Starting phenix.real_space_refine on Wed Mar 20 14:30:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xr8_22292/03_2024/6xr8_22292.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xr8_22292/03_2024/6xr8_22292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xr8_22292/03_2024/6xr8_22292.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xr8_22292/03_2024/6xr8_22292.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xr8_22292/03_2024/6xr8_22292.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xr8_22292/03_2024/6xr8_22292.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 120 5.16 5 C 17511 2.51 5 N 4431 2.21 5 O 5565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B ARG 1107": "NH1" <-> "NH2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C ARG 509": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C ARG 765": "NH1" <-> "NH2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C ARG 1107": "NH1" <-> "NH2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "C PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27627 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 8666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 8666 Classifications: {'peptide': 1107} Link IDs: {'PTRANS': 51, 'TRANS': 1055} Chain breaks: 4 Chain: "B" Number of atoms: 8666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 8666 Classifications: {'peptide': 1107} Link IDs: {'PTRANS': 51, 'TRANS': 1055} Chain breaks: 4 Chain: "C" Number of atoms: 8666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 8666 Classifications: {'peptide': 1107} Link IDs: {'PTRANS': 51, 'TRANS': 1055} Chain breaks: 4 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, '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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "2" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "5" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "9" 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: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "GA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "JA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "MA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "PA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "SA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, '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: "cA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "fA" 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: "hA" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "kA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "oA" 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: "qA" 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: "sA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "vA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "yA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "1A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "4A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "7A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, '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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 14.41, per 1000 atoms: 0.52 Number of scatterers: 27627 At special positions: 0 Unit cell: (142.725, 143.55, 197.175, 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 120 16.00 O 5565 8.00 N 4431 7.00 C 17511 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " MAN n 3 " - " MAN n 4 " " MAN7A 3 " - " MAN7A 4 " " MANSA 3 " - " MANSA 4 " ALPHA1-4 " NAG 5 2 " - " MAN 5 3 " " NAG I 2 " - " MAN I 3 " " NAG Q 2 " - " MAN Q 3 " " NAG Y 2 " - " MAN Y 3 " " NAG b 2 " - " MAN b 3 " " NAG e 2 " - " MAN e 3 " " NAG h 2 " - " MAN h 3 " " NAG k 2 " - " MAN k 3 " " NAG n 2 " - " MAN n 3 " " NAG x 2 " - " MAN x 3 " " NAG1A 2 " - " MAN1A 3 " " NAG4A 2 " - " MAN4A 3 " " NAG7A 2 " - " MAN7A 3 " " NAGDA 2 " - " MANDA 3 " " NAGGA 2 " - " MANGA 3 " " NAGJA 2 " - " MANJA 3 " " NAGMA 2 " - " MANMA 3 " " NAGPA 2 " - " MANPA 3 " " NAGSA 2 " - " MANSA 3 " " NAGcA 2 " - " MANcA 3 " " NAGkA 2 " - " MANkA 3 " " NAGsA 2 " - " MANsA 3 " " NAGvA 2 " - " MANvA 3 " " NAGyA 2 " - " MANyA 3 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 9 1 " - " NAG 9 2 " " NAG I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG N 1 " - " NAG N 2 " " NAG Q 1 " - " NAG Q 2 " " NAG U 1 " - " NAG U 2 " " NAG W 1 " - " NAG W 2 " " NAG Y 1 " - " NAG Y 2 " " NAG b 1 " - " NAG b 2 " " NAG e 1 " - " NAG e 2 " " NAG h 1 " - " NAG h 2 " " NAG k 1 " - " NAG k 2 " " NAG n 1 " - " NAG n 2 " " NAG x 1 " - " NAG x 2 " " NAG1A 1 " - " NAG1A 2 " " NAG4A 1 " - " NAG4A 2 " " NAG7A 1 " - " NAG7A 2 " " NAGBA 1 " - " NAGBA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGGA 1 " - " NAGGA 2 " " NAGJA 1 " - " NAGJA 2 " " NAGMA 1 " - " NAGMA 2 " " NAGPA 1 " - " NAGPA 2 " " NAGSA 1 " - " NAGSA 2 " " NAGcA 1 " - " NAGcA 2 " " NAGfA 1 " - " NAGfA 2 " " NAGhA 1 " - " NAGhA 2 " " NAGkA 1 " - " NAGkA 2 " " NAGoA 1 " - " NAGoA 2 " " NAGqA 1 " - " NAGqA 2 " " NAGsA 1 " - " NAGsA 2 " " NAGvA 1 " - " NAGvA 2 " " NAGyA 1 " - " NAGyA 2 " BETA1-6 " NAG 2 1 " - " FUC 2 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG N 1 " - " FUC N 3 " " NAGhA 1 " - " FUChA 3 " NAG-ASN " NAG 0 1 " - " ASN B 17 " " NAG 2 1 " - " ASN B1074 " " NAG 5 1 " - " ASN B 122 " " NAG 9 1 " - " ASN B 331 " " NAG A1402 " - " ASN A 343 " " NAG A1403 " - " ASN A 603 " " NAG A1404 " - " ASN A 657 " " NAG A1405 " - " ASN A 709 " " NAG A1406 " - " ASN A 149 " " NAG A1407 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 343 " " NAG B1403 " - " ASN B 603 " " NAG B1404 " - " ASN B 657 " " NAG B1405 " - " ASN B 709 " " NAG B1406 " - " ASN B 149 " " NAG B1407 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 343 " " NAG C1403 " - " ASN C 603 " " NAG C1404 " - " ASN C 657 " " NAG C1405 " - " ASN C 709 " " NAG C1406 " - " ASN C 149 " " NAG C1407 " - " ASN C1158 " " NAG I 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 17 " " NAG N 1 " - " ASN A1074 " " NAG Q 1 " - " ASN A 122 " " NAG U 1 " - " ASN A 331 " " NAG W 1 " - " ASN A 165 " " NAG Y 1 " - " ASN A 234 " " NAG b 1 " - " ASN A 282 " " NAG e 1 " - " ASN A 616 " " NAG h 1 " - " ASN A 801 " " NAG k 1 " - " ASN A1098 " " NAG n 1 " - " ASN A1134 " " NAG x 1 " - " ASN B 717 " " NAG1A 1 " - " ASN C 801 " " NAG4A 1 " - " ASN C1098 " " NAG7A 1 " - " ASN C1134 " " NAGBA 1 " - " ASN B 165 " " NAGDA 1 " - " ASN B 234 " " NAGGA 1 " - " ASN B 282 " " NAGJA 1 " - " ASN B 616 " " NAGMA 1 " - " ASN B 801 " " NAGPA 1 " - " ASN B1098 " " NAGSA 1 " - " ASN B1134 " " NAGcA 1 " - " ASN C 717 " " NAGfA 1 " - " ASN C 17 " " NAGhA 1 " - " ASN C1074 " " NAGkA 1 " - " ASN C 122 " " NAGoA 1 " - " ASN C 331 " " NAGqA 1 " - " ASN C 165 " " NAGsA 1 " - " ASN C 234 " " NAGvA 1 " - " ASN C 282 " " NAGyA 1 " - " ASN C 616 " Time building additional restraints: 12.48 Conformation dependent library (CDL) restraints added in 4.7 seconds 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6216 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 56 sheets defined 27.2% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.52 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.585A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.259A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.223A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.082A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.564A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 841 removed outlier: 4.038A pdb=" N LEU A 841 " --> pdb=" O GLY A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 848 removed outlier: 3.692A pdb=" N ALA A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.587A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.859A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 3.702A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A1161 " --> pdb=" O LYS A1157 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.525A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.927A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 3.871A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.113A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 842 through 848 removed outlier: 3.814A pdb=" N ALA B 846 " --> pdb=" O GLY B 842 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG B 847 " --> pdb=" O ASP B 843 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 848 " --> pdb=" O ILE B 844 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 842 through 848' Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.616A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.682A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.562A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 3.864A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.277A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.077A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.815A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.361A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.548A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 841 removed outlier: 4.027A pdb=" N LEU C 841 " --> pdb=" O GLY C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 848 removed outlier: 3.709A pdb=" N ALA C 846 " --> pdb=" O GLY C 842 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG C 847 " --> pdb=" O ASP C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.617A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.597A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.792A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 3.850A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER C1161 " --> pdb=" O LYS C1157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.226A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.226A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.591A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.083A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.798A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.436A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.714A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.250A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.525A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.477A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.883A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.883A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.939A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.690A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.903A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.467A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.841A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.304A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.270A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC2, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AC3, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC4, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.991A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.991A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.583A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.012A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.908A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.564A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 13.089A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.896A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.705A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.495A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 324 through 328 removed outlier: 3.856A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.907A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.683A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.835A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.614A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.884A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.335A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.338A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE4, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.268A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.268A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.663A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.717A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.995A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.295A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.510A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.868A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.875A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.745A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.881A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF8, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.893A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.320A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG2, first strand: chain 'C' and resid 1094 through 1097 1150 hydrogen bonds defined for protein. 