Starting phenix.real_space_refine on Tue Feb 20 12:30:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnw_26021/02_2024/7tnw_26021_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnw_26021/02_2024/7tnw_26021.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/7tnw_26021/02_2024/7tnw_26021.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnw_26021/02_2024/7tnw_26021.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnw_26021/02_2024/7tnw_26021_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnw_26021/02_2024/7tnw_26021_neut.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= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17712 2.51 5 N 4485 2.21 5 O 5529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C ARG 78": "NH1" <-> "NH2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C ASP 737": "OD1" <-> "OD2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "C ASP 1146": "OD1" <-> "OD2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A ASP 737": "OD1" <-> "OD2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 994": "OD1" <-> "OD2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "A ASP 1146": "OD1" <-> "OD2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B ASP 737": "OD1" <-> "OD2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B ASP 775": "OD1" <-> "OD2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 994": "OD1" <-> "OD2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "B ASP 1146": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27846 Number of models: 1 Model: "" Number of chains: 39 Chain: "C" Number of atoms: 8789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8789 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 3 Chain: "A" Number of atoms: 8789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8789 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 3 Chain: "B" Number of atoms: 8789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8789 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 3 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: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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: 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: "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: "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 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 Time building chain proxies: 14.38, per 1000 atoms: 0.52 Number of scatterers: 27846 At special positions: 0 Unit cell: (148.57, 143.59, 196.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 5529 8.00 N 4485 7.00 C 17712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 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=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 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 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 G 2 " - " MAN G 3 " " NAG H 2 " - " MAN H 3 " " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG M 2 " - " MAN M 3 " " NAG N 2 " - " MAN N 3 " " NAG P 2 " - " MAN P 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 a 2 " - " MAN a 3 " " NAG c 2 " - " MAN c 3 " " NAG d 2 " - " MAN d 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 " 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 " BETA1-6 " NAG L 1 " - " FUC L 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG W 1 " - " FUC W 3 " " NAG h 1 " - " FUC h 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1158 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1158 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1158 " " NAG D 1 " - " ASN C 17 " " NAG E 1 " - " ASN C 122 " " NAG F 1 " - " ASN C 165 " " NAG G 1 " - " ASN C 234 " " NAG H 1 " - " ASN C 282 " " NAG I 1 " - " ASN C 616 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG L 1 " - " ASN C1074 " " NAG M 1 " - " ASN C1098 " " NAG N 1 " - " ASN C1134 " " NAG O 1 " - " ASN A 17 " " NAG P 1 " - " ASN A 122 " " NAG Q 1 " - " ASN A 165 " " NAG R 1 " - " ASN A 234 " " NAG S 1 " - " ASN A 282 " " NAG T 1 " - " ASN A 616 " " NAG U 1 " - " ASN A 717 " " NAG V 1 " - " ASN A 801 " " NAG W 1 " - " ASN A1074 " " NAG X 1 " - " ASN A1098 " " NAG Y 1 " - " ASN A1134 " " NAG Z 1 " - " ASN B 17 " " NAG a 1 " - " ASN B 122 " " NAG b 1 " - " ASN B 165 " " NAG c 1 " - " ASN B 234 " " NAG d 1 " - " ASN B 282 " " NAG e 1 " - " ASN B 616 " " NAG f 1 " - " ASN B 717 " " NAG g 1 " - " ASN B 801 " " NAG h 1 " - " ASN B1074 " " NAG i 1 " - " ASN B1098 " " NAG j 1 " - " ASN B1134 " Time building additional restraints: 12.32 Conformation dependent library (CDL) restraints added in 4.7 seconds 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6312 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 48 sheets defined 27.6% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'C' and resid 147 through 150 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.666A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 removed outlier: 3.773A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.173A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.534A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 623 removed outlier: 3.847A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 639 removed outlier: 3.665A pdb=" N TYR C 636 " --> pdb=" O TRP C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 757 through 783 removed outlier: 3.948A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.518A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 4.060A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 847 removed outlier: 4.170A pdb=" N ILE C 844 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.850A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.665A 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 removed outlier: 3.502A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.547A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.313A 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 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.814A pdb=" N GLU C 990 " --> pdb=" O LYS C 986 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1142 through 1160 removed outlier: 4.372A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 150 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: 3.666A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.773A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.173A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.534A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 removed outlier: 3.846A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 639 removed outlier: 3.666A pdb=" N TYR A 636 " --> pdb=" O TRP A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 783 removed outlier: 3.948A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.518A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 