Starting phenix.real_space_refine on Tue Feb 20 11:15:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbp_24984/02_2024/7sbp_24984.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbp_24984/02_2024/7sbp_24984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbp_24984/02_2024/7sbp_24984.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbp_24984/02_2024/7sbp_24984.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbp_24984/02_2024/7sbp_24984.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbp_24984/02_2024/7sbp_24984.pdb" } resolution = 3.1 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= 0.003 sd= 0.042 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 117 5.16 5 C 17553 2.51 5 N 4461 2.21 5 O 5562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 452": "NH1" <-> "NH2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A ASP 796": "OD1" <-> "OD2" Residue "A ASP 820": "OD1" <-> "OD2" Residue "A TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 843": "OD1" <-> "OD2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ASP 1101": "OD1" <-> "OD2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B ASP 737": "OD1" <-> "OD2" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B ASP 839": "OD1" <-> "OD2" Residue "B ASP 843": "OD1" <-> "OD2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B ASP 936": "OD1" <-> "OD2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "B PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C ARG 634": "NH1" <-> "NH2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C ASP 820": "OD1" <-> "OD2" Residue "C ASP 843": "OD1" <-> "OD2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C ASP 1101": "OD1" <-> "OD2" Residue "C ASP 1127": "OD1" <-> "OD2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "C GLU 1151": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27693 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 8688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8688 Classifications: {'peptide': 1110} Link IDs: {'PTRANS': 53, 'TRANS': 1056} Chain breaks: 4 Chain: "B" Number of atoms: 8688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8688 Classifications: {'peptide': 1110} Link IDs: {'PTRANS': 53, 'TRANS': 1056} Chain breaks: 4 Chain: "C" Number of atoms: 8688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8688 Classifications: {'peptide': 1110} Link IDs: {'PTRANS': 53, 'TRANS': 1056} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: "F" 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: "G" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'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: "J" 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: 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: "L" 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: "M" 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: 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: "O" 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "R" 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: "S" 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "V" 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: "W" 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: "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: "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: "Z" 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: "a" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: "d" 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: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: "i" 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: "j" 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: "l" 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: "m" 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: "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: 14.11, per 1000 atoms: 0.51 Number of scatterers: 27693 At special positions: 0 Unit cell: (150.162, 146.862, 196.366, 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 117 16.00 O 5562 8.00 N 4461 7.00 C 17553 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=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 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=2.02 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.01 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 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=1.99 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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 ALPHA1-4 " NAG E 2 " - " MAN E 3 " " NAG F 2 " - " MAN F 3 " " NAG G 2 " - " MAN G 3 " " NAG I 2 " - " MAN I 3 " " NAG J 2 " - " MAN J 3 " " NAG L 2 " - " MAN L 3 " " NAG M 2 " - " MAN M 3 " " NAG N 2 " - " MAN N 3 " " NAG O 2 " - " MAN O 3 " " NAG Q 2 " - " MAN Q 3 " " NAG R 2 " - " MAN R 3 " " NAG S 2 " - " MAN S 3 " " NAG U 2 " - " MAN U 3 " " NAG V 2 " - " MAN V 3 " " NAG X 2 " - " MAN X 3 " " NAG Y 2 " - " MAN Y 3 " " NAG Z 2 " - " MAN Z 3 " " NAG a 2 " - " MAN a 3 " " NAG c 2 " - " MAN c 3 " " NAG d 2 " - " MAN d 3 " " NAG e 2 " - " MAN e 3 " " NAG g 2 " - " MAN g 3 " " NAG h 2 " - " MAN h 3 " " NAG j 2 " - " MAN j 3 " " NAG k 2 " - " MAN k 3 " " NAG l 2 " - " MAN l 3 " " NAG m 2 " - " MAN m 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " BETA1-6 " NAG K 1 " - " FUC K 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG W 1 " - " FUC W 3 " " NAG i 1 " - " FUC i 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 149 " " NAG A1403 " - " ASN A 331 " " NAG A1404 " - " ASN A 603 " " NAG A1405 " - " ASN A 657 " " NAG A1406 " - " ASN A 709 " " NAG A1407 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 331 " " NAG B1404 " - " ASN B 603 " " NAG B1405 " - " ASN B 657 " " NAG B1406 " - " ASN B 709 " " NAG B1407 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 603 " " NAG C1405 " - " ASN C 657 " " NAG C1406 " - " ASN C 709 " " NAG C1407 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 282 " " NAG H 1 " - " ASN A 616 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN A 165 " " NAG O 1 " - " ASN A 343 " " NAG P 1 " - " ASN B 17 " " NAG Q 1 " - " ASN B 122 " " NAG R 1 " - " ASN B 234 " " NAG S 1 " - " ASN B 282 " " NAG T 1 " - " ASN B 616 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 801 " " NAG W 1 " - " ASN B1074 " " NAG X 1 " - " ASN B1098 " " NAG Y 1 " - " ASN B1134 " " NAG Z 1 " - " ASN B 165 " " NAG a 1 " - " ASN B 343 " " NAG b 1 " - " ASN C 17 " " NAG c 1 " - " ASN C 122 " " NAG d 1 " - " ASN C 234 " " NAG e 1 " - " ASN C 282 " " NAG f 1 " - " ASN C 616 " " NAG g 1 " - " ASN C 717 " " NAG h 1 " - " ASN C 801 " " NAG i 1 " - " ASN C1074 " " NAG j 1 " - " ASN C1098 " " NAG k 1 " - " ASN C1134 " " NAG l 1 " - " ASN C 165 " " NAG m 1 " - " ASN C 343 " Time building additional restraints: 12.97 Conformation dependent library (CDL) restraints added in 5.0 seconds 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6240 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 47 sheets defined 27.3% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.861A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.972A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.187A 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 634 through 639 removed outlier: 3.580A pdb=" N GLY A 639 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.510A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.787A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.620A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.714A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 removed outlier: 4.425A pdb=" N ARG A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.532A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) 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 removed outlier: 4.450A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) 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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.800A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.242A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.789A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.839A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.750A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.834A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 618 through 623 removed outlier: 4.473A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 639 removed outlier: 4.118A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.044A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.466A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 843 through 848 removed outlier: 4.282A pdb=" N ARG B 847 " --> pdb=" O ASP B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.647A 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 removed outlier: 4.298A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.921A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1160 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.719A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.951A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.240A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 409 removed outlier: 3.858A 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 616 through 620 Processing helix chain 'C' and resid 635 through 639 removed outlier: 3.977A pdb=" N