3126 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: 13.04 Time building geometry restraints manager: 13.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8575 1.34 - 1.46: 6894 1.46 - 1.58: 12606 1.58 - 1.70: 2 1.70 - 1.82: 150 Bond restraints: 28227 Sorted by residual: bond pdb=" C1 FUChA 3 " pdb=" C2 FUChA 3 " ideal model delta sigma weight residual 1.528 1.590 -0.062 2.00e-02 2.50e+03 9.75e+00 bond pdb=" N VAL A 62 " pdb=" CA VAL A 62 " ideal model delta sigma weight residual 1.459 1.424 0.035 1.19e-02 7.06e+03 8.65e+00 bond pdb=" C1 FUC N 3 " pdb=" C2 FUC N 3 " ideal model delta sigma weight residual 1.528 1.585 -0.057 2.00e-02 2.50e+03 8.15e+00 bond pdb=" C5 MANPA 3 " pdb=" O5 MANPA 3 " ideal model delta sigma weight residual 1.418 1.472 -0.054 2.00e-02 2.50e+03 7.29e+00 bond pdb=" C1 NAG C1401 " pdb=" O5 NAG C1401 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.66e+00 ... (remaining 28222 not shown) Histogram of bond angle deviations from ideal: 100.28 - 107.04: 872 107.04 - 113.79: 16263 113.79 - 120.55: 10495 120.55 - 127.30: 10512 127.30 - 134.06: 246 Bond angle restraints: 38388 Sorted by residual: angle pdb=" N VAL A 62 " pdb=" CA VAL A 62 " pdb=" C VAL A 62 " ideal model delta sigma weight residual 108.23 101.58 6.65 1.53e+00 4.27e-01 1.89e+01 angle pdb=" N TRP A 258 " pdb=" CA TRP A 258 " pdb=" C TRP A 258 " ideal model delta sigma weight residual 108.19 113.32 -5.13 1.29e+00 6.01e-01 1.58e+01 angle pdb=" N TRP B 258 " pdb=" CA TRP B 258 " pdb=" C TRP B 258 " ideal model delta sigma weight residual 108.19 113.30 -5.11 1.29e+00 6.01e-01 1.57e+01 angle pdb=" N TRP C 258 " pdb=" CA TRP C 258 " pdb=" C TRP C 258 " ideal model delta sigma weight residual 108.19 113.30 -5.11 1.29e+00 6.01e-01 1.57e+01 angle pdb=" N THR A 602 " pdb=" CA THR A 602 " pdb=" C THR A 602 " ideal model delta sigma weight residual 111.28 107.60 3.68 1.09e+00 8.42e-01 1.14e+01 ... (remaining 38383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.60: 17499 24.60 - 49.19: 625 49.19 - 73.79: 130 73.79 - 98.38: 87 98.38 - 122.98: 40 Dihedral angle restraints: 18381 sinusoidal: 8712 harmonic: 9669 Sorted by residual: dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual -86.00 -157.93 71.93 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual -86.00 -157.19 71.19 1 1.00e+01 1.00e-02 6.50e+01 dihedral pdb=" CB CYS C 840 " pdb=" SG CYS C 840 " pdb=" SG CYS C 851 " pdb=" CB CYS C 851 " ideal model delta sinusoidal sigma weight residual -86.00 -150.93 64.93 1 1.00e+01 1.00e-02 5.53e+01 ... (remaining 18378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.338: 4682 0.338 - 0.676: 10 0.676 - 1.013: 0 1.013 - 1.351: 1 1.351 - 1.689: 1 Chirality restraints: 4694 Sorted by residual: chirality pdb=" C1 NAG A1407 " pdb=" ND2 ASN A1158 " pdb=" C2 NAG A1407 " pdb=" O5 NAG A1407 " both_signs ideal model delta sigma weight residual False -2.40 -0.71 -1.69 2.00e-01 2.50e+01 7.13e+01 chirality pdb=" C1 NAG A1404 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A1404 " pdb=" O5 NAG A1404 " both_signs ideal model delta sigma weight residual False -2.40 -1.32 -1.08 2.00e-01 2.50e+01 2.90e+01 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.00 0.60 2.00e-01 2.50e+01 8.87e+00 ... (remaining 4691 not shown) Planarity restraints: 4844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.275 2.00e-02 2.50e+03 4.08e-01 2.08e+03 pdb=" CG ASN A 331 " -0.117 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.146 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.733 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " 0.429 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 657 " 0.270 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" CG ASN A 657 " -0.092 2.00e-02 2.50e+03 pdb=" OD1 ASN A 657 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 657 " -0.495 2.00e-02 2.50e+03 pdb=" C1 NAG A1404 " 0.327 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 717 " 0.245 2.00e-02 2.50e+03 2.32e-01 6.72e+02 pdb=" CG ASN A 717 " -0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN A 717 " -0.106 2.00e-02 2.50e+03 pdb=" ND2 ASN A 717 " -0.336 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.279 2.00e-02 2.50e+03 ... (remaining 4841 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 387 2.65 - 3.21: 25952 3.21 - 3.78: 40993 3.78 - 4.34: 61575 4.34 - 4.90: 99461 Nonbonded interactions: 228368 Sorted by model distance: nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.089 2.440 nonbonded pdb=" OE1 GLU C 406 " pdb=" OH TYR C 495 " model vdw 2.101 2.440 nonbonded pdb=" NZ LYS C 97 " pdb=" O GLN C 183 " model vdw 2.112 2.520 nonbonded pdb=" ND2 ASN A 61 " pdb=" C1 NAG A1401 " model vdw 2.149 3.550 nonbonded pdb=" C HIS A 69 " pdb=" N ALA A 260 " model vdw 2.167 3.350 ... (remaining 228363 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 '9' selection = chain 'BA' selection = chain 'L' selection = chain 'U' selection = chain 'W' selection = chain 'fA' selection = chain 'oA' selection = chain 'qA' } ncs_group { reference = (chain '1A' and resid 1 through 2) selection = (chain '2' and resid 1 through 2) selection = (chain '4A' and resid 1 through 2) selection = (chain '5' and resid 1 through 2) selection = (chain 'DA' and resid 1 through 2) selection = (chain 'GA' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'JA' and resid 1 through 2) selection = (chain 'MA' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'PA' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'cA' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'hA' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'kA' and resid 1 through 2) selection = (chain 'sA' and resid 1 through 2) selection = (chain 'vA' and resid 1 through 2) selection = (chain 'x' and resid 1 through 2) selection = (chain 'yA' and resid 1 through 2) } ncs_group { reference = chain '7A' selection = chain 'SA' selection = chain 'n' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 24.900 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 77.870 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.310 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 28227 Z= 0.329 Angle : 0.714 7.309 38388 Z= 0.362 Chirality : 0.060 1.689 4694 Planarity : 0.003 0.057 4788 Dihedral : 15.807 122.977 12030 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.49 % Favored : 97.45 % Rotamer: Outliers : 0.73 % Allowed : 4.04 % Favored : 95.23 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 3291 helix: -0.83 (0.17), residues: 756 sheet: 0.41 (0.19), residues: 738 loop : -1.39 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 258 HIS 0.004 0.001 HIS A 146 PHE 0.012 0.001 PHE A 79 TYR 0.010 0.001 TYR A 145 ARG 0.003 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 583 time to evaluate : 2.