4.061A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 847 removed outlier: 4.169A pdb=" N ILE A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.850A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.665A 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 removed outlier: 3.501A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.547A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.313A 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 977 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.815A pdb=" N GLU A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1142 through 1160 removed outlier: 4.372A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.666A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 372 removed outlier: 3.773A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.173A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.534A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.846A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.665A pdb=" N TYR B 636 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 757 through 783 removed outlier: 3.949A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.518A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 4.060A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 847 removed outlier: 4.169A pdb=" N ILE B 844 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.850A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.664A 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 removed outlier: 3.502A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.547A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.313A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.814A pdb=" N GLU B 990 " --> pdb=" O LYS B 986 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1142 through 1160 removed outlier: 4.372A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.616A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.342A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.949A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.918A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.356A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.363A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.778A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.387A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.826A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.989A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE C 144 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.356A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.211A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.164A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.157A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.993A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.110A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 701 through 704 removed outlier: 6.690A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LYS A 790 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ASN C 703 " --> pdb=" O LYS A 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.044A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.956A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.280A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 787 through 790 removed outlier: 3.748A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.428A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.616A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.949A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.918A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.363A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.778A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.388A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.827A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.989A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE A 144 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.211A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.164A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.158A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.993A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.110A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.681A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.044A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.956A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.281A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.427A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.616A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.949A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.918A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.363A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.778A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.387A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.826A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.989A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE B 144 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.211A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.158A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.993A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.110A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.044A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.956A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.280A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.428A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) 1117 hydrogen bonds defined for protein. 3000 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: 13.09 Time building geometry restraints manager: 13.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4683 1.31 - 1.44: 7457 1.44 - 1.57: 16174 1.57 - 1.69: 3 1.69 - 1.82: 150 Bond restraints: 28467 Sorted by residual: bond pdb=" C ARG C 995 " pdb=" O ARG C 995 " ideal model delta sigma weight residual 1.236 1.185 0.052 1.16e-02 7.43e+03 2.00e+01 bond pdb=" C ARG A 995 " pdb=" O ARG A 995 " ideal model delta sigma weight residual 1.236 1.185 0.052 1.16e-02 7.43e+03 2.00e+01 bond pdb=" C ARG B 995 " pdb=" O ARG B 995 " ideal model delta sigma weight residual 1.236 1.185 0.052 1.16e-02 7.43e+03 1.99e+01 bond pdb=" CA ARG C1014 " pdb=" CB ARG C1014 " ideal model delta sigma weight residual 1.529 1.460 0.069 1.58e-02 4.01e+03 1.91e+01 bond pdb=" CA ARG B1014 " pdb=" CB ARG B1014 " ideal model delta sigma weight residual 1.529 1.460 0.069 1.58e-02 4.01e+03 1.89e+01 ... (remaining 28462 not shown) Histogram of bond angle deviations from ideal: 98.05 - 105.54: 656 105.54 - 113.03: 14083 113.03 - 120.52: 14084 120.52 - 128.01: 9775 128.01 - 135.50: 111 Bond angle restraints: 38709 Sorted by residual: angle pdb=" N ARG A1091 " pdb=" CA ARG