GLY C 639 " --> pdb=" O TYR C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 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: 3.936A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.631A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.604A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 846 removed outlier: 3.605A pdb=" N ILE C 844 " --> pdb=" O LEU C 841 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA C 846 " --> pdb=" O ASP C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.876A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.574A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.542A 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 945 through 965 removed outlier: 3.793A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) 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 984 removed outlier: 3.564A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.083A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1159 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.915A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.901A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.937A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.509A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.763A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.578A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.302A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.392A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 7.040A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.956A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.661A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.508A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.874A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.953A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.577A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.009A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.843A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.926A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.904A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.685A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.842A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.471A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.185A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.146A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.961A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.699A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.229A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.579A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.529A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.945A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.262A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.440A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.005A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.642A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.967A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 134 through 145 removed outlier: 8.054A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.122A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 328 removed outlier: 7.048A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.045A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.735A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.876A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.233A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.570A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 2967 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: 13.51 Time building geometry restraints manager: 13.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4438 1.30 - 1.43: 7441 1.43 - 1.56: 16279 1.56 - 1.69: 0 1.69 - 1.82: 144 Bond restraints: 28302 Sorted by residual: bond pdb=" C PRO C 217 " pdb=" N HIS C 218 " ideal model delta sigma weight residual 1.331 1.245 0.086 1.42e-02 4.96e+03 3.63e+01 bond pdb=" C TYR A 279 " pdb=" O TYR A 279 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.22e-02 6.72e+03 2.78e+01 bond pdb=" C ARG A 328 " pdb=" O ARG A 328 " ideal model delta sigma weight residual 1.234 1.178 0.057 1.11e-02 8.12e+03 2.62e+01 bond pdb=" C ARG B1019 " pdb=" O ARG B1019 " ideal model delta sigma weight residual 1.237 1.179 0.058 1.16e-02 7.43e+03 2.51e+01 bond pdb=" C ARG C1019 " pdb=" O ARG C1019 " ideal model delta sigma weight residual 1.236 1.177 0.059 1.19e-02 7.06e+03 2.45e+01 ... (remaining 28297 not shown) Histogram of bond angle deviations from ideal: 97.10 - 104.83: 441 104.83 - 112.56: 13331 112.56 - 120.29: 14064 120.29 - 128.03: 10544 128.03 - 135.76: 128 Bond angle restraints: 38508 Sorted by residual: angle pdb=" N CYS B 525 " pdb=" CA CYS B 525 " pdb=" C CYS B 525 " ideal model delta sigma weight residual 108.38 121.43 -13.05 1.35e+00 5.49e-01 9.34e+01 angle pdb=" N ARG B1107 " pdb=" CA ARG B1107 " pdb=" C ARG B1107 " ideal model delta sigma weight residual 112.38 122.72 -10.34 1.22e+00 6.72e-01 7.18e+01 angle pdb=" N THR A 618 " pdb=" CA THR A 618 " pdb=" C THR A 618 " ideal model delta sigma weight residual 113.20 102.98 10.22 1.21e+00 6.83e-01 7.14e+01 angle pdb=" C GLY B 526 " pdb=" N PRO B 527 " pdb=" CA PRO B 527 " ideal model delta sigma weight residual 120.83 128.09 -7.26 1.02e+00 9.61e-01 5.06e+01 angle pdb=" N PRO C 217 " pdb=" CA PRO C 217 " pdb=" C PRO C 217 " ideal model delta sigma weight residual 111.15 121.68 -10.53 1.58e+00 4.01e-01 4.44e+01 ... (remaining 38503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.61: 17548 25.61 - 51.23: 585 51.23 - 76.84: 164 76.84 - 102.46: 59 102.46 - 128.07: 70 Dihedral angle restraints: 18426 sinusoidal: 8724 harmonic: 9702 Sorted by residual: dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -168.49 82.49 1 1.00e+01 1.00e-02 8.35e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual -86.00 -165.22 79.22 1 1.00e+01 1.00e-02 7.80e+01 dihedral pdb=" C LEU C 24 " pdb=" N LEU C 24 " pdb=" CA LEU C 24 " pdb=" CB LEU C 24 " ideal model delta harmonic sigma weight residual -122.60 -143.79 21.19 0 2.50e+00 1.60e-01 7.18e+01 ... (remaining 18423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.271: 4651 0.271 - 0.542: 56 0.542 - 0.813: 7 0.813 - 1.084: 0 1.084 - 1.355: 2 Chirality restraints: 4716 Sorted by residual: chirality pdb=" C1 MAN F 3 " pdb=" O4 NAG F 2 " pdb=" C2 MAN F 3 " pdb=" O5 MAN F 3 " both_signs ideal model delta sigma weight residual False 2.40 2.16 0.24 2.00e-02 2.50e+03 1.49e+02 chirality pdb=" C1 MAN O 3 " pdb=" O4 NAG O 2 " pdb=" C2 MAN O 3 " pdb=" O5 MAN O 3 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-02 2.50e+03 7.09e+01 chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.66e+01 ... (remaining 4713 not shown) Planarity restraints: 4860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 104 " -0.186 2.00e-02 2.50e+03 9.85e-02 2.43e+02 pdb=" CG TRP C 104 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP C 104 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP C 104 " 0.097 2.00e-02 2.50e+03 pdb=" NE1 TRP C 104 " 0.070 2.00e-02 2.50e+03 pdb=" CE2 TRP C 104 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP C 104 " 0.139 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 104 " -0.112 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 104 " 0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP C 104 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 122 " -0.097 2.00e-02 2.50e+03 1.11e-01 1.54e+02 pdb=" CG ASN B 122 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN B 122 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN B 122 " 0.182 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " -0.134 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1134 " 0.099 2.00e-02 2.50e+03 9.98e-02 1.25e+02 pdb=" CG ASN A1134 " -0.061 2.00e-02 2.50e+03 pdb=" OD1 ASN A1134 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A1134 " -0.146 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " 0.121 2.00e-02 2.50e+03 ... (remaining 4857 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 192 2.64 - 3.21: 24650 3.21 - 3.77: 41212 3.77 - 4.34: 58914 4.34 - 4.90: 93951 Nonbonded interactions: 218919 Sorted by model distance: nonbonded pdb=" O ARG C 634 " pdb=" NH1 ARG C 634 " model vdw 2.078 2.520 nonbonded pdb=" NH1 ARG C 905 " pdb=" O LEU C1049 " model vdw 2.214 2.520 nonbonded pdb=" NH1 ARG B 905 " pdb=" O LEU B1049 " model vdw 2.228 2.520 nonbonded pdb=" OG SER C 349 " pdb=" O ARG C 452 " model vdw 2.230 2.440 nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.247 2.440 ... (remaining 218914 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'P' selection = chain 'T' selection = chain 'b' selection = chain 'f' } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'F' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'l' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) } 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: 6.850 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: 0.040 Extract box with map and model: 23.000 Check model and map are aligned: 0.420 Set scattering table: 0.220 Process input model: 79.180 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 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 : 0.015 0.086 28302 Z= 0.931 Angle : 1.789 13.048 38508 Z= 1.169 Chirality : 0.110 1.355 4716 Planarity : 0.012 0.125 4803 Dihedral : 17.092 128.074 12051 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.03 % Favored : 92.30 % Rotamer: Outliers : 1.38 % Allowed : 5.27 % Favored : 93.35 % Cbeta Deviations : 0.48 % 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: -1.85 (0.13), residues: 3300 helix: -1.19 (0.16), residues: 747 sheet: -0.33 (0.18), residues: 738 loop : -1.64 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.186 0.032 TRP C 104 HIS 0.014 0.003 HIS A1159 PHE 0.105 0.013 PHE C 133 TYR 0.119 0.021 TYR C 660 ARG 0.008 0.001 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 787 time to evaluate : 3.