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 PHE cc_start: 0.8529 (t80) cc_final: 0.8301 (t80) REVERT: A 567 ARG cc_start: 0.7236 (mtt90) cc_final: 0.6994 (mpt180) REVERT: A 661 GLU cc_start: 0.7726 (tt0) cc_final: 0.7431 (mp0) REVERT: A 872 GLN cc_start: 0.8458 (mt0) cc_final: 0.7982 (mt0) REVERT: B 528 LYS cc_start: 0.7658 (mtpp) cc_final: 0.7349 (mttp) REVERT: B 844 ILE cc_start: 0.4401 (OUTLIER) cc_final: 0.3840 (mm) REVERT: C 265 TYR cc_start: 0.8257 (p90) cc_final: 0.7981 (p90) REVERT: C 462 LYS cc_start: 0.7580 (mtmt) cc_final: 0.7294 (mmtt) REVERT: C 755 GLN cc_start: 0.7162 (mm-40) cc_final: 0.6735 (mt0) REVERT: C 844 ILE cc_start: 0.4195 (OUTLIER) cc_final: 0.3761 (mm) outliers start: 21 outliers final: 10 residues processed: 600 average time/residue: 1.3613 time to fit residues: 953.0211 Evaluate side-chains 296 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 284 time to evaluate : 3.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 844 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 5.9990 chunk 250 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 85 optimal weight: 0.0870 chunk 168 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 258 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 157 optimal weight: 0.0070 chunk 192 optimal weight: 3.9990 chunk 299 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 409 GLN A 437 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 804 GLN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 317 ASN B 409 GLN B 437 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 764 ASN ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 437 ASN C 474 GLN C 519 HIS C 580 GLN C 779 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28227 Z= 0.207 Angle : 0.666 11.812 38388 Z= 0.328 Chirality : 0.046 0.578 4694 Planarity : 0.004 0.039 4788 Dihedral : 13.484 106.682 6101 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.66 % Allowed : 11.95 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3291 helix: 0.76 (0.18), residues: 783 sheet: 0.42 (0.18), residues: 816 loop : -1.26 (0.13), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 258 HIS 0.004 0.001 HIS A 66 PHE 0.019 0.001 PHE C 157 TYR 0.020 0.001 TYR B1067 ARG 0.009 0.001 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 312 time to evaluate : 2.995 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: A 66 HIS cc_start: 0.7177 (OUTLIER) cc_final: 0.6638 (t-90) REVERT: A 81 ASN cc_start: 0.7588 (p0) cc_final: 0.7202 (p0) REVERT: A 462 LYS cc_start: 0.7912 (mtmt) cc_final: 0.7693 (mmtt) REVERT: A 568 ASP cc_start: 0.7791 (m-30) cc_final: 0.7250 (m-30) REVERT: A 602 THR cc_start: 0.6868 (m) cc_final: 0.6400 (p) REVERT: A 618 THR cc_start: 0.6045 (OUTLIER) cc_final: 0.5842 (p) REVERT: A 661 GLU cc_start: 0.7678 (tt0) cc_final: 0.7368 (mp0) REVERT: A 755 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6398 (mp10) REVERT: A 872 GLN cc_start: 0.8435 (mt0) cc_final: 0.7963 (mt0) REVERT: B 81 ASN cc_start: 0.7544 (p0) cc_final: 0.7196 (p0) REVERT: B 462 LYS cc_start: 0.7872 (mtmt) cc_final: 0.7544 (mmtt) REVERT: B 568 ASP cc_start: 0.7754 (m-30) cc_final: 0.7204 (m-30) REVERT: B 755 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6098 (mp10) REVERT: B 844 ILE cc_start: 0.4599 (OUTLIER) cc_final: 0.4271 (mt) REVERT: B 900 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8822 (mtm) REVERT: C 157 PHE cc_start: 0.7709 (t80) cc_final: 0.7436 (t80) REVERT: C 462 LYS cc_start: 0.7815 (mtmt) cc_final: 0.7526 (mmtt) REVERT: C 755 GLN cc_start: 0.6880 (mm-40) cc_final: 0.6472 (mt0) outliers start: 77 outliers final: 35 residues processed: 366 average time/residue: 1.1721 time to fit residues: 512.6505 Evaluate side-chains 286 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 245 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 249 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 300 optimal weight: 4.9990 chunk 324 optimal weight: 0.5980 chunk 267 optimal weight: 6.9990 chunk 297 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN A 804 GLN A 836 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 836 GLN B 919 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN C 957 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 28227 Z= 0.376 Angle : 0.719 14.619 38388 Z= 0.349 Chirality : 0.048 0.440 4694 Planarity : 0.004 0.045 4788 Dihedral : 13.031 107.966 6093 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.21 % Allowed : 12.85 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3291 helix: 0.99 (0.19), residues: 789 sheet: 0.20 (0.18), residues: 765 loop : -1.12 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 152 HIS 0.006 0.001 HIS C1083 PHE 0.017 0.002 PHE A 543 TYR 0.021 0.002 TYR C1067 ARG 0.008 0.001 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 284 time to evaluate : 3.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7241 (OUTLIER) cc_final: 0.6710 (t-90) REVERT: A 81 ASN cc_start: 0.7866 (p0) cc_final: 0.7642 (p0) REVERT: A 319 ARG cc_start: 0.7783 (ptp90) cc_final: 0.7318 (ptm160) REVERT: A 462 LYS cc_start: 0.7863 (mtmt) cc_final: 0.7603 (mmtt) REVERT: A 568 ASP cc_start: 0.7864 (m-30) cc_final: 0.7381 (m-30) REVERT: A 602 THR cc_start: 0.7779 (m) cc_final: 0.7422 (p) REVERT: A 661 GLU cc_start: 0.7826 (tt0) cc_final: 0.7487 (mp0) REVERT: A 725 GLU cc_start: 0.8349 (tt0) cc_final: 0.8016 (tt0) REVERT: A 755 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.6407 (mp10) REVERT: A 872 GLN cc_start: 0.8493 (mt0) cc_final: 0.8048 (mt0) REVERT: B 81 ASN cc_start: 0.7864 (p0) cc_final: 0.7492 (p0) REVERT: B 132 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7928 (mt-10) REVERT: B 153 MET cc_start: 0.7229 (tpp) cc_final: 0.6812 (ttt) REVERT: B 158 ARG cc_start: 0.6779 (mtt90) cc_final: 0.6151 (mmm-85) REVERT: B 462 LYS cc_start: 0.7920 (mtmt) cc_final: 0.7598 (mmtt) REVERT: B 568 ASP cc_start: 0.7841 (m-30) cc_final: 0.7345 (m-30) REVERT: B 725 GLU cc_start: 0.8458 (tt0) cc_final: 0.8113 (tt0) REVERT: B 755 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6140 (mp10) REVERT: C 113 LYS cc_start: 0.7618 (mtpt) cc_final: 