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7680 (ttpt) REVERT: H 63 PHE cc_start: 0.7420 (m-80) cc_final: 0.6452 (m-80) REVERT: H 66 LYS cc_start: 0.7756 (ptmt) cc_final: 0.7279 (tptp) REVERT: H 100 PHE cc_start: 0.7221 (m-80) cc_final: 0.6424 (m-80) REVERT: M 77 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7988 (tt) REVERT: M 100 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8750 (mmm) REVERT: Q 71 ARG cc_start: 0.9487 (OUTLIER) cc_final: 0.8405 (pmt-80) REVERT: Q 76 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8008 (t0) REVERT: Q 100 ASP cc_start: 0.7564 (p0) cc_final: 0.7298 (p0) REVERT: R 81 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8676 (tp30) REVERT: h 62 LYS cc_start: 0.9329 (tppt) cc_final: 0.9009 (ttpp) REVERT: h 86 ASP cc_start: 0.7444 (m-30) cc_final: 0.7120 (m-30) REVERT: h 100 PHE cc_start: 0.7053 (m-80) cc_final: 0.6440 (m-80) REVERT: q 28 ASN cc_start: 0.9044 (t0) cc_final: 0.8664 (t0) REVERT: q 73 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8548 (tp) REVERT: q 76 ASP cc_start: 0.9068 (t0) cc_final: 0.8780 (t70) REVERT: q 100 ASP cc_start: 0.8091 (p0) cc_final: 0.7594 (p0) REVERT: r 1 GLU cc_start: 0.9119 (pt0) cc_final: 0.8492 (mt-10) REVERT: 2 95 MET cc_start: 0.8922 (ptm) cc_final: 0.8021 (ppp) REVERT: 2 125 LEU cc_start: 0.9392 (tt) cc_final: 0.9118 (tt) REVERT: 2 271 MET cc_start: 0.8174 (mmt) cc_final: 0.7871 (mmm) REVERT: A 601 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7850 (ttpt) REVERT: A 654 GLU cc_start: 0.9017 (tp30) cc_final: 0.8668 (tp30) REVERT: c 571 TRP cc_start: 0.8409 (m-10) cc_final: 0.8190 (m-10) REVERT: c 626 MET cc_start: 0.8243 (tpp) cc_final: 0.7124 (tpp) REVERT: c 630 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8771 (pt0) REVERT: d 95 MET cc_start: 0.9202 (ppp) cc_final: 0.8558 (ppp) REVERT: d 271 MET cc_start: 0.8183 (mmt) cc_final: 0.7790 (mmm) REVERT: d 452 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8712 (mm) REVERT: d 475 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8451 (mmm) outliers start: 118 outliers final: 90 residues processed: 323 average time/residue: 0.4332 time to fit residues: 226.3853 Evaluate side-chains 332 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 229 time to evaluate : 3.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 53 LYS Chi-restraints excluded: chain 3 residue 98 TYR Chi-restraints excluded: chain 4 residue 35 ASN Chi-restraints excluded: chain 4 residue 52 LEU Chi-restraints excluded: chain 4 residue 58 ASN Chi-restraints excluded: chain 4 residue 102 THR Chi-restraints excluded: chain 4 residue 107 THR Chi-restraints excluded: chain 5 residue 100 GLU Chi-restraints excluded: chain 5 residue 100 MET Chi-restraints excluded: chain 6 residue 25 GLU Chi-restraints excluded: chain 6 residue 90 ILE Chi-restraints excluded: chain 7 residue 56 SER Chi-restraints excluded: chain 7 residue 60 ASP Chi-restraints excluded: chain 7 residue 78 LEU Chi-restraints excluded: chain 7 residue 100 LEU Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain 8 residue 34 ILE Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 71 ARG Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 43 HIS Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 98 CYS Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 53 LYS Chi-restraints excluded: chain h residue 98 TYR Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain m residue 100 MET Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 90 ILE Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 73 LEU Chi-restraints excluded: chain r residue 51 THR Chi-restraints excluded: chain r residue 56 SER Chi-restraints excluded: chain r residue 78 LEU Chi-restraints excluded: chain r residue 81 GLU Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 113 ASP Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain 2 residue 494 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 601 LYS Chi-restraints excluded: chain c residue 608 VAL Chi-restraints excluded: chain c residue 630 GLN Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 122 LEU Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 255 VAL Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 373 THR Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 452 LEU Chi-restraints excluded: chain d residue 475 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 6.9990 chunk 346 optimal weight: 8.9990 chunk 315 optimal weight: 6.9990 chunk 336 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 146 optimal weight: 30.0000 chunk 264 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 304 optimal weight: 9.9990 chunk 318 optimal weight: 4.9990 chunk 335 optimal weight: 0.0040 overall best weight: 3.