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8257 (mttt) cc_final: 0.8007 (mtmm) REVERT: A 52 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8268 (tm-30) REVERT: A 81 ASN cc_start: 0.8879 (m-40) cc_final: 0.8380 (m-40) REVERT: A 237 ARG cc_start: 0.7637 (mtm-85) cc_final: 0.7308 (mtm-85) REVERT: A 319 ARG cc_start: 0.8432 (ttp-110) cc_final: 0.8132 (ttm110) REVERT: A 351 TYR cc_start: 0.8303 (p90) cc_final: 0.7986 (p90) REVERT: A 354 ASN cc_start: 0.8222 (t0) cc_final: 0.7963 (t0) REVERT: A 396 TYR cc_start: 0.7840 (m-80) cc_final: 0.7270 (m-80) REVERT: A 421 TYR cc_start: 0.7516 (m-80) cc_final: 0.6958 (m-10) REVERT: A 462 LYS cc_start: 0.8660 (mmmm) cc_final: 0.8361 (mmmm) REVERT: A 495 TYR cc_start: 0.7937 (m-80) cc_final: 0.7700 (m-80) REVERT: A 540 ASN cc_start: 0.8366 (m-40) cc_final: 0.8165 (m-40) REVERT: A 555 SER cc_start: 0.8926 (t) cc_final: 0.8466 (p) REVERT: A 565 PHE cc_start: 0.7475 (m-80) cc_final: 0.7028 (m-80) REVERT: A 574 ASP cc_start: 0.8018 (p0) cc_final: 0.7756 (p0) REVERT: A 578 ASP cc_start: 0.6928 (m-30) cc_final: 0.6305 (m-30) REVERT: A 584 ILE cc_start: 0.9073 (mm) cc_final: 0.8708 (mm) REVERT: A 585 LEU cc_start: 0.7957 (mt) cc_final: 0.7648 (mt) REVERT: A 596 SER cc_start: 0.8827 (m) cc_final: 0.8506 (p) REVERT: A 643 PHE cc_start: 0.8183 (t80) cc_final: 0.7796 (t80) REVERT: A 658 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.8191 (p0) REVERT: A 663 ASP cc_start: 0.7985 (t0) cc_final: 0.7684 (t0) REVERT: A 702 GLU cc_start: 0.8242 (tp30) cc_final: 0.7922 (tp30) REVERT: A 708 SER cc_start: 0.9022 (t) cc_final: 0.8694 (p) REVERT: A 736 VAL cc_start: 0.9082 (t) cc_final: 0.8865 (m) REVERT: A 758 SER cc_start: 0.8295 (t) cc_final: 0.8080 (t) REVERT: A 788 ILE cc_start: 0.9131 (mm) cc_final: 0.8787 (mm) REVERT: A 796 ASP cc_start: 0.7990 (t0) cc_final: 0.7719 (t0) REVERT: A 912 THR cc_start: 0.9022 (m) cc_final: 0.8714 (p) REVERT: A 986 LYS cc_start: 0.8329 (ttmm) cc_final: 0.8107 (ttpt) REVERT: A 994 ASP cc_start: 0.8035 (t70) cc_final: 0.7705 (t0) REVERT: A 1100 THR cc_start: 0.8987 (m) cc_final: 0.8757 (p) REVERT: B 58 PHE cc_start: 0.9170 (m-10) cc_final: 0.8868 (m-80) REVERT: B 140 PHE cc_start: 0.7779 (p90) cc_final: 0.7560 (p90) REVERT: B 191 GLU cc_start: 0.7542 (pt0) cc_final: 0.7289 (pt0) REVERT: B 287 ASP cc_start: 0.7917 (t0) cc_final: 0.7595 (t0) REVERT: B 298 GLU cc_start: 0.8109 (tt0) cc_final: 0.7562 (tm-30) REVERT: B 301 CYS cc_start: 0.6950 (t) cc_final: 0.6274 (t) REVERT: B 319 ARG cc_start: 0.8463 (ttp-110) cc_final: 0.8195 (ptm-80) REVERT: B 369 TYR cc_start: 0.7030 (t80) cc_final: 0.6821 (t80) REVERT: B 396 TYR cc_start: 0.7965 (m-80) cc_final: 0.7333 (m-10) REVERT: B 462 LYS cc_start: 0.8835 (mmtm) cc_final: 0.8518 (mtmm) REVERT: B 465 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7538 (mt-10) REVERT: B 490 PHE cc_start: 0.8339 (t80) cc_final: 0.8094 (t80) REVERT: B 574 ASP cc_start: 0.7913 (p0) cc_final: 0.7712 (p0) REVERT: B 596 SER cc_start: 0.9078 (m) cc_final: 0.8828 (m) REVERT: B 738 CYS cc_start: 0.5870 (t) cc_final: 0.5534 (t) REVERT: B 762 GLN cc_start: 0.8047 (tt0) cc_final: 0.7819 (tt0) REVERT: B 790 LYS cc_start: 0.8711 (ptpp) cc_final: 0.8433 (ptmt) REVERT: B 796 ASP cc_start: 0.7988 (t0) cc_final: 0.7656 (t0) REVERT: B 808 ASP cc_start: 0.7909 (t0) cc_final: 0.7671 (t0) REVERT: B 814 LYS cc_start: 0.8516 (mmtm) cc_final: 0.8226 (mptt) REVERT: B 985 ASP cc_start: 0.7777 (p0) cc_final: 0.7360 (p0) REVERT: B 994 ASP cc_start: 0.7973 (t70) cc_final: 0.7607 (t0) REVERT: B 1005 GLN cc_start: 0.7636 (mt0) cc_final: 0.7418 (mt0) REVERT: B 1073 LYS cc_start: 0.8591 (mttm) cc_final: 0.8377 (mttm) REVERT: B 1149 LYS cc_start: 0.8778 (tmtt) cc_final: 0.8486 (tppp) REVERT: C 54 LEU cc_start: 0.8753 (mt) cc_final: 0.8537 (mt) REVERT: C 116 SER cc_start: 0.8742 (m) cc_final: 0.8388 (p) REVERT: C 135 PHE cc_start: 0.7065 (m-80) cc_final: 0.6517 (m-80) REVERT: C 191 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7131 (mt-10) REVERT: C 342 PHE cc_start: 0.8438 (m-80) cc_final: 0.8192 (m-80) REVERT: C 360 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8166 (t0) REVERT: C 402 ILE cc_start: 0.8531 (pt) cc_final: 0.8258 (pt) REVERT: C 420 ASP cc_start: 0.7428 (m-30) cc_final: 0.7086 (m-30) REVERT: C 436 TRP cc_start: 0.8174 (p90) cc_final: 0.7850 (p90) REVERT: C 455 LEU cc_start: 0.8249 (tp) cc_final: 0.8011 (mt) REVERT: C 512 VAL cc_start: 0.9320 (t) cc_final: 0.9007 (m) REVERT: C 563 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8163 (mm-40) REVERT: C 581 THR cc_start: 0.8922 (p) cc_final: 0.8606 (t) REVERT: C 583 GLU cc_start: 0.7315 (mp0) cc_final: 0.7114 (mp0) REVERT: C 586 ASP cc_start: 0.8194 (t70) cc_final: 0.7859 (t0) REVERT: C 737 ASP cc_start: 0.7512 (t0) cc_final: 0.7234 (t0) REVERT: C 776 LYS cc_start: 0.8624 (tttm) cc_final: 0.8246 (tttm) REVERT: C 780 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7469 (mm-30) REVERT: C 796 ASP cc_start: 0.7974 (t0) cc_final: 0.7495 (t0) REVERT: C 817 PHE cc_start: 0.8715 (t80) cc_final: 0.8341 (t80) REVERT: C 907 ASN cc_start: 0.8692 (t0) cc_final: 0.8409 (t0) REVERT: C 912 THR cc_start: 0.8784 (m) cc_final: 0.8435 (p) REVERT: C 935 GLN cc_start: 0.8630 (tp-100) cc_final: 0.7795 (tp-100) REVERT: C 985 ASP cc_start: 0.7585 (p0) cc_final: 0.7352 (p0) REVERT: C 994 ASP cc_start: 0.7905 (t70) cc_final: 0.7609 (t0) REVERT: C 1101 ASP cc_start: 0.7424 (m-30) cc_final: 0.7195 (m-30) outliers start: 40 outliers final: 13 residues processed: 814 average time/residue: 0.4401 time to fit residues: 541.9678 Evaluate side-chains 668 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 652 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 843 ASP Chi-restraints excluded: chain C residue 1014 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 281 optimal weight: 3.9990 chunk 252 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 261 optimal weight: 0.7980 chunk 101 optimal weight: 0.3980 chunk 158 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 302 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1119 ASN B 125 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 955 ASN B 969 ASN B1010 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 563 GLN C 580 GLN C 675 GLN C 960 ASN C1108 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28302 Z= 0.250 Angle : 0.775 10.784 38508 Z= 0.387 Chirality : 0.048 0.242 4716 Planarity : 0.004 0.048 4803 Dihedral : 14.872 113.838 6129 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.91 % Favored : 95.88 % Rotamer: Outliers : 2.28 % Allowed : 9.89 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3300 helix: 0.72 (0.19), residues: 753 sheet: -0.00 (0.19), residues: 708 loop : -1.34 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 64 HIS 0.010 0.001 HIS C 207 PHE 0.020 0.002 PHE A 192 TYR 0.022 0.002 TYR A 265 ARG 0.007 0.001 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 656 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.7982 (m) cc_final: 0.7727 (m) REVERT: A 41 LYS cc_start: 0.8174 (mttt) cc_final: 0.7937 (mtmm) REVERT: A 158 ARG cc_start: 0.7260 (mmt-90) cc_final: 0.7032 (mmt-90) REVERT: A 190 ARG cc_start: 0.7356 (tpp80) cc_final: 0.7004 (tpp80) REVERT: A 207 HIS cc_start: 0.7722 (p90) cc_final: 0.6981 (p-80) REVERT: A 237 ARG cc_start: 0.7705 (mtm-85) cc_final: 0.7415 (mtm-85) REVERT: A 242 LEU cc_start: 0.7941 (mt) cc_final: 0.7614 (mt) REVERT: A 271 GLN cc_start: 0.7867 (mp10) cc_final: 0.7449 (mp10) REVERT: A 319 ARG cc_start: 0.8427 (ttp-110) cc_final: 0.8173 (ttm110) REVERT: A 351 TYR cc_start: 0.8305 (p90) cc_final: 0.7886 (p90) REVERT: A 354 ASN cc_start: 0.8316 (t0) cc_final: 0.8107 (t0) REVERT: A 360 ASN cc_start: 0.8514 (t0) cc_final: 0.8297 (t0) REVERT: A 408 ARG cc_start: 0.8132 (ptm-80) cc_final: 0.7846 (ptm-80) REVERT: A 565 PHE cc_start: 0.7387 (m-80) cc_final: 0.7099 (m-80) REVERT: A 591 SER cc_start: 0.7749 (t) cc_final: 0.7357 (t) REVERT: A 643 PHE cc_start: 0.8160 (t80) cc_final: 0.7796 (t80) REVERT: A 663 ASP cc_start: 0.7961 (t0) cc_final: 0.7673 (t0) REVERT: A 736 VAL cc_start: 0.9047 (t) cc_final: 0.8704 (m) REVERT: A 737 ASP cc_start: 0.7369 (p0) cc_final: 0.7003 (p0) REVERT: A 796 ASP cc_start: 0.8078 (t0) cc_final: 0.7857 (t0) REVERT: A 994 ASP cc_start: 0.8170 (t70) cc_final: 0.7844 (t0) REVERT: A 995 ARG cc_start: 0.8387 (mtt-85) cc_final: 0.8164 (mtp180) REVERT: A 1072 GLU cc_start: 0.7763 (pm20) cc_final: 0.7353 (pm20) REVERT: B 118 LEU cc_start: 0.8378 (tp) cc_final: 0.8161 (tp) REVERT: B 140 PHE cc_start: 0.8204 (p90) cc_final: 0.7893 (p90) REVERT: B 281 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7839 (pp20) REVERT: B 319 ARG cc_start: 0.8528 (ttp-110) cc_final: 0.8158 (ptm-80) REVERT: B 351 TYR cc_start: 0.8373 (p90) cc_final: 0.7922 (p90) REVERT: B 369 TYR cc_start: 0.6937 (t80) cc_final: 0.6656 (t80) REVERT: B 490 PHE cc_start: 0.8232 (t80) cc_final: 0.7833 (t80) REVERT: B 523 THR cc_start: 0.8046 (p) cc_final: 0.7514 (t) REVERT: B 568 ASP cc_start: 0.8012 (t0) cc_final: 0.7778 (t0) REVERT: B 578 ASP cc_start: 0.7902 (t0) cc_final: 0.7570 (t70) REVERT: B 661 GLU cc_start: 0.7198 (pm20) cc_final: 0.6956 (pm20) REVERT: B 726 ILE cc_start: 0.9134 (mt) cc_final: 0.8934 (mm) REVERT: B 738 CYS cc_start: 0.5775 (t) cc_final: 0.5432 (t) REVERT: B 796 ASP cc_start: 0.8070 (t0) cc_final: 0.7765 (t0) REVERT: B 808 ASP cc_start: 0.7938 (t0) cc_final: 0.7662 (t0) REVERT: B 994 ASP cc_start: 0.8091 (t70) cc_final: 0.7722 (t0) REVERT: B 1072 GLU cc_start: 0.8049 (pm20) cc_final: 0.7601 (pm20) REVERT: C 65 PHE cc_start: 0.8604 (m-80) cc_final: 0.8129 (m-80) REVERT: C 195 LYS cc_start: 0.8550 (mtpp) cc_final: 0.8250 (ttmm) REVERT: C 278 LYS cc_start: 0.8497 (tttt) cc_final: 0.8173 (ttpt) REVERT: C 298 GLU cc_start: 0.8454 (tp30) cc_final: 0.8153 (tp30) REVERT: C 351 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.8161 (p90) REVERT: C 374 PHE cc_start: 0.7932 (m-80) cc_final: 0.7627 (m-80) REVERT: C 402 ILE cc_start: 0.8399 (pt) cc_final: 0.7393 (pt) REVERT: C 406 GLU cc_start: 0.7263 (pm20) cc_final: 0.6764 (pm20) REVERT: C 448 ASN cc_start: 0.7640 (t0) cc_final: 0.7282 (t0) REVERT: C 450 ASN cc_start: 0.8838 (m110) cc_final: 0.8361 (p0) REVERT: C 452 ARG cc_start: 0.7396 (ptp-110) cc_final: 0.7152 (mtm-85) REVERT: C 466 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7833 (ptp90) REVERT: C 490 PHE cc_start: 0.7998 (t80) cc_final: 0.7610 (t80) REVERT: C 492 LEU cc_start: 0.8554 (mt) cc_final: 0.8270 (mt) REVERT: C 564 GLN cc_start: 0.8150 (tp40) cc_final: 0.7868 (tp40) REVERT: C 581 THR cc_start: 0.8792 (p) cc_final: 0.8028 (t) REVERT: C 584 ILE cc_start: 0.9086 (mm) cc_final: 0.8885 (mm) REVERT: C 643 PHE cc_start: 0.8114 (t80) cc_final: 0.7794 (t80) REVERT: C 758 SER cc_start: 0.7903 (t) cc_final: 0.7615 (t) REVERT: C 776 LYS cc_start: 0.8637 (tttm) cc_final: 0.8322 (tttm) REVERT: C 780 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7485 (mm-30) REVERT: C 796 ASP cc_start: 0.8020 (t0) cc_final: 0.7664 (t0) REVERT: C 935 GLN cc_start: 0.8611 (tp-100) cc_final: 0.8237 (tt0) REVERT: C 1119 ASN cc_start: 0.8579 (m-40) cc_final: 0.8288 (m-40) outliers start: 66 outliers final: 34 residues processed: 693 average time/residue: 0.4376 time to fit residues: 472.5931 Evaluate side-chains 617 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 580 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 843 ASP Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 975 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 168 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 251 optimal weight: 0.6980 chunk 205 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 302 optimal weight: 1.9990 chunk 327 optimal weight: 0.5980 chunk 269 optimal weight: 3.9990 chunk 300 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 243 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1005 GLN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 804 GLN B1005 GLN B1010 GLN C 66 HIS C 360 ASN C1159 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28302 Z= 0.228 Angle : 0.721 11.303 38508 Z= 0.351 Chirality : 0.046 0.295 4716 Planarity : 0.004 0.058 4803 Dihedral : 13.711 110.696 6110 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.61 % Favored : 95.18 % Rotamer: Outliers : 2.76 % Allowed : 12.27 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % 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: -0.55 (0.14), residues: 3300 helix: 1.29 (0.19), residues: 771 sheet: -0.18 (0.18), residues: 759 loop : -1.22 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 64 HIS 0.011 0.001 HIS C 207 PHE 0.027 0.002 PHE B 643 TYR 0.021 0.002 TYR B 396 ARG 0.007 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 611 time to evaluate : 3.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8432 (tp) cc_final: 0.8231 (tp) REVERT: A 158 ARG cc_start: 0.7275 (mmt-90) cc_final: 0.7060 (mmt-90) REVERT: A 190 ARG cc_start: 0.7286 (tpp80) cc_final: 0.6809 (tpp80) REVERT: A 271 GLN cc_start: 0.7816 (mp10) cc_final: 0.7329 (mp10) REVERT: A 319 ARG cc_start: 0.8427 (ttp-110) cc_final: 0.8163 (ttm110) REVERT: A 351 TYR cc_start: 0.8335 (p90) cc_final: 0.7883 (p90) REVERT: A 354 ASN cc_start: 0.8308 (t0) cc_final: 0.8086 (t0) REVERT: A 360 ASN cc_start: 0.8577 (t0) cc_final: 0.8330 (t0) REVERT: A 398 ASP cc_start: 0.6855 (m-30) cc_final: 0.6358 (m-30) REVERT: A 408 ARG cc_start: 0.8131 (ptm-80) cc_final: 0.7914 (ptm-80) REVERT: A 565 PHE cc_start: 0.7451 (m-80) cc_final: 0.7174 (m-80) REVERT: A 643 PHE cc_start: 0.8209 (t80) cc_final: 0.7745 (t80) REVERT: A 663 ASP cc_start: 0.7802 (t0) cc_final: 0.7522 (t0) REVERT: A 790 LYS cc_start: 0.8715 (ptpp) cc_final: 0.8351 (ptpp) REVERT: A 796 ASP cc_start: 0.8093 (t0) cc_final: 0.7887 (t0) REVERT: A 804 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7950 (tp40) REVERT: A 994 ASP cc_start: 0.8165 (t70) cc_final: 0.7831 (t0) REVERT: A 995 ARG cc_start: 0.8376 (mtt-85) cc_final: 0.8118 (mtp180) REVERT: A 1072 GLU cc_start: 0.7739 (pm20) cc_final: 0.7432 (pm20) REVERT: B 140 PHE cc_start: 0.8224 (p90) cc_final: 0.7914 (p90) REVERT: B 319 ARG cc_start: 0.8546 (ttp-110) cc_final: 0.8109 (ptm-80) REVERT: B 351 TYR cc_start: 0.8390 (p90) cc_final: 0.7895 (p90) REVERT: B 403 ARG cc_start: 0.7287 (ttp-110) cc_final: 0.6954 (ttp-110) REVERT: B 465 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7552 (mt-10) REVERT: B 490 PHE cc_start: 0.8171 (t80) cc_final: 0.7784 (t80) REVERT: B 523 THR cc_start: 0.8231 (p) cc_final: 0.7668 (t) REVERT: B 578 ASP cc_start: 0.7896 (t0) cc_final: 0.7544 (t70) REVERT: B 591 SER cc_start: 0.8847 (t) cc_final: 0.8487 (p) REVERT: B 661 GLU cc_start: 0.7106 (pm20) cc_final: 0.6798 (pm20) REVERT: B 776 LYS cc_start: 0.8738 (ttmm) cc_final: 0.8487 (tttt) REVERT: B 796 ASP cc_start: 0.8158 (t0) cc_final: 0.7833 (t0) REVERT: B 994 ASP cc_start: 0.8064 (t70) cc_final: 0.7641 (t0) REVERT: B 1072 GLU cc_start: 0.8063 (pm20) cc_final: 0.7615 (pm20) REVERT: C 52 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8428 (tm-30) REVERT: C 146 HIS cc_start: 0.6463 (m-70) cc_final: 0.6189 (m170) REVERT: C 191 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7218 (mp0) REVERT: C 278 LYS cc_start: 0.8573 (tttt) cc_final: 0.8297 (ttpt) REVERT: C 298 GLU cc_start: 0.8484 (tp30) cc_final: 0.8223 (tp30) REVERT: C 347 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.6411 (m-80) REVERT: C 351 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.8176 (p90) REVERT: C 360 ASN cc_start: 0.8375 (t0) cc_final: 0.8088 (t0) REVERT: C 368 LEU cc_start: 0.8975 (pp) cc_final: 0.8648 (pp) REVERT: C 389 ASP cc_start: 0.7570 (m-30) cc_final: 0.7319 (t0) REVERT: C 402 ILE cc_start: 0.8426 (pt) cc_final: 0.8190 (pt) REVERT: C 448 ASN cc_start: 0.7536 (t0) cc_final: 0.7212 (t0) REVERT: C 452 ARG cc_start: 0.7495 (ptp-110) cc_final: 0.7291 (mtm-85) REVERT: C 465 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7512 (mt-10) REVERT: C 466 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7883 (ptp90) REVERT: C 490 PHE cc_start: 0.8077 (t80) cc_final: 0.7556 (t80) REVERT: C 492 LEU cc_start: 0.8542 (mt) cc_final: 0.8205 (mt) REVERT: C 564 GLN cc_start: 0.8184 (tp40) cc_final: 0.7849 (tp40) REVERT: C 581 THR cc_start: 0.8630 (p) cc_final: 0.7870 (p) REVERT: C 643 PHE cc_start: 0.8116 (t80) cc_final: 0.7813 (t80) REVERT: C 776 LYS cc_start: 0.8638 (tttm) cc_final: 0.8304 (tttm) REVERT: C 780 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7451 (mm-30) REVERT: C 796 ASP cc_start: 0.8025 (t0) cc_final: 0.7689 (t0) REVERT: C 935 GLN cc_start: 0.8576 (tp-100) cc_final: 0.8303 (tt0) REVERT: C 994 ASP cc_start: 0.7943 (t0) cc_final: 0.7686 (t0) REVERT: C 1119 ASN cc_start: 0.8558 (m-40) cc_final: 0.8274 (m-40) outliers start: 80 outliers final: 47 residues processed: 653 average time/residue: 0.4255 time to fit residues: 430.3814 Evaluate side-chains 623 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 573 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 986 LYS Chi-restraints excluded: chain C residue 1101 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 299 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 157 optimal weight: 0.0170 chunk 33 optimal weight: 0.0030 chunk 144 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 304 optimal weight: 2.9990 chunk 321 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 288 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 0.5428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 613 GLN A 804 GLN A1002 GLN A1005 GLN A1119 ASN B 388 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B1005 GLN C 66 HIS C 960 ASN C1002 GLN C1159 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 28302 Z= 0.202 Angle : 0.697 10.625 38508 Z= 0.333 Chirality : 0.045 0.254 4716 Planarity : 0.004 0.059 4803 Dihedral : 12.724 108.454 6107 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.52 % Favored : 95.30 % Rotamer: Outliers : 2.69 % Allowed : 13.82 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -0.35 (0.14), residues: 3300 helix: 1.78 (0.19), residues: 750 sheet: -0.15 (0.18), residues: 762 loop : -1.18 (0.13), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 436 HIS 0.011 0.001 HIS C 207 PHE 0.025 0.001 PHE C 168 TYR 0.018 0.001 TYR C1067 ARG 0.007 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 595 time to evaluate : 3.