0.7389 (ttpp) REVERT: C 152 TRP cc_start: 0.7142 (m100) cc_final: 0.6879 (m100) REVERT: C 157 PHE cc_start: 0.7749 (t80) cc_final: 0.7540 (t80) REVERT: C 422 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.7713 (p0) REVERT: C 462 LYS cc_start: 0.7822 (mtmt) cc_final: 0.7485 (mmtt) REVERT: C 725 GLU cc_start: 0.8560 (tt0) cc_final: 0.8281 (tt0) REVERT: C 755 GLN cc_start: 0.7011 (mm-40) cc_final: 0.6518 (mt0) REVERT: C 847 ARG cc_start: 0.4799 (mtm-85) cc_final: 0.4505 (mtt-85) outliers start: 122 outliers final: 55 residues processed: 375 average time/residue: 1.1735 time to fit residues: 526.9959 Evaluate side-chains 304 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 244 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 1.9990 chunk 225 optimal weight: 10.0000 chunk 155 optimal weight: 0.0060 chunk 33 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 301 optimal weight: 0.5980 chunk 318 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 285 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN B 317 ASN B 414 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN C 52 GLN C 901 GLN C 957 GLN C1002 GLN C1113 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28227 Z= 0.180 Angle : 0.625 13.041 38388 Z= 0.296 Chirality : 0.044 0.371 4694 Planarity : 0.003 0.051 4788 Dihedral : 12.303 105.211 6090 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.11 % Allowed : 15.34 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3291 helix: 1.38 (0.19), residues: 783 sheet: 0.42 (0.18), residues: 753 loop : -1.13 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS B 519 PHE 0.010 0.001 PHE A 238 TYR 0.027 0.001 TYR A 265 ARG 0.008 0.001 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 279 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7876 (p0) cc_final: 0.7531 (p0) REVERT: A 319 ARG cc_start: 0.7702 (ptp90) cc_final: 0.7301 (ptm160) REVERT: A 368 LEU cc_start: 0.8176 (pp) cc_final: 0.7755 (pp) REVERT: A 462 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7584 (mmtt) REVERT: A 568 ASP cc_start: 0.7838 (m-30) cc_final: 0.7421 (m-30) REVERT: A 602 THR cc_start: 0.7614 (m) cc_final: 0.7299 (p) REVERT: A 618 THR cc_start: 0.6324 (OUTLIER) cc_final: 0.6067 (p) REVERT: A 661 GLU cc_start: 0.7833 (tt0) cc_final: 0.7494 (mp0) REVERT: A 725 GLU cc_start: 0.8331 (tt0) cc_final: 0.8018 (tt0) REVERT: A 872 GLN cc_start: 0.8461 (mt0) cc_final: 0.8014 (mt0) REVERT: B 81 ASN cc_start: 0.7807 (p0) cc_final: 0.7410 (p0) REVERT: B 153 MET cc_start: 0.7247 (tpp) cc_final: 0.6847 (ttt) REVERT: B 462 LYS cc_start: 0.7927 (mtmt) cc_final: 0.7568 (mmtt) REVERT: B 568 ASP cc_start: 0.7779 (m-30) cc_final: 0.7314 (m-30) REVERT: B 755 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6016 (mp10) REVERT: B 828 LEU cc_start: 0.7009 (mp) cc_final: 0.6674 (mp) REVERT: C 81 ASN cc_start: 0.7120 (p0) cc_final: 0.6832 (p0) REVERT: C 113 LYS cc_start: 0.7630 (mtpt) cc_final: 0.7400 (ttpp) REVERT: C 152 TRP cc_start: 0.7129 (m100) cc_final: 0.6823 (m100) REVERT: C 409 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8338 (mt0) REVERT: C 422 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.7501 (p0) REVERT: C 462 LYS cc_start: 0.7850 (mtmt) cc_final: 0.7506 (mmtt) REVERT: C 725 GLU cc_start: 0.8501 (tt0) cc_final: 0.8267 (tt0) REVERT: C 755 GLN cc_start: 0.6956 (mm-40) cc_final: 0.6485 (mt0) REVERT: C 830 ASP cc_start: 0.4571 (OUTLIER) cc_final: 0.3744 (p0) REVERT: C 847 ARG cc_start: 0.4720 (mtm-85) cc_final: 0.4484 (mtt-85) REVERT: C 872 GLN cc_start: 0.8544 (mt0) cc_final: 0.8163 (mt0) outliers start: 90 outliers final: 38 residues processed: 347 average time/residue: 1.1392 time to fit residues: 476.1115 Evaluate side-chains 295 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 252 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 237 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 272 optimal weight: 0.0970 chunk 220 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 286 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 563 GLN A 779 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 474 GLN B 544 ASN B 564 GLN B 779 GLN C 52 GLN C 957 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 28227 Z= 0.317 Angle : 0.671 12.474 38388 Z= 0.320 Chirality : 0.046 0.384 4694 Planarity : 0.004 0.040 4788 Dihedral : 11.956 105.655 6088 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.11 % Allowed : 14.78 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3291 helix: 1.38 (0.19), residues: 783 sheet: 0.54 (0.19), residues: 663 loop : -1.11 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.004 0.001 HIS A 207 PHE 0.013 0.002 PHE B1121 TYR 0.027 0.002 TYR A 265 ARG 0.006 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 255 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7185 (OUTLIER) cc_final: 0.6603 (t-90) REVERT: A 81 ASN cc_start: 0.8038 (p0) cc_final: 0.7633 (p0) REVERT: A 179 LEU cc_start: 0.6623 (OUTLIER) cc_final: 0.6392 (mt) REVERT: A 319 ARG cc_start: 0.7781 (ptp90) cc_final: 0.7378 (ptm160) REVERT: A 368 LEU cc_start: 0.8234 (pp) cc_final: 0.7768 (pp) REVERT: A 462 LYS cc_start: 0.7858 (mtmt) cc_final: 0.7575 (mmtt) REVERT: A 568 ASP cc_start: 0.7901 (m-30) cc_final: 0.7506 (m-30) REVERT: A 618 THR cc_start: 0.6453 (OUTLIER) cc_final: 0.6123 (p) REVERT: A 661 GLU cc_start: 0.7823 (tt0) cc_final: 0.7503 (mp0) REVERT: A 725 GLU cc_start: 0.8393 (tt0) cc_final: 0.8061 (tt0) REVERT: A 847 ARG cc_start: 0.4560 (mtm-85) cc_final: 0.4351 (mtt180) REVERT: A 872 GLN cc_start: 0.8494 (mt0) cc_final: 0.8057 (mt0) REVERT: A 878 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8924 (tt) REVERT: A 916 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8384 (tp) REVERT: B 81 ASN cc_start: 0.7904 (p0) cc_final: 0.7521 (p0) REVERT: B 132 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: B 153 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6879 (ttt) REVERT: B 462 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7576 (mmtt) REVERT: B 568 ASP cc_start: 0.7804 (m-30) cc_final: 0.7367 (m-30) REVERT: B 725 GLU cc_start: 0.8487 (tt0) cc_final: 0.8148 (tt0) REVERT: B 755 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6064 (mp10) REVERT: B 828 LEU cc_start: 0.7302 (mp) cc_final: 0.7014 (mp) REVERT: C 152 TRP cc_start: 0.7236 (m100) cc_final: 0.6929 (m100) REVERT: C 409 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8393 (mt0) REVERT: C 422 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.7524 (p0) REVERT: C 462 LYS cc_start: 0.7866 (mtmt) cc_final: 0.7480 (mmtt) REVERT: C 725 GLU cc_start: 0.8579 (tt0) cc_final: 0.8333 (tt0) REVERT: C 755 GLN cc_start: 0.7024 (mm-40) cc_final: 0.6528 (mt0) REVERT: C 847 ARG cc_start: 0.5099 (mtm-85) cc_final: 0.4798 (mtt-85) REVERT: C 1127 ASP cc_start: 0.7547 (m-30) cc_final: 0.7229 (m-30) outliers start: 119 outliers final: 61 residues processed: 344 average time/residue: 1.1473 time to fit residues: 476.4563 Evaluate side-chains 310 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 239 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 187 optimal weight: 0.0970 chunk 78 optimal weight: 9.9990 chunk 319 optimal weight: 0.9980 chunk 265 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 779 GLN C 52 GLN C 872 GLN C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28227 Z= 0.220 Angle : 0.634 11.906 38388 Z= 0.301 Chirality : 0.045 0.371 4694 Planarity : 0.003 0.039 4788 Dihedral : 11.527 104.384 6088 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.87 % Allowed : 15.51 % Favored : 80.62 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.14), residues: 3291 helix: 1.50 (0.19), residues: 783 sheet: 0.27 (0.18), residues: 759 loop : -1.09 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS A 207 PHE 0.012 0.001 PHE B 898 TYR 0.028 0.001 TYR B 265 ARG 0.008 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 261 time to evaluate : 3.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7295 (OUTLIER) cc_final: 0.6621 (t-90) REVERT: A 81 ASN cc_start: 0.8075 (p0) cc_final: 0.7760 (p0) REVERT: A 179 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6357 (mt) REVERT: A 319 ARG cc_start: 0.7735 (ptp90) cc_final: 0.7345 (ptm160) REVERT: A 368 LEU cc_start: 0.8225 (pp) cc_final: 0.7761 (pp) REVERT: A 462 LYS cc_start: 0.7867 (mtmt) cc_final: 0.7543 (mmtt) REVERT: A 568 ASP cc_start: 0.7856 (m-30) cc_final: 0.7598 (m-30) REVERT: A 618 THR cc_start: 0.6442 (OUTLIER) cc_final: 0.6112 (p) REVERT: A 661 GLU cc_start: 0.7845 (tt0) cc_final: 0.7559 (mp0) REVERT: A 725 GLU cc_start: 0.8384 (tt0) cc_final: 0.8059 (tt0) REVERT: A 830 ASP cc_start: 0.4918 (OUTLIER) cc_final: 0.4555 (p0) REVERT: A 872 GLN cc_start: 0.8504 (mt0) cc_final: 0.8067 (mt0) REVERT: A 878 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8942 (tt) REVERT: A 916 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8362 (tp) REVERT: B 81 ASN cc_start: 0.7890 (p0) cc_final: 0.7515 (p0) REVERT: B 132 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7809 (mt-10) REVERT: B 153 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.6819 (ttt) REVERT: B 158 ARG cc_start: 0.6674 (mtt90) cc_final: 0.5996 (mmm-85) REVERT: B 331 ASN cc_start: 0.4855 (OUTLIER) cc_final: 0.4321 (m110) REVERT: B 462 LYS cc_start: 0.7933 (mtmt) cc_final: 0.7582 (mmtt) REVERT: B 568 ASP cc_start: 0.7731 (m-30) cc_final: 0.7294 (m-30) REVERT: B 755 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6034 (mp10) REVERT: B 828 LEU cc_start: 0.7382 (mp) cc_final: 0.7097 (mp) REVERT: C 115 GLN cc_start: 0.8174 (mt0) cc_final: 0.7922 (mt0) REVERT: C 152 TRP cc_start: 0.7146 (m100) cc_final: 0.6881 (m100) REVERT: C 422 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.7545 (p0) REVERT: C 462 LYS cc_start: 0.7871 (mtmt) cc_final: 0.7457 (mmtt) REVERT: C 725 GLU cc_start: 0.8560 (tt0) cc_final: 0.8309 (tt0) REVERT: C 755 GLN cc_start: 0.7059 (mm-40) cc_final: 0.6543 (mt0) REVERT: C 830 ASP cc_start: 0.4931 (OUTLIER) cc_final: 0.4220 (p0) REVERT: C 847 ARG cc_start: 0.5071 (mtm-85) cc_final: 0.4801 (mtt-85) REVERT: C 1127 ASP cc_start: 0.7559 (m-30) cc_final: 0.7271 (m-30) outliers start: 112 outliers final: 56 residues processed: 339 average time/residue: 1.1070 time to fit residues: 453.8474 Evaluate side-chains 316 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 248 time to evaluate : 3.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1043 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 chunk 180 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 318 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN B 450 ASN B 779 GLN C 52 GLN C 872 GLN C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 28227 Z= 0.337 Angle : 0.687 11.591 38388 Z= 0.328 Chirality : 0.047 0.394 4694 Planarity : 0.004 0.041 4788 Dihedral : 11.402 105.208 6088 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.66 % Allowed : 16.20 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.14), residues: 3291 helix: 1.51 (0.19), residues: 765 sheet: 0.26 (0.19), residues: 681 loop : -1.00 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 436 HIS 0.004 0.001 HIS A 207 PHE 0.017 0.002 PHE C 898 TYR 0.033 0.002 TYR A 265 ARG 0.006 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 252 time to evaluate : 2.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7280 (OUTLIER) cc_final: 0.6626 (t-90) REVERT: A 81 ASN cc_start: 0.8299 (p0) cc_final: 0.7926 (p0) REVERT: A 179 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6310 (mt) REVERT: A 319 ARG cc_start: 0.7803 (ptp90) cc_final: 0.7427 (ptm160) REVERT: A 368 LEU cc_start: 0.8219 (pp) cc_final: 0.7755 (pp) REVERT: A 462 LYS cc_start: 0.7842 (mtmt) cc_final: 0.7460 (mmtt) REVERT: A 618 THR cc_start: 0.6612 (OUTLIER) cc_final: 0.6187 (p) REVERT: A 661 GLU cc_start: 0.7958 (tt0) cc_final: 0.7590 (mp0) REVERT: A 725 GLU cc_start: 0.8404 (tt0) cc_final: 0.8066 (tt0) REVERT: A 830 ASP cc_start: 0.4927 (OUTLIER) cc_final: 0.4565 (p0) REVERT: A 872 GLN cc_start: 0.8523 (mt0) cc_final: 0.8085 (mt0) REVERT: A 878 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8940 (tt) REVERT: A 916 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8425 (tp) REVERT: B 66 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.6848 (t70) REVERT: B 81 ASN cc_start: 0.8022 (p0) cc_final: 0.7698 (p0) REVERT: B 132 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: B 153 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6792 (ttt) REVERT: B 158 ARG cc_start: 0.6848 (mtt90) cc_final: 0.6224 (mmm-85) REVERT: B 331 ASN cc_start: 0.4777 (OUTLIER) cc_final: 0.4297 (m110) REVERT: B 462 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7570 (mmtt) REVERT: B 568 ASP cc_start: 0.7800 (m-30) cc_final: 0.7411 (m-30) REVERT: B 725 GLU cc_start: 0.8507 (tt0) cc_final: 0.8154 (tt0) REVERT: B 755 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6079 (mp10) REVERT: B 916 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8546 (tp) REVERT: C 152 TRP cc_start: 0.7245 (m100) cc_final: 0.6985 (m100) REVERT: C 158 ARG cc_start: 0.7002 (mmt90) cc_final: 0.6650 (mmm-85) REVERT: C 422 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.7788 (p0) REVERT: C 462 LYS cc_start: 0.7830 (mtmt) cc_final: 0.7400 (mmtt) REVERT: C 489 TYR cc_start: 0.8231 (m-80) cc_final: 0.7642 (m-80) REVERT: C 725 GLU cc_start: 0.8576 (tt0) cc_final: 0.8312 (tt0) REVERT: C 755 GLN cc_start: 0.7088 (mm-40) cc_final: 0.6563 (mt0) REVERT: C 830 ASP cc_start: 0.5047 (OUTLIER) cc_final: 0.4474 (p0) REVERT: C 847 ARG cc_start: 0.5137 (mtm-85) cc_final: 0.4884 (mtt-85) REVERT: C 1113 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8293 (mm110) REVERT: C 1127 ASP cc_start: 0.7577 (m-30) cc_final: 0.7268 (m-30) outliers start: 106 outliers final: 70 residues processed: 334 average time/residue: 1.1220 time to fit residues: 452.5332 Evaluate side-chains 321 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 236 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 0.7980 chunk 127 optimal weight: 0.0370 chunk 189 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 202 optimal weight: 0.6980 chunk 216 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 250 optimal weight: 0.5980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN C 52 GLN C 913 GLN C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 28227 Z= 0.188 Angle : 0.629 11.525 38388 Z= 0.296 Chirality : 0.046 0.983 4694 Planarity : 0.003 0.037 4788 Dihedral : 10.828 102.639 6088 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.21 % Allowed : 16.93 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3291 helix: 1.71 (0.19), residues: 777 sheet: 0.25 (0.18), residues: 729 loop : -0.98 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.002 0.001 HIS A 207 PHE 0.013 0.001 PHE C 898 TYR 0.031 0.001 TYR B 265 ARG 0.007 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 275 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7247 (OUTLIER) cc_final: 0.6519 (t-90) REVERT: A 81 ASN cc_start: 0.8237 (p0) cc_final: 0.7889 (p0) REVERT: A 179 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6274 (mt) REVERT: A 190 ARG cc_start: 0.8092 (mtp85) cc_final: 0.7708 (mtt-85) REVERT: A 319 ARG cc_start: 0.7641 (ptp90) cc_final: 0.7291 (ptm160) REVERT: A 368 LEU cc_start: 0.8240 (pp) cc_final: 0.7783 (pp) REVERT: A 462 LYS cc_start: 0.7819 (mtmt) cc_final: 0.7536 (mmtt) REVERT: A 618 THR cc_start: 0.6596 (OUTLIER) cc_final: 0.6161 (p) REVERT: A 661 GLU cc_start: 0.7965 (tt0) cc_final: 0.7599 (mp0) REVERT: A 663 ASP cc_start: 0.8314 (t0) cc_final: 0.8082 (t0) REVERT: A 725 GLU cc_start: 0.8378 (tt0) cc_final: 0.8017 (tt0) REVERT: A 872 GLN cc_start: 0.8489 (mt0) cc_final: 0.8055 (mt0) REVERT: A 878 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8925 (tt) REVERT: A 916 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8307 (tp) REVERT: A 1113 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8494 (mm110) REVERT: B 66 HIS cc_start: 0.7318 (OUTLIER) cc_final: 0.6726 (t70) REVERT: B 81 ASN cc_start: 0.7939 (p0) cc_final: 0.7633 (p0) REVERT: B 132 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7785 (mt-10) REVERT: B 158 ARG cc_start: 0.6778 (mtt90) cc_final: 0.6038 (mmm-85) REVERT: B 331 ASN cc_start: 0.4546 (OUTLIER) cc_final: 0.4252 (m110) REVERT: B 462 LYS cc_start: 0.7917 (mtmt) cc_final: 0.7564 (mmtt) REVERT: B 568 ASP cc_start: 0.7745 (m-30) cc_final: 0.7399 (m-30) REVERT: B 725 GLU cc_start: 0.8416 (tt0) cc_final: 0.8067 (tt0) REVERT: B 916 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8496 (tp) REVERT: C 152 TRP cc_start: 0.7280 (m100) cc_final: 0.7048 (m100) REVERT: C 158 ARG cc_start: 0.6963 (mmt90) cc_final: 0.6640 (mmm-85) REVERT: C 409 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8339 (mt0) REVERT: C 422 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.7748 (p0) REVERT: C 462 LYS cc_start: 0.7792 (mtmt) cc_final: 0.7411 (mmtt) REVERT: C 725 GLU cc_start: 0.8544 (tt0) cc_final: 0.8288 (tt0) REVERT: C 755 GLN cc_start: 0.7064 (mm-40) cc_final: 0.6536 (mt0) REVERT: C 830 ASP cc_start: 0.4740 (OUTLIER) cc_final: 0.4431 (p0) REVERT: C 847 ARG cc_start: 0.5085 (mtm-85) cc_final: 0.4855 (mtt-85) REVERT: C 1127 ASP cc_start: 0.7546 (m-30) cc_final: 0.7248 (m-30) outliers start: 93 outliers final: 53 residues processed: 345 average time/residue: 1.1289 time to fit residues: 471.6341 Evaluate side-chains 310 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 244 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 987 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 3.9990 chunk 304 optimal weight: 0.5980 chunk 278 optimal weight: 0.2980 chunk 296 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 232 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 267 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN B 314 GLN B 474 GLN C 52 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28227 Z= 0.254 Angle : 0.655 11.226 38388 Z= 0.309 Chirality : 0.046 0.768 4694 Planarity : 0.003 0.039 4788 Dihedral : 10.493 102.809 6086 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.07 % Allowed : 17.31 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3291 helix: 1.79 (0.19), residues: 759 sheet: 0.10 (0.18), residues: 741 loop : -0.97 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS A 207 PHE 0.013 0.001 PHE C 898 TYR 0.033 0.001 TYR A 265 ARG 0.006 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 259 time to evaluate : 3.