A1091 " pdb=" C ARG A1091 " ideal model delta sigma weight residual 111.03 103.07 7.96 1.11e+00 8.12e-01 5.14e+01 angle pdb=" N ARG C1091 " pdb=" CA ARG C1091 " pdb=" C ARG C1091 " ideal model delta sigma weight residual 111.03 103.09 7.94 1.11e+00 8.12e-01 5.12e+01 angle pdb=" N ARG B1091 " pdb=" CA ARG B1091 " pdb=" C ARG B1091 " ideal model delta sigma weight residual 111.03 103.12 7.91 1.11e+00 8.12e-01 5.08e+01 angle pdb=" CA ASN A 422 " pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 112.60 119.57 -6.97 1.00e+00 1.00e+00 4.86e+01 angle pdb=" CA ASN B 422 " pdb=" CB ASN B 422 " pdb=" CG ASN B 422 " ideal model delta sigma weight residual 112.60 119.57 -6.97 1.00e+00 1.00e+00 4.86e+01 ... (remaining 38704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.55: 17415 24.55 - 49.11: 708 49.11 - 73.66: 198 73.66 - 98.21: 45 98.21 - 122.76: 63 Dihedral angle restraints: 18429 sinusoidal: 8625 harmonic: 9804 Sorted by residual: dihedral pdb=" N ASN C 331 " pdb=" C ASN C 331 " pdb=" CA ASN C 331 " pdb=" CB ASN C 331 " ideal model delta harmonic sigma weight residual 122.80 144.17 -21.37 0 2.50e+00 1.60e-01 7.30e+01 dihedral pdb=" N ASN A 331 " pdb=" C ASN A 331 " pdb=" CA ASN A 331 " pdb=" CB ASN A 331 " ideal model delta harmonic sigma weight residual 122.80 144.16 -21.36 0 2.50e+00 1.60e-01 7.30e+01 dihedral pdb=" N ASN B 331 " pdb=" C ASN B 331 " pdb=" CA ASN B 331 " pdb=" CB ASN B 331 " ideal model delta harmonic sigma weight residual 122.80 144.10 -21.30 0 2.50e+00 1.60e-01 7.26e+01 ... (remaining 18426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.325: 4653 0.325 - 0.649: 21 0.649 - 0.974: 6 0.974 - 1.298: 3 1.298 - 1.623: 12 Chirality restraints: 4695 Sorted by residual: chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.80e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 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 chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.78 -1.62 2.00e-01 2.50e+01 6.58e+01 ... (remaining 4692 not shown) Planarity restraints: 4896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 2 " -0.142 2.00e-02 2.50e+03 1.17e-01 1.71e+02 pdb=" C7 NAG a 2 " 0.040 2.00e-02 2.50e+03 pdb=" C8 NAG a 2 " -0.106 2.00e-02 2.50e+03 pdb=" N2 NAG a 2 " 0.187 2.00e-02 2.50e+03 pdb=" O7 NAG a 2 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 2 " -0.142 2.00e-02 2.50e+03 1.17e-01 1.70e+02 pdb=" C7 NAG P 2 " 0.040 2.00e-02 2.50e+03 pdb=" C8 NAG P 2 " -0.106 2.00e-02 2.50e+03 pdb=" N2 NAG P 2 " 0.187 2.00e-02 2.50e+03 pdb=" O7 NAG P 2 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.141 2.00e-02 2.50e+03 1.17e-01 1.70e+02 pdb=" C7 NAG E 2 " 0.039 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.106 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.186 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.022 2.00e-02 2.50e+03 ... (remaining 4893 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 873 2.74 - 3.28: 28092 3.28 - 3.82: 41990 3.82 - 4.36: 56723 4.36 - 4.90: 90540 Nonbonded interactions: 218218 Sorted by model distance: nonbonded pdb=" CZ PHE C 592 " pdb=" CE MET A 740 " model vdw 2.197 3.760 nonbonded pdb=" CE MET C 740 " pdb=" CZ PHE B 592 " model vdw 2.206 3.760 nonbonded pdb=" O MET A 900 " pdb=" CD2 TYR A 904 " model vdw 2.379 3.340 nonbonded pdb=" O MET B 900 " pdb=" CD2 TYR B 904 " model vdw 2.380 3.340 nonbonded pdb=" O MET C 900 " pdb=" CD2 TYR C 904 " model vdw 2.380 3.340 ... (remaining 218213 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 'F' selection = chain 'I' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'Z' selection = chain 'b' selection = chain 'e' } ncs_group { reference = (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 '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 'P' 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 'a' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'f' 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) } 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: 5.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 23.110 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 76.040 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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 : 0.014 0.080 28467 Z= 0.904 Angle : 1.818 10.533 38709 Z= 1.187 Chirality : 0.133 1.623 4695 Planarity : 0.013 0.117 4842 Dihedral : 16.814 122.764 11982 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.65 % Favored : 91.54 % Rotamer: Outliers : 1.81 % Allowed : 6.13 % Favored : 92.06 % Cbeta Deviations : 0.67 % 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: -1.73 (0.13), residues: 3333 helix: -1.43 (0.16), residues: 783 sheet: 0.35 (0.19), residues: 606 loop : -1.55 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.023 TRP B 64 HIS 0.011 0.003 HIS A 625 PHE 0.089 0.014 PHE A 133 TYR 0.110 0.018 TYR A 636 ARG 0.006 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 668 time to evaluate : 2.966 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: C 41 LYS cc_start: 0.8639 (mmmm) cc_final: 0.8353 (mmmm) REVERT: C 99 ASN cc_start: 0.7751 (t0) cc_final: 0.7307 (t0) REVERT: C 102 ARG cc_start: 0.7538 (mtt-85) cc_final: 0.6967 (mtt-85) REVERT: C 116 SER cc_start: 0.8734 (p) cc_final: 0.8412 (t) REVERT: C 140 PHE cc_start: 0.7981 (p90) cc_final: 0.7698 (p90) REVERT: C 176 LEU cc_start: 0.7516 (tp) cc_final: 0.7211 (tt) REVERT: C 191 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7825 (mt-10) REVERT: C 306 PHE cc_start: 0.8873 (m-80) cc_final: 0.8626 (m-80) REVERT: C 314 GLN cc_start: 0.8159 (mm110) cc_final: 0.7836 (mm-40) REVERT: C 317 ASN cc_start: 0.8376 (m110) cc_final: 0.6929 (m110) REVERT: C 351 TYR cc_start: 0.8217 (p90) cc_final: 0.7972 (p90) REVERT: C 393 THR cc_start: 0.7521 (m) cc_final: 0.7319 (p) REVERT: C 586 ASP cc_start: 0.8209 (m-30) cc_final: 0.7838 (m-30) REVERT: C 654 GLU cc_start: 0.7814 (tt0) cc_final: 0.7389 (tt0) REVERT: C 675 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7355 (pp30) REVERT: C 690 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7733 (mm-40) REVERT: C 693 ILE cc_start: 0.9342 (pt) cc_final: 0.9040 (pt) REVERT: C 755 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8342 (mp10) REVERT: C 773 GLU cc_start: 0.8140 (tp30) cc_final: 0.7924 (tt0) REVERT: C 776 LYS cc_start: 0.8836 (tttp) cc_final: 0.8518 (tttm) REVERT: C 780 GLU cc_start: 0.8556 (mt-10) cc_final: 0.7936 (mt-10) REVERT: C 790 LYS cc_start: 0.8916 (mtmt) cc_final: 0.8690 (mtpp) REVERT: C 814 LYS cc_start: 0.8781 (mptt) cc_final: 0.8540 (mttm) REVERT: C 837 TYR cc_start: 0.6573 (OUTLIER) cc_final: 0.6087 (t80) REVERT: C 849 LEU cc_start: 0.8531 (tp) cc_final: 0.8260 (tt) REVERT: C 987 VAL cc_start: 0.8965 (t) cc_final: 0.8080 (t) REVERT: C 1125 ASN cc_start: 0.8525 (p0) cc_final: 0.8148 (p0) REVERT: A 116 SER cc_start: 