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.7335 (mmt-90) cc_final: 0.7089 (mmt-90) REVERT: A 271 GLN cc_start: 0.7914 (mp10) cc_final: 0.7335 (mp10) REVERT: A 319 ARG cc_start: 0.8408 (ttp-110) cc_final: 0.8198 (ttm110) REVERT: A 351 TYR cc_start: 0.8261 (p90) cc_final: 0.7872 (p90) REVERT: A 354 ASN cc_start: 0.8302 (t0) cc_final: 0.8075 (t0) REVERT: A 360 ASN cc_start: 0.8553 (t0) cc_final: 0.8297 (t0) REVERT: A 421 TYR cc_start: 0.7778 (m-80) cc_final: 0.7409 (m-10) REVERT: A 505 TYR cc_start: 0.7703 (OUTLIER) cc_final: 0.7490 (m-80) REVERT: A 565 PHE cc_start: 0.7425 (m-80) cc_final: 0.7148 (m-80) REVERT: A 643 PHE cc_start: 0.8145 (t80) cc_final: 0.7660 (t80) REVERT: A 790 LYS cc_start: 0.8690 (ptpp) cc_final: 0.8359 (ptpp) REVERT: A 912 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8338 (p) REVERT: A 994 ASP cc_start: 0.8152 (t70) cc_final: 0.7818 (t0) REVERT: A 995 ARG cc_start: 0.8362 (mtt-85) cc_final: 0.8059 (mtp180) REVERT: B 140 PHE cc_start: 0.8215 (p90) cc_final: 0.7902 (p90) REVERT: B 190 ARG cc_start: 0.7514 (tpp-160) cc_final: 0.6758 (tpp80) REVERT: B 191 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: B 319 ARG cc_start: 0.8560 (ttp-110) cc_final: 0.8004 (ptm-80) REVERT: B 341 VAL cc_start: 0.9184 (m) cc_final: 0.8969 (p) REVERT: B 351 TYR cc_start: 0.8380 (p90) cc_final: 0.7898 (p90) REVERT: B 390 LEU cc_start: 0.8694 (tp) cc_final: 0.8465 (tp) REVERT: B 462 LYS cc_start: 0.8944 (mtmm) cc_final: 0.8514 (mttp) REVERT: B 465 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7326 (mt-10) REVERT: B 490 PHE cc_start: 0.8250 (t80) cc_final: 0.7900 (t80) REVERT: B 523 THR cc_start: 0.8293 (p) cc_final: 0.7754 (t) REVERT: B 661 GLU cc_start: 0.7076 (pm20) cc_final: 0.6776 (pm20) REVERT: B 776 LYS cc_start: 0.8725 (ttmm) cc_final: 0.8483 (tttt) REVERT: B 796 ASP cc_start: 0.8156 (t0) cc_final: 0.7820 (t0) REVERT: B 985 ASP cc_start: 0.7935 (p0) cc_final: 0.7723 (p0) REVERT: B 994 ASP cc_start: 0.8043 (t70) cc_final: 0.7571 (t0) REVERT: C 146 HIS cc_start: 0.6437 (m-70) cc_final: 0.6165 (m170) REVERT: C 158 ARG cc_start: 0.6622 (mtt180) cc_final: 0.6199 (mmm-85) REVERT: C 191 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7240 (mp0) REVERT: C 192 PHE cc_start: 0.7887 (m-80) cc_final: 0.7661 (m-10) REVERT: C 278 LYS cc_start: 0.8620 (tttt) cc_final: 0.8320 (ttpt) REVERT: C 298 GLU cc_start: 0.8484 (tp30) cc_final: 0.8173 (tp30) REVERT: C 347 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.6527 (m-80) REVERT: C 351 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.8160 (p90) REVERT: C 360 ASN cc_start: 0.8387 (t0) cc_final: 0.8106 (t0) REVERT: C 368 LEU cc_start: 0.8920 (pp) cc_final: 0.8575 (pp) REVERT: C 389 ASP cc_start: 0.7475 (m-30) cc_final: 0.7263 (t0) REVERT: C 462 LYS cc_start: 0.8984 (mmmm) cc_final: 0.8612 (mmmm) REVERT: C 490 PHE cc_start: 0.8098 (t80) cc_final: 0.7560 (t80) REVERT: C 492 LEU cc_start: 0.8522 (mt) cc_final: 0.8178 (mt) REVERT: C 564 GLN cc_start: 0.8212 (tp40) cc_final: 0.7872 (tp40) REVERT: C 643 PHE cc_start: 0.8061 (t80) cc_final: 0.7777 (t80) REVERT: C 776 LYS cc_start: 0.8637 (tttm) cc_final: 0.8218 (tttm) REVERT: C 780 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7400 (mm-30) REVERT: C 796 ASP cc_start: 0.8022 (t0) cc_final: 0.7725 (t0) REVERT: C 912 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8126 (p) REVERT: C 1119 ASN cc_start: 0.8561 (m-40) cc_final: 0.8207 (m-40) outliers start: 78 outliers final: 46 residues processed: 642 average time/residue: 0.4135 time to fit residues: 412.3319 Evaluate side-chains 612 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 560 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 986 LYS Chi-restraints excluded: chain C residue 1101 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 268 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 274 optimal weight: 0.7980 chunk 222 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 164 optimal weight: 3.9990 chunk 288 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 218 HIS A 314 GLN A 388 ASN A 613 GLN A1002 GLN A1005 GLN A1119 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 804 GLN B1005 GLN B1088 HIS C 66 HIS C 394 ASN C 804 GLN C1002 GLN C1159 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28302 Z= 0.249 Angle : 0.701 11.698 38508 Z= 0.335 Chirality : 0.046 0.272 4716 Planarity : 0.004 0.058 4803 Dihedral : 11.976 108.492 6102 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.79 % Favored : 95.03 % Rotamer: Outliers : 3.21 % Allowed : 14.37 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3300 helix: 2.06 (0.20), residues: 729 sheet: -0.17 (0.18), residues: 735 loop : -1.09 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 436 HIS 0.011 0.001 HIS C 207 PHE 0.024 0.001 PHE C 392 TYR 0.019 0.001 TYR C1067 ARG 0.007 0.001 ARG B1091 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 597 time to evaluate : 3.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.7655 (tp40) cc_final: 0.7376 (tp-100) REVERT: A 158 ARG cc_start: 0.7385 (mmt-90) cc_final: 0.7003 (mmt-90) REVERT: A 190 ARG cc_start: 0.7248 (tpp80) cc_final: 0.6907 (tpp80) REVERT: A 271 GLN cc_start: 0.7988 (mp10) cc_final: 0.7372 (mp10) REVERT: A 319 ARG cc_start: 0.8446 (ttp-110) cc_final: 0.8245 (ttm110) REVERT: A 347 PHE cc_start: 0.7300 (m-80) cc_final: 0.7003 (m-80) REVERT: A 351 TYR cc_start: 0.8304 (p90) cc_final: 0.7935 (p90) REVERT: A 354 ASN cc_start: 0.8298 (t0) cc_final: 0.8039 (t0) REVERT: A 360 ASN cc_start: 0.8584 (t0) cc_final: 0.8222 (t0) REVERT: A 421 TYR cc_start: 0.7845 (m-80) cc_final: 0.7442 (m-10) REVERT: A 505 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: A 565 PHE cc_start: 0.7471 (m-80) cc_final: 0.7197 (m-80) REVERT: A 643 PHE cc_start: 0.8157 (t80) cc_final: 0.7650 (t80) REVERT: A 790 LYS cc_start: 0.8691 (ptpp) cc_final: 0.8356 (ptpp) REVERT: A 912 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8313 (p) REVERT: A 994 ASP cc_start: 0.8182 (t70) cc_final: 0.7866 (t0) REVERT: A 995 ARG cc_start: 0.8393 (mtt-85) cc_final: 0.8034 (mtp180) REVERT: A 1002 GLN cc_start: 0.7979 (tt0) cc_final: 0.7761 (tt0) REVERT: B 140 PHE cc_start: 0.8196 (p90) cc_final: 0.7911 (p90) REVERT: B 190 ARG cc_start: 0.7496 (tpp-160) cc_final: 0.6680 (tpp80) REVERT: B 319 ARG cc_start: 0.8525 (ttp-110) cc_final: 0.8294 (ttm110) REVERT: B 351 TYR cc_start: 0.8404 (p90) cc_final: 0.7896 (p90) REVERT: B 465 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7226 (mt-10) REVERT: B 490 PHE cc_start: 0.8314 (t80) cc_final: 0.7966 (t80) REVERT: B 523 THR cc_start: 0.8353 (p) cc_final: 0.7841 (t) REVERT: B 661 GLU cc_start: 0.7129 (pm20) cc_final: 0.6822 (pm20) REVERT: B 693 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8852 (pp) REVERT: B 776 LYS cc_start: 0.8729 (ttmm) cc_final: 0.8486 (tttt) REVERT: B 790 LYS cc_start: 0.8652 (ptpp) cc_final: 0.8378 (ptpp) REVERT: B 796 ASP cc_start: 0.8155 (t0) cc_final: 0.7832 (t0) REVERT: B 986 LYS cc_start: 0.8345 (mmmt) cc_final: 0.8099 (mmmt) REVERT: B 994 ASP cc_start: 0.8064 (t70) cc_final: 0.7570 (t0) REVERT: B 1082 CYS cc_start: 0.5474 (t) cc_final: 0.5199 (t) REVERT: C 146 HIS cc_start: 0.6455 (m-70) cc_final: 0.6182 (m170) REVERT: C 191 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7275 (mp0) REVERT: C 278 LYS cc_start: 0.8664 (tttt) cc_final: 0.8344 (ttpt) REVERT: C 298 GLU cc_start: 0.8479 (tp30) cc_final: 0.8215 (tp30) REVERT: C 347 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.6498 (m-80) REVERT: C 351 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.8177 (p90) REVERT: C 360 ASN cc_start: 0.8419 (t0) cc_final: 0.8150 (t0) REVERT: C 368 LEU cc_start: 0.8941 (pp) cc_final: 0.8595 (pp) REVERT: C 462 LYS cc_start: 0.9006 (mmmm) cc_final: 0.8389 (mmmm) REVERT: C 465 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7317 (mt-10) REVERT: C 490 PHE cc_start: 0.8150 (t80) cc_final: 0.7939 (t80) REVERT: C 564 GLN cc_start: 0.8227 (tp40) cc_final: 0.7955 (tp-100) REVERT: C 643 PHE cc_start: 0.8082 (t80) cc_final: 0.7806 (t80) REVERT: C 776 LYS cc_start: 0.8646 (tttm) cc_final: 0.8256 (tttm) REVERT: C 780 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7445 (mm-30) REVERT: C 796 ASP cc_start: 0.8040 (t0) cc_final: 0.7768 (t0) REVERT: C 817 PHE cc_start: 0.8280 (t80) cc_final: 0.7919 (t80) REVERT: C 912 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8109 (p) REVERT: C 1119 ASN cc_start: 0.8584 (m-40) cc_final: 0.8237 (m-40) REVERT: C 1138 TYR cc_start: 0.8064 (t80) cc_final: 0.7830 (t80) outliers start: 93 outliers final: 66 residues processed: 653 average time/residue: 0.3988 time to fit residues: 407.1689 Evaluate side-chains 638 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 566 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 986 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1101 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 108 optimal weight: 1.9990 chunk 289 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 79 optimal weight: 0.0570 chunk 322 optimal weight: 0.8980 chunk 267 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 169 optimal weight: 0.3980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 954 GLN A1119 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 GLN B 658 ASN B1005 GLN C 66 HIS C 388 ASN C 969 ASN C1159 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 28302 Z= 0.212 Angle : 0.688 11.953 38508 Z= 0.328 Chirality : 0.045 0.269 4716 Planarity : 0.004 0.056 4803 Dihedral : 11.274 108.231 6102 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.39 % Favored : 95.42 % Rotamer: Outliers : 3.38 % Allowed : 14.96 % Favored : 81.66 % 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: -0.18 (0.14), residues: 3300 helix: 2.07 (0.20), residues: 732 sheet: -0.06 (0.18), residues: 714 loop : -1.08 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 436 HIS 0.012 0.001 HIS C 207 PHE 0.023 0.001 PHE C 392 TYR 0.018 0.001 TYR C1067 ARG 0.009 0.001 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 578 time to evaluate : 3.