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7244 (OUTLIER) cc_final: 0.6501 (t-90) REVERT: A 81 ASN cc_start: 0.8447 (p0) cc_final: 0.8079 (p0) REVERT: A 179 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6290 (mt) REVERT: A 190 ARG cc_start: 0.8093 (mtp85) cc_final: 0.7729 (mtt-85) REVERT: A 319 ARG cc_start: 0.7741 (ptp90) cc_final: 0.7361 (ptm160) REVERT: A 368 LEU cc_start: 0.8200 (pp) cc_final: 0.7761 (pp) REVERT: A 462 LYS cc_start: 0.7784 (mtmt) cc_final: 0.7572 (mmtt) REVERT: A 618 THR cc_start: 0.6606 (OUTLIER) cc_final: 0.6169 (p) REVERT: A 661 GLU cc_start: 0.7962 (tt0) cc_final: 0.7614 (mp0) REVERT: A 663 ASP cc_start: 0.8333 (t0) cc_final: 0.8130 (t0) REVERT: A 725 GLU cc_start: 0.8393 (tt0) cc_final: 0.8026 (tt0) REVERT: A 847 ARG cc_start: 0.6376 (mpt-90) cc_final: 0.6103 (mpt90) REVERT: A 872 GLN cc_start: 0.8503 (mt0) cc_final: 0.8053 (mt0) REVERT: A 878 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8944 (tt) REVERT: A 916 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8358 (tp) REVERT: A 1113 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8515 (mm110) REVERT: B 66 HIS cc_start: 0.7338 (OUTLIER) cc_final: 0.6713 (t70) REVERT: B 81 ASN cc_start: 0.8035 (p0) cc_final: 0.7735 (p0) REVERT: B 132 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7909 (mt-10) REVERT: B 158 ARG cc_start: 0.6840 (mtt90) cc_final: 0.6105 (mmm-85) REVERT: B 331 ASN cc_start: 0.4583 (OUTLIER) cc_final: 0.4339 (m110) REVERT: B 462 LYS cc_start: 0.7948 (mtmt) cc_final: 0.7580 (mmtt) REVERT: B 568 ASP cc_start: 0.7706 (m-30) cc_final: 0.7335 (m-30) REVERT: B 755 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.5988 (mp10) REVERT: B 916 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8519 (tt) REVERT: C 152 TRP cc_start: 0.7302 (m100) cc_final: 0.7069 (m100) REVERT: C 158 ARG cc_start: 0.6972 (mmt90) cc_final: 0.6649 (mmm-85) REVERT: C 409 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8421 (mt0) REVERT: C 422 ASN cc_start: 0.8401 (OUTLIER) cc_final: 0.7808 (p0) REVERT: C 462 LYS cc_start: 0.7823 (mtmt) cc_final: 0.7394 (mmtt) REVERT: C 725 GLU cc_start: 0.8563 (tt0) cc_final: 0.8305 (tt0) REVERT: C 755 GLN cc_start: 0.7062 (mm-40) cc_final: 0.6530 (mt0) REVERT: C 830 ASP cc_start: 0.4701 (OUTLIER) cc_final: 0.4483 (p0) REVERT: C 1127 ASP cc_start: 0.7567 (m-30) cc_final: 0.7301 (m-30) outliers start: 89 outliers final: 54 residues processed: 324 average time/residue: 1.1628 time to fit residues: 452.3298 Evaluate side-chains 310 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 242 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 987 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 0.6980 chunk 313 optimal weight: 0.6980 chunk 191 optimal weight: 0.3980 chunk 148 optimal weight: 0.9980 chunk 217 optimal weight: 2.9990 chunk 328 optimal weight: 1.9990 chunk 302 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 27 optimal weight: 0.0010 chunk 202 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 474 GLN B 913 GLN C 52 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN C 957 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28227 Z= 0.181 Angle : 0.622 11.294 38388 Z= 0.291 Chirality : 0.044 0.675 4694 Planarity : 0.003 0.037 4788 Dihedral : 9.889 101.467 6086 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.28 % Allowed : 18.34 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.14), residues: 3291 helix: 1.80 (0.19), residues: 780 sheet: 0.09 (0.18), residues: 741 loop : -0.86 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.002 0.001 HIS C1048 PHE 0.012 0.001 PHE C 898 TYR 0.039 0.001 TYR C 265 ARG 0.006 0.000 ARG B 567 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 267 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8480 (p0) cc_final: 0.8107 (p0) REVERT: A 179 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6253 (mt) REVERT: A 190 ARG cc_start: 0.8043 (mtp85) cc_final: 0.7704 (mtt-85) REVERT: A 319 ARG cc_start: 0.7667 (ptp90) cc_final: 0.7307 (ptm160) REVERT: A 368 LEU cc_start: 0.8262 (pp) cc_final: 0.7807 (pp) REVERT: A 462 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7622 (mmtt) REVERT: A 618 THR cc_start: 0.6588 (OUTLIER) cc_final: 0.6147 (p) REVERT: A 661 GLU cc_start: 0.7965 (tt0) cc_final: 0.7613 (mp0) REVERT: A 663 ASP cc_start: 0.8315 (t0) cc_final: 0.8094 (t0) REVERT: A 725 GLU cc_start: 0.8375 (tt0) cc_final: 0.8022 (tt0) REVERT: A 847 ARG cc_start: 0.6444 (mpt-90) cc_final: 0.6175 (mpt90) REVERT: A 872 GLN cc_start: 0.8477 (mt0) cc_final: 0.8047 (mt0) REVERT: A 878 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8920 (tt) REVERT: A 916 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8290 (tp) REVERT: A 1113 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8497 (mm110) REVERT: B 66 HIS cc_start: 0.7296 (OUTLIER) cc_final: 0.6672 (t70) REVERT: B 81 ASN cc_start: 0.8058 (p0) cc_final: 0.7757 (p0) REVERT: B 132 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7789 (mt-10) REVERT: B 158 ARG cc_start: 0.6780 (mtt90) cc_final: 0.6037 (mmm-85) REVERT: B 331 ASN cc_start: 0.4382 (OUTLIER) cc_final: 0.4120 (m110) REVERT: B 462 LYS cc_start: 0.7951 (mtmt) cc_final: 0.7573 (mmtt) REVERT: B 567 ARG cc_start: 0.7388 (mtt-85) cc_final: 0.7121 (mmt180) REVERT: B 568 ASP cc_start: 0.7641 (m-30) cc_final: 0.7320 (m-30) REVERT: B 755 GLN cc_start: 0.7147 (OUTLIER) cc_final: 0.5951 (mp10) REVERT: B 916 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8517 (tp) REVERT: C 152 TRP cc_start: 0.7338 (m100) cc_final: 0.7137 (m100) REVERT: C 158 ARG cc_start: 0.6991 (mmt90) cc_final: 0.6697 (mmm-85) REVERT: C 409 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8286 (mt0) REVERT: C 422 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.7735 (p0) REVERT: C 462 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7389 (mptm) REVERT: C 725 GLU cc_start: 0.8533 (tt0) cc_final: 0.8242 (tt0) REVERT: C 755 GLN cc_start: 0.7038 (mm-40) cc_final: 0.6517 (mt0) REVERT: C 1127 ASP cc_start: 0.7579 (m-30) cc_final: 0.7291 (m-30) outliers start: 66 outliers final: 46 residues processed: 315 average time/residue: 1.1895 time to fit residues: 453.2777 Evaluate side-chains 304 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 246 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 987 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 241 optimal weight: 0.0770 chunk 38 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 269 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 779 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.159577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.118169 restraints weight = 34048.866| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.31 r_work: 0.3125 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 28227 Z= 0.349 Angle : 0.701 11.003 38388 Z= 0.333 Chirality : 0.047 0.617 4694 Planarity : 0.004 0.041 4788 Dihedral : 9.804 103.494 6086 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.87 % Allowed : 17.93 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3291 helix: 1.65 (0.19), residues: 762 sheet: 0.09 (0.18), residues: 747 loop : -0.95 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 436 HIS 0.004 0.001 HIS A1083 PHE 0.015 0.002 PHE C 306 TYR 0.035 0.002 TYR C 265 ARG 0.006 0.000 ARG B 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9941.82 seconds wall clock time: 177 minutes 36.73 seconds (10656.73 seconds total)