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 ASN D 577 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 33045 Z= 0.364 Angle : 0.739 15.542 44907 Z= 0.353 Chirality : 0.047 0.272 5442 Planarity : 0.004 0.048 5472 Dihedral : 8.728 63.572 7435 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 3.69 % Allowed : 13.33 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.68 (0.14), residues: 3777 helix: -0.31 (0.25), residues: 450 sheet: -0.92 (0.14), residues: 1260 loop : -1.39 (0.14), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP d 427 HIS 0.006 0.001 HIS C 330 PHE 0.018 0.002 PHE 2 53 TYR 0.015 0.001 TYR 4 54 ARG 0.014 0.000 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 231 time to evaluate : 4.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 85 GLU cc_start: 0.8277 (tp30) cc_final: 0.8008 (tp30) REVERT: 5 100 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.8898 (mmm) REVERT: 7 60 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8368 (t0) REVERT: 7 81 GLU cc_start: 0.8488 (tp30) cc_final: 0.8208 (tp30) REVERT: 8 28 ASN cc_start: 0.9032 (t0) cc_final: 0.8599 (t0) REVERT: 8 71 ARG cc_start: 0.9416 (OUTLIER) cc_final: 0.7072 (pmt-80) REVERT: C 95 MET cc_start: 0.9149 (ppp) cc_final: 0.8514 (ppp) REVERT: C 104 MET cc_start: 0.8675 (tmm) cc_final: 0.8021 (tmm) REVERT: C 271 MET cc_start: 0.8324 (mmm) cc_final: 0.7948 (mmt) REVERT: C 425 ASN cc_start: 0.8595 (t0) cc_final: 0.8343 (t0) REVERT: D 530 MET cc_start: 0.7695 (ptp) cc_final: 0.7319 (mpp) REVERT: D 601 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7779 (ttpt) REVERT: H 63 PHE cc_start: 0.7491 (m-80) cc_final: 0.6545 (m-80) REVERT: H 66 LYS cc_start: 0.7829 (ptmt) cc_final: 0.7391 (tptp) REVERT: H 100 PHE cc_start: 0.7297 (m-80) cc_final: 0.6513 (m-80) REVERT: M 77 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7993 (tt) REVERT: M 100 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.8708 (mmm) REVERT: Q 71 ARG cc_start: 0.9489 (OUTLIER) cc_final: 0.8414 (pmt-80) REVERT: Q 76 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8066 (t0) REVERT: Q 100 ASP cc_start: 0.7818 (p0) cc_final: 0.7558 (p0) REVERT: h 62 LYS cc_start: 0.9343 (tppt) cc_final: 0.9029 (ttpp) REVERT: h 86 ASP cc_start: 0.7430 (m-30) cc_final: 0.7109 (m-30) REVERT: h 100 PHE cc_start: 0.7147 (m-80) cc_final: 0.6485 (m-80) REVERT: m 77 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7507 (tt) REVERT: q 28 ASN cc_start: 0.9055 (t0) cc_final: 0.8664 (t0) REVERT: q 71 ARG cc_start: 0.9518 (OUTLIER) cc_final: 0.8988 (pmt-80) REVERT: q 73 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8537 (tp) REVERT: q 76 ASP cc_start: 0.9051 (t0) cc_final: 0.8715 (t0) REVERT: q 100 ASP cc_start: 0.8224 (p0) cc_final: 0.7779 (p0) REVERT: r 1 GLU cc_start: 0.9128 (pt0) cc_final: 0.8395 (mt-10) REVERT: 2 95 MET cc_start: 0.8953 (ptm) cc_final: 0.7994 (ppp) REVERT: 2 125 LEU cc_start: 0.9416 (tt) cc_final: 0.9126 (tt) REVERT: 2 271 MET cc_start: 0.8237 (mmt) cc_final: 0.7837 (mmm) REVERT: A 601 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7992 (ttpt) REVERT: A 654 GLU cc_start: 0.9058 (tp30) cc_final: 0.8712 (tp30) REVERT: c 571 TRP cc_start: 0.8382 (m-10) cc_final: 0.7837 (m-10) REVERT: c 630 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8671 (pt0) REVERT: d 95 MET cc_start: 0.9202 (ppp) cc_final: 0.8587 (ppp) REVERT: d 271 MET cc_start: 0.8223 (mmt) cc_final: 0.7792 (mmm) REVERT: d 452 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8728 (mm) REVERT: d 475 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8480 (mmm) outliers start: 123 outliers final: 95 residues processed: 318 average time/residue: 0.4531 time to fit residues: 234.3325 Evaluate side-chains 334 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 224 time to evaluate : 3.