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.7439 (mmt-90) cc_final: 0.6881 (mmt-90) REVERT: A 190 ARG cc_start: 0.7216 (tpp80) cc_final: 0.6845 (tpp80) REVERT: A 271 GLN cc_start: 0.8013 (mp10) cc_final: 0.7686 (mp10) REVERT: A 298 GLU cc_start: 0.8416 (tp30) cc_final: 0.8104 (tp30) REVERT: A 319 ARG cc_start: 0.8433 (ttp-110) cc_final: 0.8158 (ttm110) REVERT: A 351 TYR cc_start: 0.8285 (p90) cc_final: 0.7947 (p90) REVERT: A 354 ASN cc_start: 0.8279 (t0) cc_final: 0.8026 (t0) REVERT: A 360 ASN cc_start: 0.8505 (t0) cc_final: 0.8246 (t0) REVERT: A 421 TYR cc_start: 0.7704 (m-80) cc_final: 0.7327 (m-10) REVERT: A 505 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.7417 (m-80) REVERT: A 509 ARG cc_start: 0.5525 (OUTLIER) cc_final: 0.4577 (mtp180) REVERT: A 565 PHE cc_start: 0.7455 (m-80) cc_final: 0.7170 (m-80) REVERT: A 790 LYS cc_start: 0.8690 (ptpp) cc_final: 0.8362 (ptpp) REVERT: A 994 ASP cc_start: 0.8175 (t70) cc_final: 0.7855 (t0) REVERT: A 995 ARG cc_start: 0.8368 (mtt-85) cc_final: 0.8011 (mtp180) REVERT: A 1107 ARG cc_start: 0.7941 (mtt90) cc_final: 0.7620 (mtt90) REVERT: B 108 THR cc_start: 0.6940 (OUTLIER) cc_final: 0.6527 (m) REVERT: B 140 PHE cc_start: 0.8164 (p90) cc_final: 0.7868 (p90) REVERT: B 190 ARG cc_start: 0.7490 (tpp-160) cc_final: 0.6660 (tpp-160) REVERT: B 319 ARG cc_start: 0.8526 (ttp-110) cc_final: 0.8316 (ttm110) REVERT: B 351 TYR cc_start: 0.8371 (p90) cc_final: 0.7890 (p90) REVERT: B 462 LYS cc_start: 0.8912 (mtmm) cc_final: 0.8607 (mttm) REVERT: B 465 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7427 (mt-10) REVERT: B 490 PHE cc_start: 0.8358 (t80) cc_final: 0.8019 (t80) REVERT: B 523 THR cc_start: 0.8368 (p) cc_final: 0.7845 (t) REVERT: B 578 ASP cc_start: 0.7959 (t0) cc_final: 0.7596 (t70) REVERT: B 591 SER cc_start: 0.8953 (t) cc_final: 0.8377 (p) REVERT: B 661 GLU cc_start: 0.7054 (pm20) cc_final: 0.6844 (pm20) REVERT: B 693 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8820 (pp) REVERT: B 776 LYS cc_start: 0.8711 (ttmm) cc_final: 0.8456 (tttt) REVERT: B 796 ASP cc_start: 0.8139 (t0) cc_final: 0.7819 (t0) REVERT: B 808 ASP cc_start: 0.8042 (t0) cc_final: 0.7797 (t0) REVERT: B 817 PHE cc_start: 0.8543 (t80) cc_final: 0.8007 (t80) REVERT: B 986 LYS cc_start: 0.8320 (mmmt) cc_final: 0.8058 (mmmt) REVERT: B 994 ASP cc_start: 0.8048 (t70) cc_final: 0.7529 (t0) REVERT: B 1082 CYS cc_start: 0.5420 (t) cc_final: 0.5179 (t) REVERT: C 146 HIS cc_start: 0.6448 (m-70) cc_final: 0.6182 (m170) REVERT: C 191 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7264 (mp0) REVERT: C 278 LYS cc_start: 0.8691 (tttt) cc_final: 0.8371 (ttpt) REVERT: C 298 GLU cc_start: 0.8479 (tp30) cc_final: 0.8208 (tp30) REVERT: C 347 PHE cc_start: 0.7455 (OUTLIER) cc_final: 0.6565 (m-80) REVERT: C 351 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.8126 (p90) REVERT: C 360 ASN cc_start: 0.8432 (t0) cc_final: 0.8176 (t0) REVERT: C 368 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8561 (pp) REVERT: C 462 LYS cc_start: 0.9035 (mmmm) cc_final: 0.8451 (mmmm) REVERT: C 465 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7431 (mt-10) REVERT: C 490 PHE cc_start: 0.8267 (t80) cc_final: 0.8038 (t80) REVERT: C 564 GLN cc_start: 0.8247 (tp40) cc_final: 0.7960 (tp40) REVERT: C 643 PHE cc_start: 0.8048 (t80) cc_final: 0.7766 (t80) REVERT: C 776 LYS cc_start: 0.8638 (tttm) cc_final: 0.8303 (tttm) REVERT: C 780 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7448 (mm-30) REVERT: C 796 ASP cc_start: 0.8028 (t0) cc_final: 0.7768 (t0) REVERT: C 912 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8076 (p) REVERT: C 1119 ASN cc_start: 0.8533 (m-40) cc_final: 0.8195 (m-40) REVERT: C 1138 TYR cc_start: 0.8065 (t80) cc_final: 0.7828 (t80) outliers start: 98 outliers final: 72 residues processed: 634 average time/residue: 0.4120 time to fit residues: 405.0412 Evaluate side-chains 645 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 565 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 986 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1101 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 310 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 183 optimal weight: 0.6980 chunk 235 optimal weight: 9.9990 chunk 182 optimal weight: 0.6980 chunk 271 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 320 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 195 optimal weight: 0.0570 chunk 148 optimal weight: 0.6980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 134 GLN A 314 GLN A 613 GLN A 954 GLN A1088 HIS ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B1005 GLN C 969 ASN C1088 HIS C1159 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 28302 Z= 0.214 Angle : 0.691 17.550 38508 Z= 0.327 Chirality : 0.045 0.274 4716 Planarity : 0.004 0.054 4803 Dihedral : 10.642 107.972 6102 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.45 % Favored : 95.36 % Rotamer: Outliers : 3.52 % Allowed : 15.58 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3300 helix: 2.11 (0.20), residues: 732 sheet: -0.08 (0.18), residues: 714 loop : -1.03 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 436 HIS 0.012 0.001 HIS C 207 PHE 0.023 0.001 PHE C 392 TYR 0.018 0.001 TYR C1067 ARG 0.008 0.001 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 585 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.7454 (mmt-90) cc_final: 0.6886 (mmt-90) REVERT: A 190 ARG cc_start: 0.7181 (tpp80) cc_final: 0.6964 (tpp80) REVERT: A 191 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7049 (mp0) REVERT: A 220 PHE cc_start: 0.8088 (t80) cc_final: 0.7818 (t80) REVERT: A 269 TYR cc_start: 0.6916 (m-10) cc_final: 0.6626 (m-80) REVERT: A 271 GLN cc_start: 0.8002 (mp10) cc_final: 0.7504 (mp10) REVERT: A 298 GLU cc_start: 0.8418 (tp30) cc_final: 0.8102 (tp30) REVERT: A 319 ARG cc_start: 0.8442 (ttp-110) cc_final: 0.8167 (ttm110) REVERT: A 351 TYR cc_start: 0.8280 (p90) cc_final: 0.7955 (p90) REVERT: A 354 ASN cc_start: 0.8248 (t0) cc_final: 0.8008 (t0) REVERT: A 360 ASN cc_start: 0.8516 (t0) cc_final: 0.8262 (t0) REVERT: A 421 TYR cc_start: 0.7747 (m-80) cc_final: 0.7279 (m-10) REVERT: A 523 THR cc_start: 0.8400 (p) cc_final: 0.8041 (t) REVERT: A 565 PHE cc_start: 0.7428 (m-80) cc_final: 0.7137 (m-80) REVERT: A 607 GLN cc_start: 0.8312 (mt0) cc_final: 0.8059 (mt0) REVERT: A 658 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8429 (p0) REVERT: A 790 LYS cc_start: 0.8691 (ptpp) cc_final: 0.8363 (ptpp) REVERT: A 994 ASP cc_start: 0.8184 (t70) cc_final: 0.7866 (t0) REVERT: A 995 ARG cc_start: 0.8365 (mtt-85) cc_final: 0.7999 (mtp180) REVERT: B 108 THR cc_start: 0.6962 (OUTLIER) cc_final: 0.6539 (m) REVERT: B 140 PHE cc_start: 0.8149 (p90) cc_final: 0.7837 (p90) REVERT: B 191 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6980 (mt-10) REVERT: B 319 ARG cc_start: 0.8537 (ttp-110) cc_final: 0.8336 (ttm110) REVERT: B 351 TYR cc_start: 0.8376 (p90) cc_final: 0.7890 (p90) REVERT: B 414 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8131 (mm-40) REVERT: B 465 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7312 (mt-10) REVERT: B 490 PHE cc_start: 0.8373 (t80) cc_final: 0.8020 (t80) REVERT: B 523 THR cc_start: 0.8393 (p) cc_final: 0.7865 (t) REVERT: B 578 ASP cc_start: 0.7970 (t0) cc_final: 0.7601 (t70) REVERT: B 661 GLU cc_start: 0.7063 (pm20) cc_final: 0.6819 (pm20) REVERT: B 693 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8792 (pp) REVERT: B 776 LYS cc_start: 0.8697 (ttmm) cc_final: 0.8450 (tttt) REVERT: B 796 ASP cc_start: 0.8155 (t0) cc_final: 0.7827 (t0) REVERT: B 808 ASP cc_start: 0.8036 (t0) cc_final: 0.7774 (t0) REVERT: B 823 PHE cc_start: 0.8208 (t80) cc_final: 0.7709 (t80) REVERT: B 986 LYS cc_start: 0.8280 (mmmt) cc_final: 0.8059 (mmmt) REVERT: B 994 ASP cc_start: 0.8045 (t70) cc_final: 0.7554 (t0) REVERT: B 995 ARG cc_start: 0.8301 (mtt-85) cc_final: 0.8012 (mtt-85) REVERT: B 1082 CYS cc_start: 0.5443 (t) cc_final: 0.5182 (t) REVERT: C 146 HIS cc_start: 0.6475 (m-70) cc_final: 0.6206 (m170) REVERT: C 191 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7313 (mp0) REVERT: C 278 LYS cc_start: 0.8698 (tttt) cc_final: 0.8384 (ttpt) REVERT: C 347 