0.8672 (p) cc_final: 0.8448 (t) REVERT: A 140 PHE cc_start: 0.8128 (p90) cc_final: 0.7844 (p90) REVERT: A 190 ARG cc_start: 0.8051 (mtt90) cc_final: 0.7540 (mtm-85) REVERT: A 191 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7764 (mt-10) REVERT: A 287 ASP cc_start: 0.8497 (t0) cc_final: 0.8230 (t0) REVERT: A 314 GLN cc_start: 0.8287 (mm110) cc_final: 0.7881 (mm-40) REVERT: A 317 ASN cc_start: 0.8349 (m110) cc_final: 0.6945 (m110) REVERT: A 353 TRP cc_start: 0.8382 (p-90) cc_final: 0.8149 (p-90) REVERT: A 564 GLN cc_start: 0.7896 (tp40) cc_final: 0.7692 (tp-100) REVERT: A 581 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8335 (p) REVERT: A 586 ASP cc_start: 0.8315 (m-30) cc_final: 0.7972 (m-30) REVERT: A 615 VAL cc_start: 0.8660 (t) cc_final: 0.8206 (p) REVERT: A 632 THR cc_start: 0.8514 (m) cc_final: 0.8270 (p) REVERT: A 654 GLU cc_start: 0.7629 (tt0) cc_final: 0.7313 (tt0) REVERT: A 675 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7277 (pp30) REVERT: A 737 ASP cc_start: 0.7853 (t0) cc_final: 0.7527 (t0) REVERT: A 740 MET cc_start: 0.8457 (ttp) cc_final: 0.8236 (ttm) REVERT: A 755 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8367 (mp10) REVERT: A 765 ARG cc_start: 0.8488 (ttp-110) cc_final: 0.8274 (ttp80) REVERT: A 773 GLU cc_start: 0.8166 (tp30) cc_final: 0.7916 (tt0) REVERT: A 780 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8259 (mt-10) REVERT: A 790 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8568 (mtpp) REVERT: A 837 TYR cc_start: 0.6614 (OUTLIER) cc_final: 0.6085 (t80) REVERT: A 1005 GLN cc_start: 0.8602 (tp40) cc_final: 0.8049 (tp40) REVERT: A 1125 ASN cc_start: 0.8542 (p0) cc_final: 0.8144 (p0) REVERT: B 153 MET cc_start: 0.5896 (tmm) cc_final: 0.5577 (tmm) REVERT: B 191 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7868 (mt-10) REVERT: B 239 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7443 (tm-30) REVERT: B 287 ASP cc_start: 0.8582 (t0) cc_final: 0.8342 (t0) REVERT: B 314 GLN cc_start: 0.8346 (mm110) cc_final: 0.7896 (mm-40) REVERT: B 317 ASN cc_start: 0.8418 (m110) cc_final: 0.7363 (m-40) REVERT: B 353 TRP cc_start: 0.8383 (p-90) cc_final: 0.7852 (p-90) REVERT: B 393 THR cc_start: 0.7619 (m) cc_final: 0.7395 (p) REVERT: B 400 PHE cc_start: 0.7528 (p90) cc_final: 0.7302 (p90) REVERT: B 402 ILE cc_start: 0.8416 (pt) cc_final: 0.8155 (pt) REVERT: B 557 LYS cc_start: 0.8982 (mtmm) cc_final: 0.8746 (mtmt) REVERT: B 581 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8105 (p) REVERT: B 615 VAL cc_start: 0.8698 (t) cc_final: 0.8224 (p) REVERT: B 654 GLU cc_start: 0.7816 (tt0) cc_final: 0.7612 (tt0) REVERT: B 661 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7945 (mm-30) REVERT: B 737 ASP cc_start: 0.7726 (t0) cc_final: 0.7432 (t0) REVERT: B 765 ARG cc_start: 0.8389 (ttp-110) cc_final: 0.8157 (ttm-80) REVERT: B 790 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8486 (mtpp) REVERT: B 804 GLN cc_start: 0.7964 (mt0) cc_final: 0.7758 (mt0) REVERT: B 811 LYS cc_start: 0.8259 (ttmm) cc_final: 0.7746 (tttp) REVERT: B 814 LYS cc_start: 0.8789 (mptt) cc_final: 0.8573 (mptt) REVERT: B 820 ASP cc_start: 0.8282 (t70) cc_final: 0.8037 (t0) REVERT: B 837 TYR cc_start: 0.6641 (OUTLIER) cc_final: 0.6114 (t80) outliers start: 53 outliers final: 10 residues processed: 707 average time/residue: 0.4222 time to fit residues: 454.3374 Evaluate side-chains 527 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 510 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 837 TYR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 837 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 281 optimal weight: 0.6980 chunk 252 optimal weight: 0.9990 chunk 140 optimal weight: 0.0050 chunk 86 optimal weight: 0.4980 chunk 170 optimal weight: 0.0970 chunk 134 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 194 optimal weight: 0.7980 chunk 302 optimal weight: 0.9980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 394 ASN C 417 ASN C 450 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 836 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 394 ASN A 417 ASN A 613 GLN A 836 GLN B 394 ASN B 417 ASN B 450 ASN B 481 ASN B 613 GLN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 836 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 28467 Z= 0.240 Angle : 0.792 13.198 38709 Z= 0.393 Chirality : 0.055 0.737 4695 Planarity : 0.004 0.052 4842 Dihedral : 14.088 111.794 5920 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.90 % Allowed : 10.16 % Favored : 86.95 % 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: -0.67 (0.14), residues: 3333 helix: 0.71 (0.19), residues: 768 sheet: 0.27 (0.18), residues: 726 loop : -1.28 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 64 HIS 0.005 0.001 HIS B 519 PHE 0.024 0.002 PHE A1148 TYR 0.019 0.002 TYR C 265 ARG 0.010 0.001 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 532 time to evaluate : 2.911 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: C 41 LYS cc_start: 0.8770 (mmmm) cc_final: 0.8349 (mmmm) REVERT: C 99 ASN cc_start: 0.8229 (t0) cc_final: 0.7803 (t0) REVERT: C 102 ARG cc_start: 0.7473 (mtt-85) cc_final: 0.6987 (mtt-85) REVERT: C 129 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7453 (ptmm) REVERT: C 140 PHE cc_start: 0.8027 (p90) cc_final: 0.7791 (p90) REVERT: C 287 ASP cc_start: 0.8565 (t0) cc_final: 0.8286 (t0) REVERT: C 306 PHE cc_start: 0.8930 (m-80) cc_final: 0.8631 (m-80) REVERT: C 317 ASN cc_start: 0.8420 (m110) cc_final: 0.7942 (m-40) REVERT: C 558 LYS cc_start: 0.8786 (mmmm) cc_final: 0.8584 (mmmm) REVERT: C 586 ASP cc_start: 0.8170 (m-30) cc_final: 0.7708 (m-30) REVERT: C 654 GLU cc_start: 0.7695 (tt0) cc_final: 0.7311 (tt0) REVERT: C 675 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7230 (pp30) REVERT: C 690 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7576 (mm-40) REVERT: C 693 ILE cc_start: 0.9418 (pt) cc_final: 0.9015 (pt) REVERT: C 776 LYS cc_start: 0.8819 (tttp) cc_final: 0.8604 (tttp) REVERT: C 780 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8145 (mt-10) REVERT: C 790 LYS cc_start: 0.8939 (mtmt) cc_final: 0.8655 (mtpp) REVERT: C 811 LYS cc_start: 0.8513 (ttmm) cc_final: 0.8239 (ttmm) REVERT: A 41 LYS cc_start: 0.8813 (mmmm) cc_final: 0.8518 (mmmm) REVERT: A 99 ASN cc_start: 0.8075 (t0) cc_final: 0.7848 (t0) REVERT: A 137 ASN cc_start: 0.8562 (t0) cc_final: 0.8329 (p0) REVERT: A 140 PHE cc_start: 0.8120 (p90) cc_final: 0.7912 (p90) REVERT: A 287 ASP cc_start: 0.8589 (t0) cc_final: 0.8328 (t0) REVERT: A 317 ASN cc_start: 0.8366 (m110) cc_final: 0.7920 (m-40) REVERT: A 380 TYR cc_start: 0.7910 (m-80) cc_final: 0.6912 (m-80) REVERT: A 577 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8488 (ptm160) REVERT: A 581 THR cc_start: 0.8718 (p) cc_final: 0.8387 (p) REVERT: A 586 ASP cc_start: 0.8195 (m-30) cc_final: 0.7934 (m-30) REVERT: A 632 THR cc_start: 0.8535 (m) cc_final: 0.8186 (p) REVERT: A 654 GLU cc_start: 0.7619 (tt0) cc_final: 0.7170 (tt0) REVERT: A 675 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7265 (pp30) REVERT: A 693 ILE cc_start: 0.9413 (pt) cc_final: 0.9148 (pt) REVERT: A 755 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8615 (mm-40) REVERT: A 776 LYS cc_start: 0.8859 (tttp) cc_final: 0.8513 (tttp) REVERT: A 790 LYS cc_start: 0.8894 (mtmt) cc_final: 0.8553 (mtpp) REVERT: A 820 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8075 (m-30) REVERT: A 950 ASP cc_start: 0.8114 (m-30) cc_final: 0.7880 (m-30) REVERT: A 1005 GLN cc_start: 0.8628 (tp40) cc_final: 0.8155 (tp40) REVERT: B 41 LYS cc_start: 0.8701 (mmmm) cc_final: 0.8414 (mmmm) REVERT: B 80 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.6935 (p0) REVERT: B 95 ILE cc_start: 0.8990 (tt) cc_final: 0.8790 (tt) REVERT: B 105 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8577 (mt) REVERT: B 121 ASN cc_start: 0.6073 (t0) cc_final: 0.5807 (t0) REVERT: B 153 MET cc_start: 0.6034 (tmm) cc_final: 0.5571 (tmm) REVERT: B 191 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7678 (mt-10) REVERT: B 317 ASN cc_start: 0.8221 (m110) cc_final: 0.7986 (m110) REVERT: B 323 THR cc_start: 0.8445 (p) cc_final: 0.8185 (p) REVERT: B 338 PHE cc_start: 0.7435 (m-80) cc_final: 0.6973 (m-80) REVERT: B 369 TYR cc_start: 0.7109 (t80) cc_final: 0.6799 (t80) REVERT: B 422 ASN cc_start: 0.6454 (OUTLIER) cc_final: 0.5040 (p0) REVERT: B 466 ARG cc_start: 0.6726 (OUTLIER) cc_final: 0.5992 (ptp90) REVERT: B 557 LYS cc_start: 0.8904 (mtmm) cc_final: 0.8697 (mtmt) REVERT: B 649 CYS cc_start: 0.6916 (t) cc_final: 0.6499 (t) REVERT: B 654 GLU cc_start: 0.7741 (tt0) cc_final: 0.7495 (tt0) REVERT: B 790 LYS cc_start: 0.8829 (mtmt) cc_final: 0.8463 (mtpp) REVERT: B 811 LYS cc_start: 0.8462 (ttmm) cc_final: 0.7998 (ttmm) REVERT: B 820 ASP cc_start: 0.8372 (t70) cc_final: 0.8052 (m-30) REVERT: B 957 GLN cc_start: 0.8525 (tt0) cc_final: 0.8279 (tm-30) REVERT: B 964 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8688 (mtmm) REVERT: B 995 ARG cc_start: 0.8092 (mtt-85) cc_final: 0.7679 (mtt-85) outliers start: 85 outliers final: 40 residues processed: 581 average time/residue: 0.4165 time to fit residues: 371.9187 Evaluate side-chains 510 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 460 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1152 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 168 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 251 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 chunk 327 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 chunk 300 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 450 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1011 GLN A 121 ASN A 218 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 271 GLN B 417 ASN B 519 HIS ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.120 28467 Z= 0.500 Angle : 0.830 9.650 38709 Z= 0.410 Chirality : 0.055 0.660 4695 Planarity : 0.005 0.044 4842 Dihedral : 13.492 109.911 5901 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.16 % Allowed : 12.03 % Favored : 83.81 % 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: -0.72 (0.14), residues: 3333 helix: 0.88 (0.19), residues: 783 sheet: 0.19 (0.18), residues: 696 loop : -1.39 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 436 HIS 0.008 0.001 HIS C1064 PHE 0.023 0.003 PHE B 86 TYR 0.025 0.002 TYR C1067 ARG 0.009 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 494 time to evaluate : 3.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 LYS cc_start: 0.8813 (mmmm) cc_final: 0.8425 (mmmm) REVERT: C 102 ARG cc_start: 0.7502 (mtt-85) cc_final: 0.7185 (mmt90) REVERT: C 317 ASN cc_start: 0.8317 (m110) cc_final: 0.8101 (m110) REVERT: C 377 PHE cc_start: 0.6904 (OUTLIER) cc_final: 0.6540 (t80) REVERT: C 398 ASP cc_start: 0.7366 (m-30) cc_final: 0.6909 (t0) REVERT: C 586 ASP cc_start: 0.8224 (m-30) cc_final: 0.7744 (m-30) REVERT: C 654 GLU cc_start: 0.7695 (tt0) cc_final: 0.7242 (tt0) REVERT: C 675 GLN cc_start: 0.7731 (pt0) cc_final: 0.7449 (pp30) REVERT: C 693 ILE cc_start: 0.9421 (pt) cc_final: 0.9051 (pt) REVERT: C 773 GLU cc_start: 0.7955 (tt0) cc_final: 0.7726 (tt0) REVERT: C 780 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8328 (mt-10) REVERT: C 790 LYS cc_start: 0.8940 (mtmt) cc_final: 0.8637 (mtpp) REVERT: C 811 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8064 (ttmm) REVERT: C 820 ASP cc_start: 0.8459 (t0) cc_final: 0.8084 (m-30) REVERT: C 1072 GLU cc_start: 0.8766 (pm20) cc_final: 0.8480 (pm20) REVERT: C 1148 PHE cc_start: 0.6677 (OUTLIER) cc_final: 0.6328 (p90) REVERT: A 41 LYS cc_start: 0.8870 (mmmm) cc_final: 0.8561 (mmmm) REVERT: A 116 SER cc_start: 0.8679 (m) cc_final: 0.8470 (p) REVERT: A 137 ASN cc_start: 0.8492 (t0) cc_final: 0.8077 (p0) REVERT: A 287 ASP cc_start: 0.8653 (t0) cc_final: 0.8442 (t0) REVERT: A 377 PHE cc_start: 0.6921 (OUTLIER) cc_final: 0.6511 (t80) REVERT: A 551 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8843 (t) REVERT: A 571 ASP cc_start: 0.8609 (t0) cc_final: 0.8357 (t0) REVERT: A 586 ASP cc_start: 0.8260 (m-30) cc_final: 0.7998 (m-30) REVERT: A 632 THR cc_start: 0.8611 (m) cc_final: 0.8270 (p) REVERT: A 654 GLU cc_start: 0.7712 (tt0) cc_final: 0.7209 (tt0) REVERT: A 755 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8595 (mm-40) REVERT: A 790 LYS cc_start: 0.8949 (mtmt) cc_final: 0.8641 (mtpp) REVERT: A 820 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8026 (m-30) REVERT: A 859 THR cc_start: 0.8854 (m) cc_final: 0.8424 (p) REVERT: A 950 ASP cc_start: 0.8161 (m-30) cc_final: 0.7892 (m-30) REVERT: A 977 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8416 (mp) REVERT: A 1005 GLN cc_start: 0.8782 (tp40) cc_final: 0.8409 (tp40) REVERT: A 1072 GLU cc_start: 0.8707 (pm20) cc_final: 0.8265 (pm20) REVERT: B 41 LYS cc_start: 0.8774 (mmmm) cc_final: 0.8382 (mmmm) REVERT: B 80 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7287 (p0) REVERT: B 105 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8666 (mt) REVERT: B 153 MET cc_start: 0.5565 (tmm) cc_final: 0.4988 (tmm) REVERT: B 186 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.6422 (m-80) REVERT: B 191 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7620 (mt-10) REVERT: B 317 ASN cc_start: 0.8269 (m110) cc_final: 0.8049 (m110) REVERT: B 377 PHE cc_start: 0.6840 (OUTLIER) cc_final: 0.6356 (t80) REVERT: B 390 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8792 (mm) REVERT: B 400 PHE cc_start: 0.7528 (p90) cc_final: 0.7270 (p90) REVERT: B 516 GLU cc_start: 0.7223 (tp30) cc_final: 0.6963 (tp30) REVERT: B 654 GLU cc_start: 0.7735 (tt0) cc_final: 0.7472 (tt0) REVERT: B 790 LYS cc_start: 0.8862 (mtmt) cc_final: 0.8537 (mtmm) REVERT: B 964 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8795 (mtmm) REVERT: B 995 ARG cc_start: 0.8276 (mtt-85) cc_final: 0.7819 (mtt-85) outliers start: 122 outliers final: 72 residues processed: 568 average time/residue: 0.4386 time to fit residues: 387.3506 Evaluate side-chains 541 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 457 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 299 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 157 optimal weight: 0.0770 chunk 33 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 203 optimal weight: 0.5980 chunk 304 optimal weight: 0.6980 chunk 321 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 288 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 314 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN A 121 ASN A 188 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 417 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 28467 Z= 0.228 Angle : 0.735 9.973 38709 Z= 0.355 Chirality : 0.050 0.540 4695 Planarity : 0.004 0.035 4842 Dihedral : 12.716 108.236 5891 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.14 % Allowed : 14.35 % Favored : 82.52 % 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: -0.46 (0.14), residues: 3333 helix: 1.21 (0.19), residues: 774 sheet: 0.17 (0.18), residues: 723 loop : -1.20 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 436 HIS 0.003 0.001 HIS C1159 PHE 0.039 0.002 PHE C 338 TYR 0.021 0.001 TYR A 421 ARG 0.005 0.001 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 496 time to evaluate : 3.028 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: C 32 PHE cc_start: 0.8413 (m-80) cc_final: 0.8156 (m-80) REVERT: C 41 LYS cc_start: 0.8805 (mmmm) cc_final: 0.8406 (mmtp) REVERT: C 129 LYS cc_start: 0.7848 (tttt) cc_final: 0.7590 (ptmm) REVERT: C 317 ASN cc_start: 0.8287 (m110) cc_final: 0.8045 (m110) REVERT: C 377 PHE cc_start: 0.6762 (OUTLIER) cc_final: 0.6353 (t80) REVERT: C 398 ASP cc_start: 0.7380 (m-30) cc_final: 0.6816 (t0) REVERT: C 434 ILE cc_start: 0.7360 (mp) cc_final: 0.6992 (mt) REVERT: C 465 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7028 (tp30) REVERT: C 586 ASP cc_start: 0.8151 (m-30) cc_final: 0.7730 (m-30) REVERT: C 615 VAL cc_start: 0.8867 (t) cc_final: 0.8663 (p) REVERT: C 654 GLU cc_start: 0.7601 (tt0) cc_final: 0.7169 (tt0) REVERT: C 693 ILE cc_start: 0.9419 (pt) cc_final: 0.9053 (pt) REVERT: C 773 GLU cc_start: 0.7915 (tt0) cc_final: 0.7699 (tt0) REVERT: C 780 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8270 (mt-10) REVERT: C 790 LYS cc_start: 0.8902 (mtmt) cc_final: 0.8561 (mtpp) REVERT: C 811 LYS cc_start: 0.8538 (ttmm) cc_final: 0.7932 (ttmm) REVERT: C 820 ASP cc_start: 0.8428 (t0) cc_final: 0.8028 (m-30) REVERT: C 977 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8083 (mp) REVERT: C 1072 GLU cc_start: 0.8601 (pm20) cc_final: 0.8338 (pm20) REVERT: C 1148 PHE cc_start: 0.6274 (OUTLIER) cc_final: 0.5984 (p90) REVERT: A 41 LYS cc_start: 0.8846 (mmmm) cc_final: 0.8508 (mmmm) REVERT: A 116 SER cc_start: 0.8683 (m) cc_final: 0.8435 (p) REVERT: A 129 LYS cc_start: 0.7955 (tttt) cc_final: 0.7587 (ptmm) REVERT: A 190 ARG cc_start: 0.8177 (mtt90) cc_final: 0.7863 (mtt90) REVERT: A 239 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7874 (tm-30) REVERT: A 287 ASP cc_start: 0.8629 (t0) cc_final: 0.8416 (t0) REVERT: A 586 ASP cc_start: 0.8204 (m-30) cc_final: 0.7895 (m-30) REVERT: A 632 THR cc_start: 0.8565 (m) cc_final: 0.8158 (p) REVERT: A 654 GLU cc_start: 0.7709 (tt0) cc_final: 0.7218 (tt0) REVERT: A 755 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8476 (mp10) REVERT: A 790 LYS cc_start: 0.8889 (mtmt) cc_final: 0.8571 (mtpp) REVERT: A 814 LYS cc_start: 0.8841 (mmtm) cc_final: 0.8311 (mmtt) REVERT: A 820 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.7979 (m-30) REVERT: A 950 ASP cc_start: 0.8111 (m-30) cc_final: 0.7724 (m-30) REVERT: A 977 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8316 (mp) REVERT: A 1005 GLN cc_start: 0.8702 (tp40) cc_final: 0.8378 (tp40) REVERT: A 1072 GLU cc_start: 0.8533 (pm20) cc_final: 0.8103 (pm20) REVERT: B 41 LYS cc_start: 0.8737 (mmmm) cc_final: 0.8333 (UNCLASSIFIED) REVERT: B 105 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8691 (mt) REVERT: B 129 LYS cc_start: 0.7997 (tttt) cc_final: 0.7752 (ptmm) REVERT: B 153 MET cc_start: 0.5520 (OUTLIER) cc_final: 0.4924 (tmm) REVERT: B 177 MET cc_start: 0.6566 (OUTLIER) cc_final: 0.6266 (mmm) REVERT: B 191 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7669 (mt-10) REVERT: B 317 ASN cc_start: 0.8262 (m110) cc_final: 0.8008 (m110) REVERT: B 390 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8816 (mp) REVERT: B 516 GLU cc_start: 0.7039 (tp30) cc_final: 0.6743 (tp30) REVERT: B 571 ASP cc_start: 0.8426 (t0) cc_final: 0.7889 (t0) REVERT: B 592 PHE cc_start: 0.8406 (p90) cc_final: 0.8172 (p90) REVERT: B 654 GLU cc_start: 0.7687 (tt0) cc_final: 0.7441 (tt0) REVERT: B 737 ASP cc_start: 0.7618 (t0) cc_final: 0.7410 (t0) REVERT: B 740 MET cc_start: 0.8881 (tpp) cc_final: 0.8477 (tpp) REVERT: B 790 LYS cc_start: 0.8870 (mtmt) cc_final: 0.8437 (mtmm) REVERT: B 811 LYS cc_start: 0.8492 (ttmm) cc_final: 0.8265 (ttmm) REVERT: B 995 ARG cc_start: 0.8092 (mtt-85) cc_final: 0.7678 (mtt-85) outliers start: 92 outliers final: 52 residues processed: 552 average time/residue: 0.4282 time to fit residues: 361.8758 Evaluate side-chains 524 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 463 time to evaluate : 3.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain C residue 1149 LYS Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1149 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 268 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 239 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 274 optimal weight: 1.9990 chunk 222 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 164 optimal weight: 0.0030 chunk 288 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN A 66 HIS A 121 ASN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B 121 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 28467 Z= 0.305 Angle : 0.741 9.923 38709 Z= 0.358 Chirality : 0.050 0.498 4695 Planarity : 0.004 0.037 4842 Dihedral : 12.220 106.627 5889 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.72 % Allowed : 14.76 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3333 helix: 1.28 (0.20), residues: 774 sheet: 0.23 (0.19), residues: 666 loop : -1.17 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 436 HIS 0.004 0.001 HIS C1064 PHE 0.020 0.002 PHE B 338 TYR 0.021 0.002 TYR C1067 ARG 0.006 0.001 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 492 time to evaluate : 2.973 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: C 41 LYS cc_start: 0.8814 (mmmm) cc_final: 