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 53 LYS Chi-restraints excluded: chain 3 residue 98 TYR Chi-restraints excluded: chain 4 residue 52 LEU Chi-restraints excluded: chain 4 residue 58 ASN Chi-restraints excluded: chain 4 residue 102 THR Chi-restraints excluded: chain 4 residue 107 THR Chi-restraints excluded: chain 5 residue 100 GLU Chi-restraints excluded: chain 5 residue 100 MET Chi-restraints excluded: chain 6 residue 25 GLU Chi-restraints excluded: chain 6 residue 90 ILE Chi-restraints excluded: chain 7 residue 56 SER Chi-restraints excluded: chain 7 residue 60 ASP Chi-restraints excluded: chain 7 residue 78 LEU Chi-restraints excluded: chain 7 residue 100 LEU Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain 8 residue 34 ILE Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 71 ARG Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 43 HIS Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 98 CYS Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 53 LYS Chi-restraints excluded: chain h residue 98 TYR Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain m residue 100 MET Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 90 ILE Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 71 ARG Chi-restraints excluded: chain q residue 73 LEU Chi-restraints excluded: chain r residue 56 SER Chi-restraints excluded: chain r residue 78 LEU Chi-restraints excluded: chain r residue 81 GLU Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain 2 residue 494 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 573 ILE Chi-restraints excluded: chain c residue 601 LYS Chi-restraints excluded: chain c residue 608 VAL Chi-restraints excluded: chain c residue 630 GLN Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 122 LEU Chi-restraints excluded: chain d residue 215 ILE Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 255 VAL Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 373 THR Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 452 LEU Chi-restraints excluded: chain d residue 475 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 20.0000 chunk 356 optimal weight: 6.9990 chunk 217 optimal weight: 8.9990 chunk 168 optimal weight: 3.9990 chunk 247 optimal weight: 7.9990 chunk 373 optimal weight: 0.8980 chunk 343 optimal weight: 2.9990 chunk 297 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 229 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 33045 Z= 0.345 Angle : 0.738 15.506 44907 Z= 0.352 Chirality : 0.047 0.275 5442 Planarity : 0.004 0.048 5472 Dihedral : 8.627 62.864 7435 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 3.48 % Allowed : 13.54 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.64 (0.14), residues: 3777 helix: -0.32 (0.25), residues: 450 sheet: -0.90 (0.14), residues: 1260 loop : -1.36 (0.14), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP d 427 HIS 0.006 0.001 HIS C 330 PHE 0.015 0.002 PHE d 288 TYR 0.016 0.001 TYR 4 54 ARG 0.008 0.000 ARG L 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 235 time to evaluate : 3.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 85 GLU cc_start: 0.8284 (tp30) cc_final: 0.8018 (tp30) REVERT: 5 77 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7755 (tt) REVERT: 5 100 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8900 (mmm) REVERT: 7 33 MET cc_start: 0.8866 (tpp) cc_final: 0.8467 (tpp) REVERT: 7 60 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8395 (t0) REVERT: 7 81 GLU cc_start: 0.8448 (tp30) cc_final: 0.8159 (tp30) REVERT: 8 28 ASN cc_start: 0.9007 (t0) cc_final: 0.8616 (t0) REVERT: 8 71 ARG cc_start: 0.9412 (OUTLIER) cc_final: 0.7056 (pmt-80) REVERT: C 95 MET cc_start: 0.9169 (ppp) cc_final: 0.8512 (ppp) REVERT: C 271 MET cc_start: 0.8326 (mmm) cc_final: 0.7936 (mmt) REVERT: C 425 ASN cc_start: 0.8566 (t0) cc_final: 0.8341 (t0) REVERT: D 530 MET cc_start: 0.7706 (ptp) cc_final: 0.7340 (mpp) REVERT: D 601 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7765 (ttpt) REVERT: H 33 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7386 (tp30) REVERT: H 63 PHE cc_start: 0.7569 (m-80) cc_final: 0.6660 (m-80) REVERT: H 66 LYS cc_start: 0.7785 (ptmt) cc_final: 0.7396 (tptp) REVERT: H 94 ARG cc_start: 0.6292 (OUTLIER) cc_final: 0.5741 (tmm160) REVERT: H 100 PHE cc_start: 0.7311 (m-80) cc_final: 0.6406 (m-80) REVERT: M 77 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7923 (tt) REVERT: M 100 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8744 (mmm) REVERT: Q 71 ARG cc_start: 0.9499 (OUTLIER) cc_final: 0.8513 (pmt-80) REVERT: Q 76 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8049 (t0) REVERT: Q 100 ASP cc_start: 0.7855 (p0) cc_final: 0.7597 (p0) REVERT: h 62 LYS cc_start: 0.9347 (tppt) cc_final: 0.9115 (ttpp) REVERT: h 86 ASP cc_start: 0.7428 (m-30) cc_final: 0.7111 (m-30) REVERT: h 100 PHE cc_start: 0.7167 (m-80) cc_final: 0.6515 (m-80) REVERT: m 77 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7513 (tt) REVERT: q 28 ASN cc_start: 0.9055 (t0) cc_final: 0.8659 (t0) REVERT: q 71 ARG cc_start: 0.9517 (OUTLIER) cc_final: 0.8974 (pmt-80) REVERT: q 73 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8559 (tp) REVERT: q 76 ASP cc_start: 0.9029 (t0) cc_final: 0.8728 (t0) REVERT: q 100 ASP cc_start: 0.8185 (p0) cc_final: 0.7805 (p0) REVERT: r 1 GLU cc_start: 0.9133 (pt0) cc_final: 0.8400 (mt-10) REVERT: 2 95 MET cc_start: 0.8969 (ptm) cc_final: 0.7988 (ppp) REVERT: 2 125 LEU cc_start: 0.9409 (tt) cc_final: 0.9125 (tt) REVERT: 2 271 MET cc_start: 0.8220 (mmt) cc_final: 0.7774 (mmm) REVERT: A 601 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8114 (ttpt) REVERT: A 654 GLU cc_start: 0.9051 (tp30) cc_final: 0.8711 (tp30) REVERT: c 571 TRP cc_start: 0.8364 (m-10) cc_final: 0.7819 (m-10) REVERT: c 630 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8717 (pt0) REVERT: d 95 MET cc_start: 0.9204 (ppp) cc_final: 0.8565 (ppp) REVERT: d 125 LEU cc_start: 0.9292 (tt) cc_final: 0.9036 (tt) REVERT: d 271 MET cc_start: 0.8167 (mmt) cc_final: 0.7725 (mmm) REVERT: d 452 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8730 (mm) REVERT: d 475 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8466 (mmm) outliers start: 116 outliers final: 92 residues processed: 317 average time/residue: 0.4520 time to fit residues: 230.0410 Evaluate side-chains 337 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 227 time to evaluate : 3.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 53 LYS Chi-restraints excluded: chain 3 residue 98 TYR Chi-restraints excluded: chain 4 residue 52 LEU Chi-restraints excluded: chain 4 residue 58 ASN Chi-restraints excluded: chain 4 residue 102 THR Chi-restraints excluded: chain 4 residue 107 THR Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 5 residue 100 GLU Chi-restraints excluded: chain 5 residue 100 MET Chi-restraints excluded: chain 6 residue 25 GLU Chi-restraints excluded: chain 6 residue 90 ILE Chi-restraints excluded: chain 7 residue 56 SER Chi-restraints excluded: chain 7 residue 60 ASP Chi-restraints excluded: chain 7 residue 78 LEU Chi-restraints excluded: chain 7 residue 100 LEU Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain 8 residue 34 ILE Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 71 ARG Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 43 HIS Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 98 CYS Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 53 LYS Chi-restraints excluded: chain h residue 98 TYR Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain m residue 100 MET Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 90 ILE Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 71 ARG Chi-restraints excluded: chain q residue 73 LEU Chi-restraints excluded: chain r residue 56 SER Chi-restraints excluded: chain r residue 78 LEU Chi-restraints excluded: chain r residue 100 LEU Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain 2 residue 494 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 601 LYS Chi-restraints excluded: chain c residue 608 VAL Chi-restraints excluded: chain c residue 630 GLN Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 122 LEU Chi-restraints excluded: chain d residue 215 ILE Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 255 VAL Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 373 THR Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 452 LEU Chi-restraints excluded: chain d residue 475 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 0.8980 chunk 316 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 274 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 305 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 23 ASN ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN M 23 ASN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.060188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.043394 restraints weight = 196741.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.044417 restraints weight = 105695.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.045063 restraints weight = 75272.166| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33045 Z= 0.172 Angle : 0.670 16.211 44907 Z= 0.319 Chirality : 0.046 0.266 5442 Planarity : 0.004 0.051 5472 Dihedral : 8.046 59.738 7435 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.40 % Allowed : 14.68 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.38 (0.14), residues: 3777 helix: 0.03 (0.26), residues: 432 sheet: -0.56 (0.14), residues: 1272 loop : -1.34 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 427 HIS 0.003 0.001 HIS 3 35 PHE 0.016 0.001 PHE d 288 TYR 0.041 0.001 TYR q 100 ARG 0.006 0.000 ARG L 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6040.55 seconds wall clock time: 113 minutes 5.80 seconds (6785.80 seconds total)