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.6655 (m-80) REVERT: C 351 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.8153 (p90) REVERT: C 360 ASN cc_start: 0.8443 (t0) cc_final: 0.8199 (t0) REVERT: C 368 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8551 (pp) REVERT: C 462 LYS cc_start: 0.9051 (mmmm) cc_final: 0.8417 (mmmm) REVERT: C 465 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7406 (mt-10) REVERT: C 490 PHE cc_start: 0.8300 (t80) cc_final: 0.8042 (t80) REVERT: C 564 GLN cc_start: 0.8260 (tp40) cc_final: 0.7939 (tp40) REVERT: C 643 PHE cc_start: 0.8028 (t80) cc_final: 0.7776 (t80) REVERT: C 710 ASN cc_start: 0.8900 (p0) cc_final: 0.8661 (p0) REVERT: C 776 LYS cc_start: 0.8643 (tttm) cc_final: 0.8297 (tttm) REVERT: C 780 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7454 (mm-30) REVERT: C 796 ASP cc_start: 0.8043 (t0) cc_final: 0.7794 (t0) REVERT: C 912 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8065 (p) REVERT: C 994 ASP cc_start: 0.7972 (t0) cc_final: 0.7761 (t0) REVERT: C 1119 ASN cc_start: 0.8512 (m-40) cc_final: 0.8198 (m-40) REVERT: C 1138 TYR cc_start: 0.8076 (t80) cc_final: 0.7800 (t80) outliers start: 102 outliers final: 74 residues processed: 648 average time/residue: 0.4095 time to fit residues: 412.3890 Evaluate side-chains 645 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 563 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 986 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1101 ASP Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 198 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 218 optimal weight: 0.2980 chunk 158 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 252 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 658 ASN A 954 GLN A1005 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B1005 GLN C 188 ASN C 901 GLN C1159 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 28302 Z= 0.242 Angle : 0.695 14.431 38508 Z= 0.330 Chirality : 0.045 0.282 4716 Planarity : 0.004 0.052 4803 Dihedral : 10.167 108.942 6102 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.70 % Favored : 95.12 % Rotamer: Outliers : 3.14 % Allowed : 16.27 % Favored : 80.59 % 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: 3300 helix: 2.14 (0.20), residues: 732 sheet: -0.10 (0.18), residues: 714 loop : -1.03 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 436 HIS 0.012 0.001 HIS C 207 PHE 0.030 0.001 PHE C 392 TYR 0.018 0.001 TYR C1067 ARG 0.009 0.001 ARG B1091 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 585 time to evaluate : 3.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.7482 (mmt-90) cc_final: 0.6901 (mmt-90) REVERT: A 191 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7073 (mp0) REVERT: A 220 PHE cc_start: 0.8111 (t80) cc_final: 0.7790 (t80) REVERT: A 271 GLN cc_start: 0.8070 (mp10) cc_final: 0.7394 (mp10) REVERT: A 278 LYS cc_start: 0.8925 (tttt) cc_final: 0.8588 (ttmt) REVERT: A 298 GLU cc_start: 0.8426 (tp30) cc_final: 0.8107 (tp30) REVERT: A 319 ARG cc_start: 0.8453 (ttp-110) cc_final: 0.8091 (ttm110) REVERT: A 354 ASN cc_start: 0.8239 (t0) cc_final: 0.7971 (t0) REVERT: A 360 ASN cc_start: 0.8526 (t0) cc_final: 0.8275 (t0) REVERT: A 421 TYR cc_start: 0.7656 (m-80) cc_final: 0.7195 (m-10) REVERT: A 523 THR cc_start: 0.8503 (p) cc_final: 0.8111 (t) REVERT: A 565 PHE cc_start: 0.7433 (m-80) cc_final: 0.7147 (m-80) REVERT: A 607 GLN cc_start: 0.8320 (mt0) cc_final: 0.8092 (mt0) REVERT: A 790 LYS cc_start: 0.8695 (ptpp) cc_final: 0.8342 (ptpp) REVERT: A 994 ASP cc_start: 0.8203 (t70) cc_final: 0.7887 (t0) REVERT: B 108 THR cc_start: 0.6881 (OUTLIER) cc_final: 0.6439 (m) REVERT: B 140 PHE cc_start: 0.8148 (p90) cc_final: 0.7831 (p90) REVERT: B 190 ARG cc_start: 0.7554 (tpp-160) cc_final: 0.6677 (tpp80) REVERT: B 191 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7168 (mt-10) REVERT: B 351 TYR cc_start: 0.8389 (p90) cc_final: 0.7893 (p90) REVERT: B 414 GLN cc_start: 0.8486 (mm-40) cc_final: 0.7947 (mm110) REVERT: B 462 LYS cc_start: 0.8897 (mtmm) cc_final: 0.8544 (mtmm) REVERT: B 465 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7306 (mt-10) REVERT: B 490 PHE cc_start: 0.8362 (t80) cc_final: 0.8009 (t80) REVERT: B 523 THR cc_start: 0.8409 (p) cc_final: 0.7867 (t) REVERT: B 578 ASP cc_start: 0.7933 (t0) cc_final: 0.7562 (t70) REVERT: B 661 GLU cc_start: 0.7140 (pm20) cc_final: 0.6897 (pm20) REVERT: B 693 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8789 (pp) REVERT: B 776 LYS cc_start: 0.8694 (ttmm) cc_final: 0.8446 (tttt) REVERT: B 796 ASP cc_start: 0.8155 (t0) cc_final: 0.7838 (t0) REVERT: B 808 ASP cc_start: 0.8032 (t0) cc_final: 0.7776 (t0) REVERT: B 817 PHE cc_start: 0.8521 (t80) cc_final: 0.8291 (t80) REVERT: B 823 PHE cc_start: 0.8207 (t80) cc_final: 0.7699 (t80) REVERT: B 986 LYS cc_start: 0.8281 (mmmt) cc_final: 0.8079 (mmmt) REVERT: B 994 ASP cc_start: 0.8058 (t70) cc_final: 0.7751 (t0) REVERT: B 995 ARG cc_start: 0.8293 (mtt-85) cc_final: 0.8004 (mtt-85) REVERT: B 1073 LYS cc_start: 0.8568 (mtpp) cc_final: 0.8113 (mttm) REVERT: B 1082 CYS cc_start: 0.5399 (t) cc_final: 0.5118 (t) REVERT: C 191 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7325 (mp0) REVERT: C 278 LYS cc_start: 0.8719 (tttt) cc_final: 0.8379 (ttpt) REVERT: C 298 GLU cc_start: 0.8545 (tp30) cc_final: 0.8261 (tp30) REVERT: C 347 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.6699 (m-80) REVERT: C 351 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.8151 (p90) REVERT: C 360 ASN cc_start: 0.8495 (t0) cc_final: 0.8257 (t0) REVERT: C 368 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8567 (pp) REVERT: C 490 PHE cc_start: 0.8313 (t80) cc_final: 0.8035 (t80) REVERT: C 564 GLN cc_start: 0.8254 (tp40) cc_final: 0.7934 (tp40) REVERT: C 643 PHE cc_start: 0.8043 (t80) cc_final: 0.7746 (t80) REVERT: C 710 ASN cc_start: 0.8931 (p0) cc_final: 0.8693 (p0) REVERT: C 776 LYS cc_start: 0.8641 (tttm) cc_final: 0.8276 (tttm) REVERT: C 780 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7489 (mm-30) REVERT: C 796 ASP cc_start: 0.8044 (t0) cc_final: 0.7806 (t0) REVERT: C 912 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8058 (p) REVERT: C 933 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8431 (ttmm) REVERT: C 994 ASP cc_start: 0.7978 (t0) cc_final: 0.7746 (t0) REVERT: C 1119 ASN cc_start: 0.8518 (m-40) cc_final: 0.8187 (m-40) REVERT: C 1138 TYR cc_start: 0.8075 (t80) cc_final: 0.7842 (t80) outliers start: 91 outliers final: 76 residues processed: 639 average time/residue: 0.4070 time to fit residues: 399.4789 Evaluate side-chains 647 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 564 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1101 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 291 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 chunk 280 optimal weight: 0.9990 chunk 299 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 234 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 270 optimal weight: 0.2980 chunk 282 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 314 GLN A 613 GLN A 655 HIS A 954 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B1005 GLN C1159 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 28302 Z= 0.280 Angle : 0.719 13.926 38508 Z= 0.344 Chirality : 0.046 0.286 4716 Planarity : 0.004 0.061 4803 Dihedral : 9.955 110.436 6100 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.79 % Favored : 95.03 % Rotamer: Outliers : 3.10 % Allowed : 17.34 % Favored : 79.56 % 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: -0.18 (0.14), residues: 3300 helix: 1.94 (0.20), residues: 750 sheet: -0.10 (0.18), residues: 744 loop : -1.04 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 104 HIS 0.012 0.001 HIS C 207 PHE 0.027 0.001 PHE A 643 TYR 0.019 0.001 TYR A1138 ARG 0.010 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 571 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.7415 (mmt-90) cc_final: 0.6786 (mmt-90) REVERT: A 220 PHE cc_start: 0.8121 (t80) cc_final: 0.7802 (t80) REVERT: A 271 GLN cc_start: 0.8139 (mp10) cc_final: 0.7432 (mp10) REVERT: A 278 LYS cc_start: 0.8937 (tttt) cc_final: 0.8625 (ttmt) REVERT: A 298 GLU cc_start: 0.8432 (tp30) cc_final: 0.8117 (tp30) REVERT: A 319 ARG cc_start: 0.8429 (ttp-110) cc_final: 0.8167 (ttm110) REVERT: A 353 TRP cc_start: 0.8347 (p-90) cc_final: 0.8018 (p-90) REVERT: A 354 ASN cc_start: 0.8254 (t0) cc_final: 0.8004 (t0) REVERT: A 360 ASN cc_start: 0.8535 (t0) cc_final: 0.8290 (t0) REVERT: A 398 ASP cc_start: 0.7013 (m-30) cc_final: 0.6596 (m-30) REVERT: A 421 TYR cc_start: 0.7739 (m-80) cc_final: 0.7335 (m-10) REVERT: A 523 THR cc_start: 0.8619 (p) cc_final: 0.8252 (t) REVERT: A 565 PHE cc_start: 0.7469 (m-80) cc_final: 0.7190 (m-80) REVERT: A 646 ARG cc_start: 0.8226 (mtm-85) cc_final: 0.8016 (mtm-85) REVERT: A 994 ASP cc_start: 0.8232 (t70) cc_final: 0.7924 (t0) REVERT: B 140 PHE cc_start: 0.8173 (p90) cc_final: 0.7845 (p90) REVERT: B 190 ARG cc_start: 0.7536 (tpp-160) cc_final: 0.7160 (tpp80) REVERT: B 191 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7226 (mt-10) REVERT: B 351 TYR cc_start: 0.8415 (p90) cc_final: 0.7954 (p90) REVERT: B 414 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8010 (mm110) REVERT: B 465 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7305 (mt-10) REVERT: B 490 PHE cc_start: 