0.8384 (mmmm) REVERT: C 116 SER cc_start: 0.8817 (m) cc_final: 0.8535 (t) REVERT: C 129 LYS cc_start: 0.7849 (tttt) cc_final: 0.7612 (ptmm) REVERT: C 317 ASN cc_start: 0.8307 (m110) cc_final: 0.8094 (m110) REVERT: C 377 PHE cc_start: 0.6829 (OUTLIER) cc_final: 0.6370 (t80) REVERT: C 398 ASP cc_start: 0.7319 (m-30) cc_final: 0.6735 (t0) REVERT: C 434 ILE cc_start: 0.7443 (mp) cc_final: 0.7100 (mt) REVERT: C 586 ASP cc_start: 0.8127 (m-30) cc_final: 0.7729 (m-30) REVERT: C 654 GLU cc_start: 0.7634 (tt0) cc_final: 0.7314 (tt0) REVERT: C 675 GLN cc_start: 0.7436 (pp30) cc_final: 0.7027 (pp30) REVERT: C 690 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7632 (mm110) REVERT: C 790 LYS cc_start: 0.8919 (mtmt) cc_final: 0.8601 (mtpp) REVERT: C 811 LYS cc_start: 0.8577 (ttmm) cc_final: 0.8001 (ttmm) REVERT: C 820 ASP cc_start: 0.8437 (t0) cc_final: 0.8034 (m-30) REVERT: C 828 LEU cc_start: 0.8837 (tp) cc_final: 0.8593 (tt) REVERT: C 977 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8143 (mp) REVERT: C 1072 GLU cc_start: 0.8676 (pm20) cc_final: 0.8423 (pm20) REVERT: C 1148 PHE cc_start: 0.6415 (OUTLIER) cc_final: 0.6116 (p90) REVERT: A 41 LYS cc_start: 0.8838 (mmmm) cc_final: 0.8468 (mmmm) REVERT: A 116 SER cc_start: 0.8679 (m) cc_final: 0.8429 (p) REVERT: A 129 LYS cc_start: 0.7973 (tttt) cc_final: 0.7649 (ptmm) REVERT: A 135 PHE cc_start: 0.7841 (m-80) cc_final: 0.7521 (m-80) REVERT: A 239 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7840 (tm-30) REVERT: A 377 PHE cc_start: 0.6993 (OUTLIER) cc_final: 0.6543 (t80) REVERT: A 586 ASP cc_start: 0.8164 (m-30) cc_final: 0.7910 (m-30) REVERT: A 632 THR cc_start: 0.8555 (m) cc_final: 0.8077 (p) REVERT: A 654 GLU cc_start: 0.7762 (tt0) cc_final: 0.7348 (tt0) REVERT: A 675 GLN cc_start: 0.7310 (pp30) cc_final: 0.6906 (pp30) REVERT: A 755 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8480 (mp10) REVERT: A 776 LYS cc_start: 0.8832 (tttp) cc_final: 0.8602 (tttm) REVERT: A 790 LYS cc_start: 0.8894 (mtmt) cc_final: 0.8602 (mtpp) REVERT: A 814 LYS cc_start: 0.8840 (mmtm) cc_final: 0.8308 (mmtt) REVERT: A 820 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.7977 (m-30) REVERT: A 950 ASP cc_start: 0.8127 (m-30) cc_final: 0.7742 (m-30) REVERT: A 977 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8358 (mp) REVERT: A 1005 GLN cc_start: 0.8734 (tp40) cc_final: 0.8396 (tp40) REVERT: A 1072 GLU cc_start: 0.8595 (pm20) cc_final: 0.8131 (pm20) REVERT: B 41 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8398 (mmmm) REVERT: B 80 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.7112 (p0) REVERT: B 81 ASN cc_start: 0.7762 (t0) cc_final: 0.7320 (t0) REVERT: B 129 LYS cc_start: 0.8022 (tttt) cc_final: 0.7687 (ptmm) REVERT: B 153 MET cc_start: 0.5447 (OUTLIER) cc_final: 0.4891 (tmm) REVERT: B 177 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.6369 (mmm) REVERT: B 191 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7657 (mt-10) REVERT: B 239 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: B 317 ASN cc_start: 0.8280 (m110) cc_final: 0.8059 (m110) REVERT: B 377 PHE cc_start: 0.6828 (OUTLIER) cc_final: 0.6371 (t80) REVERT: B 390 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8821 (mp) REVERT: B 400 PHE cc_start: 0.7471 (p90) cc_final: 0.7099 (p90) REVERT: B 455 LEU cc_start: 0.8299 (mt) cc_final: 0.8040 (tt) REVERT: B 466 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.6128 (ptp90) REVERT: B 516 GLU cc_start: 0.7098 (tp30) cc_final: 0.6799 (tp30) REVERT: B 557 LYS cc_start: 0.9056 (mtmt) cc_final: 0.8645 (mtmm) REVERT: B 571 ASP cc_start: 0.8456 (t0) cc_final: 0.7925 (t0) REVERT: B 654 GLU cc_start: 0.7701 (tt0) cc_final: 0.7444 (tt0) REVERT: B 790 LYS cc_start: 0.8862 (mtmt) cc_final: 0.8405 (mtmm) REVERT: B 995 ARG cc_start: 0.8145 (mtt-85) cc_final: 0.7716 (mtt-85) outliers start: 109 outliers final: 68 residues processed: 555 average time/residue: 0.4279 time to fit residues: 365.0764 Evaluate side-chains 545 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 464 time to evaluate : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 839 ASP Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1149 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 108 optimal weight: 0.8980 chunk 289 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 188 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 322 optimal weight: 0.9980 chunk 267 optimal weight: 0.2980 chunk 149 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 564 GLN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 28467 Z= 0.258 Angle : 0.726 13.269 38709 Z= 0.350 Chirality : 0.049 0.496 4695 Planarity : 0.004 0.036 4842 Dihedral : 11.759 106.055 5888 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.58 % Allowed : 15.88 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.38 (0.14), residues: 3333 helix: 1.30 (0.20), residues: 777 sheet: 0.37 (0.19), residues: 660 loop : -1.19 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP A 436 HIS 0.003 0.001 HIS C1064 PHE 0.030 0.001 PHE C 338 TYR 0.021 0.001 TYR C 380 ARG 0.006 0.001 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 494 time to evaluate : 3.188 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: C 41 LYS cc_start: 0.8807 (mmmm) cc_final: 0.8382 (mmmm) REVERT: C 105 ILE cc_start: 0.8899 (mp) cc_final: 0.8673 (mp) REVERT: C 129 LYS cc_start: 0.7828 (tttt) cc_final: 0.7588 (ptmm) REVERT: C 190 ARG cc_start: 0.8106 (mtt90) cc_final: 0.7836 (mtt90) REVERT: C 377 PHE cc_start: 0.6771 (OUTLIER) cc_final: 0.6393 (t80) REVERT: C 398 ASP cc_start: 0.7273 (m-30) cc_final: 0.6681 (t0) REVERT: C 434 ILE cc_start: 0.7525 (mp) cc_final: 0.7231 (mt) REVERT: C 455 LEU cc_start: 0.8705 (tp) cc_final: 0.8461 (mt) REVERT: C 465 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7243 (tp30) REVERT: C 558 LYS cc_start: 0.8863 (mmmm) cc_final: 0.8568 (mmmm) REVERT: C 586 ASP cc_start: 0.8082 (m-30) cc_final: 0.7744 (m-30) REVERT: C 649 CYS cc_start: 0.6662 (t) cc_final: 0.6194 (t) REVERT: C 654 GLU cc_start: 0.7630 (tt0) cc_final: 0.7295 (tt0) REVERT: C 675 GLN cc_start: 0.7452 (pp30) cc_final: 0.6975 (pp30) REVERT: C 690 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7630 (mm-40) REVERT: C 811 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8008 (ttmm) REVERT: C 820 ASP cc_start: 0.8434 (t0) cc_final: 0.8007 (m-30) REVERT: C 828 LEU cc_start: 0.8894 (tp) cc_final: 0.8662 (tt) REVERT: C 977 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8113 (mp) REVERT: C 1072 GLU cc_start: 0.8646 (pm20) cc_final: 0.8404 (pm20) REVERT: C 1148 PHE cc_start: 0.6350 (OUTLIER) cc_final: 0.6122 (p90) REVERT: A 41 LYS cc_start: 0.8839 (mmmm) cc_final: 0.8447 (mmmm) REVERT: A 100 ILE cc_start: 0.9101 (mp) cc_final: 0.8856 (mp) REVERT: A 116 SER cc_start: 0.8645 (m) cc_final: 