0.8386 (t80) cc_final: 0.8041 (t80) REVERT: B 523 THR cc_start: 0.8419 (p) cc_final: 0.7870 (t) REVERT: B 578 ASP cc_start: 0.7952 (t0) cc_final: 0.7589 (t70) REVERT: B 693 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8807 (pp) REVERT: B 725 GLU cc_start: 0.7443 (tt0) cc_final: 0.7209 (tt0) REVERT: B 796 ASP cc_start: 0.8164 (t0) cc_final: 0.7849 (t0) REVERT: B 808 ASP cc_start: 0.7873 (t0) cc_final: 0.7590 (t0) REVERT: B 817 PHE cc_start: 0.8530 (t80) cc_final: 0.8089 (t80) REVERT: B 823 PHE cc_start: 0.8217 (t80) cc_final: 0.7701 (t80) REVERT: B 986 LYS cc_start: 0.8275 (mmmt) cc_final: 0.7983 (mmmt) REVERT: B 994 ASP cc_start: 0.7966 (t70) cc_final: 0.7709 (t0) REVERT: B 1073 LYS cc_start: 0.8574 (mtpp) cc_final: 0.8112 (mttm) REVERT: B 1082 CYS cc_start: 0.5398 (t) cc_final: 0.5109 (t) REVERT: B 1123 SER cc_start: 0.9140 (OUTLIER) cc_final: 0.8700 (t) REVERT: C 191 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7416 (mp0) REVERT: C 278 LYS cc_start: 0.8748 (tttt) cc_final: 0.8378 (ttpt) REVERT: C 298 GLU cc_start: 0.8557 (tp30) cc_final: 0.8278 (tp30) REVERT: C 347 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.6602 (m-80) REVERT: C 351 TYR cc_start: 0.8506 (p90) cc_final: 0.8154 (p90) REVERT: C 360 ASN cc_start: 0.8527 (t0) cc_final: 0.8304 (t0) REVERT: C 368 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8595 (pp) REVERT: C 490 PHE cc_start: 0.8332 (t80) cc_final: 0.8032 (t80) REVERT: C 564 GLN cc_start: 0.8258 (tp40) cc_final: 0.7934 (tp40) REVERT: C 643 PHE cc_start: 0.8078 (t80) cc_final: 0.7753 (t80) REVERT: C 710 ASN cc_start: 0.8947 (p0) cc_final: 0.8711 (p0) REVERT: C 776 LYS cc_start: 0.8649 (tttm) cc_final: 0.8291 (ttpp) REVERT: C 780 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7441 (mm-30) REVERT: C 796 ASP cc_start: 0.8047 (t0) cc_final: 0.7834 (t0) REVERT: C 814 LYS cc_start: 0.8345 (mmpt) cc_final: 0.8126 (mptt) REVERT: C 912 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.8044 (p) REVERT: C 1119 ASN cc_start: 0.8537 (m-40) cc_final: 0.8197 (m-40) REVERT: C 1138 TYR cc_start: 0.8133 (t80) cc_final: 0.7856 (t80) outliers start: 90 outliers final: 74 residues processed: 628 average time/residue: 0.4438 time to fit residues: 428.8605 Evaluate side-chains 642 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 562 time to evaluate : 3.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1101 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 196 optimal weight: 0.3980 chunk 316 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 219 optimal weight: 0.9980 chunk 331 optimal weight: 0.7980 chunk 305 optimal weight: 0.5980 chunk 264 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 204 optimal weight: 0.8980 chunk 161 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 613 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 955 ASN B1005 GLN C1159 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 28302 Z= 0.214 Angle : 0.710 16.377 38508 Z= 0.338 Chirality : 0.045 0.272 4716 Planarity : 0.004 0.048 4803 Dihedral : 9.525 109.269 6100 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.33 % Favored : 95.48 % Rotamer: Outliers : 2.55 % Allowed : 18.24 % 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: -0.11 (0.14), residues: 3300 helix: 2.09 (0.20), residues: 732 sheet: -0.07 (0.18), residues: 741 loop : -1.01 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 104 HIS 0.013 0.001 HIS C 207 PHE 0.040 0.001 PHE C 817 TYR 0.018 0.001 TYR C1067 ARG 0.009 0.001 ARG C 567 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 577 time to evaluate : 2.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6458 (mtt180) cc_final: 0.6051 (ttt180) REVERT: A 158 ARG cc_start: 0.7385 (mmt-90) cc_final: 0.6804 (mmt-90) REVERT: A 191 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7008 (mp0) REVERT: A 220 PHE cc_start: 0.8079 (t80) cc_final: 0.7801 (t80) REVERT: A 271 GLN cc_start: 0.8089 (mp10) cc_final: 0.7424 (mp10) REVERT: A 278 LYS cc_start: 0.8941 (tttt) cc_final: 0.8608 (ttmt) REVERT: A 298 GLU cc_start: 0.8425 (tp30) cc_final: 0.8109 (tp30) REVERT: A 319 ARG cc_start: 0.8408 (ttp-110) cc_final: 0.8059 (ttm110) REVERT: A 354 ASN cc_start: 0.8262 (t0) cc_final: 0.8018 (t0) REVERT: A 360 ASN cc_start: 0.8485 (t0) cc_final: 0.8257 (t0) REVERT: A 421 TYR cc_start: 0.7694 (m-80) cc_final: 0.7182 (m-10) REVERT: A 505 TYR cc_start: 0.7364 (m-80) cc_final: 0.6632 (m-80) REVERT: A 523 THR cc_start: 0.8647 (p) cc_final: 0.8279 (t) REVERT: A 646 ARG cc_start: 0.8178 (mtm-85) cc_final: 0.7963 (mtm-85) REVERT: A 790 LYS cc_start: 0.8640 (ptpp) cc_final: 0.8276 (ptpp) REVERT: A 794 ILE cc_start: 0.9000 (mt) cc_final: 0.8724 (tp) REVERT: A 804 GLN cc_start: 0.8354 (mm110) cc_final: 0.7976 (mm-40) REVERT: A 935 GLN cc_start: 0.8423 (tt0) cc_final: 0.7926 (tt0) REVERT: A 994 ASP cc_start: 0.8197 (t70) cc_final: 0.7856 (t0) REVERT: B 108 THR cc_start: 0.6953 (OUTLIER) cc_final: 0.6473 (m) REVERT: B 140 PHE cc_start: 0.8079 (p90) cc_final: 0.7760 (p90) REVERT: B 190 ARG cc_start: 0.7501 (tpp-160) cc_final: 0.6663 (tpp80) REVERT: B 191 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7208 (mt-10) REVERT: B 403 ARG cc_start: 0.7655 (ttp-110) cc_final: 0.7092 (ttp80) REVERT: B 414 GLN cc_start: 0.8454 (mm-40) cc_final: 0.7971 (mm110) REVERT: B 465 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7251 (mt-10) REVERT: B 490 PHE cc_start: 0.8356 (t80) cc_final: 0.8019 (t80) REVERT: B 523 THR cc_start: 0.8447 (p) cc_final: 0.7887 (t) REVERT: B 546 LEU cc_start: 0.8752 (tp) cc_final: 0.8507 (tt) REVERT: B 578 ASP cc_start: 0.7999 (t0) cc_final: 0.7612 (t70) REVERT: B 661 GLU cc_start: 0.7138 (pm20) cc_final: 0.6919 (pm20) REVERT: B 693 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8770 (pp) REVERT: B 776 LYS cc_start: 0.8662 (ttmm) cc_final: 0.8415 (tttt) REVERT: B 796 ASP cc_start: 0.8147 (t0) cc_final: 0.7830 (t0) REVERT: B 808 ASP cc_start: 0.7919 (t0) cc_final: 0.7657 (t0) REVERT: B 823 PHE cc_start: 0.8177 (t80) cc_final: 0.7678 (t80) REVERT: B 994 ASP cc_start: 0.7889 (t70) cc_final: 0.7644 (t0) REVERT: B 1073 LYS cc_start: 0.8567 (mtpp) cc_final: 0.8115 (mttm) REVERT: B 1082 CYS cc_start: 0.5320 (t) cc_final: 0.5036 (t) REVERT: B 1123 SER cc_start: 0.9136 (OUTLIER) cc_final: 0.8701 (t) REVERT: C 88 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.8102 (m-30) REVERT: C 158 ARG cc_start: 0.7203 (mtt180) cc_final: 0.6232 (mtp180) REVERT: C 191 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7419 (mp0) REVERT: C 278 LYS cc_start: 0.8754 (tttt) cc_final: 0.8401 (ttpt) REVERT: C 298 GLU cc_start: 0.8539 (tp30) cc_final: 0.8249 (tp30) REVERT: C 347 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6721 (m-80) REVERT: C 351 TYR cc_start: 0.8488 (p90) cc_final: 0.8150 (p90) REVERT: C 360 ASN cc_start: 0.8453 (t0) cc_final: 0.8067 (t0) REVERT: C 368 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8578 (pp) REVERT: C 490 PHE cc_start: 0.8328 (t80) cc_final: 0.8010 (t80) REVERT: C 563 GLN cc_start: 0.8527 (mm-40) cc_final: 0.7780 (mm-40) REVERT: C 564 GLN cc_start: 0.8257 (tp40) cc_final: 0.7947 (tp40) REVERT: C 658 ASN cc_start: 0.8660 (p0) cc_final: 0.8395 (p0) REVERT: C 710 ASN cc_start: 0.8912 (p0) cc_final: 0.8693 (p0) REVERT: C 776 LYS cc_start: 0.8626 (tttm) cc_final: 0.8251 (ttpp) REVERT: C 780 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7423 (mm-30) REVERT: C 933 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8318 (mtmm) REVERT: C 1119 ASN cc_start: 0.8500 (m-40) cc_final: 0.8193 (m-40) REVERT: C 1138 TYR cc_start: 0.8104 (t80) cc_final: 0.7839 (t80) outliers start: 74 outliers final: 60 residues processed: 626 average time/residue: 0.4453 time to fit residues: 434.4807 Evaluate side-chains 625 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 558 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1101 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 209 optimal weight: 1.9990 chunk 281 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 243 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 264 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 271 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 613 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 955 ASN B1005 GLN C 655 HIS C1002 GLN C1159 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.111834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.089495 restraints weight = 61022.113| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.57 r_work: 0.3257 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.300 28302 Z= 0.316 Angle : 0.832 59.185 38508 Z= 0.433 Chirality : 0.048 1.060 4716 Planarity : 0.004 0.047 4803 Dihedral : 9.522 109.268 6100 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.39 % Favored : 95.42 % Rotamer: Outliers : 2.79 % Allowed : 18.89 % Favored : 78.32 % Cbeta Deviations : 0.06 % 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: -0.12 (0.14), residues: 3300 helix: 2.09 (0.20), residues: 732 sheet: -0.08 (0.18), residues: 741 loop : -1.01 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 353 HIS 0.011 0.001 HIS C 207 PHE 0.035 0.001 PHE C 855 TYR 0.019 0.001 TYR A 380 ARG 0.021 0.001 ARG C 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7946.60 seconds wall clock time: 144 minutes 7.73 seconds (8647.73 seconds total)