0.8375 (p) REVERT: A 129 LYS cc_start: 0.7942 (tttt) cc_final: 0.7604 (ptmm) REVERT: A 186 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.6549 (m-80) REVERT: A 239 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7856 (tm-30) REVERT: A 377 PHE cc_start: 0.6960 (OUTLIER) cc_final: 0.6496 (t80) REVERT: A 586 ASP cc_start: 0.8155 (m-30) cc_final: 0.7857 (m-30) REVERT: A 654 GLU cc_start: 0.7726 (tt0) cc_final: 0.7314 (tt0) REVERT: A 675 GLN cc_start: 0.7285 (pp30) cc_final: 0.6885 (pp30) REVERT: A 755 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8461 (mp10) REVERT: A 790 LYS cc_start: 0.8879 (mtmt) cc_final: 0.8584 (mtpp) REVERT: A 811 LYS cc_start: 0.8481 (ttmm) cc_final: 0.7963 (ttmm) REVERT: A 820 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.7943 (m-30) REVERT: A 950 ASP cc_start: 0.8129 (m-30) cc_final: 0.7701 (m-30) REVERT: A 977 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8344 (mp) REVERT: A 1005 GLN cc_start: 0.8711 (tp40) cc_final: 0.8366 (tp40) REVERT: A 1072 GLU cc_start: 0.8547 (pm20) cc_final: 0.8096 (pm20) REVERT: B 41 LYS cc_start: 0.8767 (mmmm) cc_final: 0.8353 (mmmm) REVERT: B 81 ASN cc_start: 0.7896 (t0) cc_final: 0.7534 (t0) REVERT: B 129 LYS cc_start: 0.8006 (tttt) cc_final: 0.7662 (ptmm) REVERT: B 153 MET cc_start: 0.5439 (OUTLIER) cc_final: 0.4867 (tmm) REVERT: B 177 MET cc_start: 0.6678 (OUTLIER) cc_final: 0.6326 (mmm) REVERT: B 190 ARG cc_start: 0.8196 (mtt90) cc_final: 0.7556 (mtt90) REVERT: B 191 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7588 (mt-10) REVERT: B 317 ASN cc_start: 0.8278 (m110) cc_final: 0.8006 (m110) REVERT: B 377 PHE cc_start: 0.6647 (OUTLIER) cc_final: 0.6111 (t80) REVERT: B 390 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8803 (mp) REVERT: B 400 PHE cc_start: 0.7467 (p90) cc_final: 0.7057 (p90) REVERT: B 455 LEU cc_start: 0.8189 (mt) cc_final: 0.7959 (mt) REVERT: B 466 ARG cc_start: 0.6623 (OUTLIER) cc_final: 0.6153 (ptp90) REVERT: B 516 GLU cc_start: 0.7134 (tp30) cc_final: 0.6768 (tp30) REVERT: B 571 ASP cc_start: 0.8483 (t0) cc_final: 0.7960 (t0) REVERT: B 586 ASP cc_start: 0.8267 (m-30) cc_final: 0.7947 (m-30) REVERT: B 654 GLU cc_start: 0.7701 (tt0) cc_final: 0.7428 (tt0) REVERT: B 773 GLU cc_start: 0.7896 (tt0) cc_final: 0.7644 (tt0) REVERT: B 790 LYS cc_start: 0.8864 (mtmt) cc_final: 0.8401 (mtmm) REVERT: B 995 ARG cc_start: 0.8070 (mtt-85) cc_final: 0.7664 (mtt-85) outliers start: 105 outliers final: 72 residues processed: 555 average time/residue: 0.4139 time to fit residues: 353.7733 Evaluate side-chains 557 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 473 time to evaluate : 3.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 839 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1149 LYS 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: 8.9990 chunk 183 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 271 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 320 optimal weight: 0.8980 chunk 200 optimal weight: 0.9980 chunk 195 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS C 121 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN A 121 ASN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 613 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 28467 Z= 0.355 Angle : 0.764 11.165 38709 Z= 0.369 Chirality : 0.050 0.526 4695 Planarity : 0.004 0.037 4842 Dihedral : 11.552 105.279 5888 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.19 % Allowed : 16.09 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.45 (0.14), residues: 3333 helix: 1.34 (0.20), residues: 768 sheet: 0.35 (0.20), residues: 624 loop : -1.25 (0.13), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 436 HIS 0.005 0.001 HIS C1064 PHE 0.017 0.002 PHE B 140 TYR 0.023 0.002 TYR C 380 ARG 0.007 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 488 time to evaluate : 3.215 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: C 41 LYS cc_start: 0.8811 (mmmm) cc_final: 0.8404 (mmmm) REVERT: C 105 ILE cc_start: 0.8895 (mp) cc_final: 0.8686 (mp) REVERT: C 129 LYS cc_start: 0.7841 (tttt) cc_final: 0.7597 (ptmm) REVERT: C 190 ARG cc_start: 0.8141 (mtt90) cc_final: 0.7803 (mtt90) REVERT: C 377 PHE cc_start: 0.6818 (OUTLIER) cc_final: 0.6441 (t80) REVERT: C 398 ASP cc_start: 0.7273 (m-30) cc_final: 0.6679 (t0) REVERT: C 434 ILE cc_start: 0.7525 (mp) cc_final: 0.7241 (mt) REVERT: C 586 ASP cc_start: 0.8025 (m-30) cc_final: 0.7734 (m-30) REVERT: C 649 CYS cc_start: 0.6642 (t) cc_final: 0.6175 (t) REVERT: C 654 GLU cc_start: 0.7609 (tt0) cc_final: 0.7259 (tt0) REVERT: C 675 GLN cc_start: 0.7421 (pp30) cc_final: 0.6948 (pp30) REVERT: C 690 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7695 (mm-40) REVERT: C 811 LYS cc_start: 0.8636 (ttmm) cc_final: 0.8347 (ttmm) REVERT: C 828 LEU cc_start: 0.8903 (tp) cc_final: 0.8683 (tt) REVERT: C 977 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8170 (mp) REVERT: C 1072 GLU cc_start: 0.8695 (pm20) cc_final: 0.8475 (pm20) REVERT: A 41 LYS cc_start: 0.8849 (mmmm) cc_final: 0.8418 (mmmm) REVERT: A 100 ILE cc_start: 0.9096 (mp) cc_final: 0.8852 (mp) REVERT: A 116 SER cc_start: 0.8638 (m) cc_final: 0.8426 (p) REVERT: A 239 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7912 (tm-30) REVERT: A 377 PHE cc_start: 0.6980 (OUTLIER) cc_final: 0.6509 (t80) REVERT: A 586 ASP cc_start: 0.8131 (m-30) cc_final: 0.7876 (m-30) REVERT: A 646 ARG cc_start: 0.8585 (mmm-85) cc_final: 0.8251 (mmm160) REVERT: A 654 GLU cc_start: 0.7732 (tt0) cc_final: 0.7319 (tt0) REVERT: A 675 GLN cc_start: 0.7300 (pp30) cc_final: 0.6922 (pp30) REVERT: A 755 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8468 (mp10) REVERT: A 776 LYS cc_start: 0.8811 (tttp) cc_final: 0.8527 (tttm) REVERT: A 790 LYS cc_start: 0.8901 (mtmt) cc_final: 0.8595 (mtpp) REVERT: A 811 LYS cc_start: 0.8514 (ttmm) cc_final: 0.8027 (ttmm) REVERT: A 820 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.7969 (m-30) REVERT: A 950 ASP cc_start: 0.8152 (m-30) cc_final: 0.7753 (m-30) REVERT: A 977 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8432 (mp) REVERT: A 1072 GLU cc_start: 0.8613 (pm20) cc_final: 0.8139 (pm20) REVERT: B 41 LYS cc_start: 0.8763 (mmmm) cc_final: 0.8313 (mmmm) REVERT: B 81 ASN cc_start: 0.7876 (t0) cc_final: 0.7350 (t0) REVERT: B 121 ASN cc_start: 0.6971 (OUTLIER) cc_final: 0.6723 (t0) REVERT: B 129 LYS cc_start: 0.8013 (tttt) cc_final: 0.7684 (ptmm) REVERT: B 153 MET cc_start: 0.5389 (OUTLIER) cc_final: 0.4877 (tmm) REVERT: B 177 MET cc_start: 0.6732 (OUTLIER) cc_final: 0.6369 (mmm) REVERT: B 191 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7615 (mt-10) REVERT: B 239 GLN cc_start: 0.7935 (tt0) cc_final: 0.7543 (tt0) REVERT: B 317 ASN cc_start: 0.8266 (m110) cc_final: 0.8009 (m110) REVERT: B 377 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.6327 (t80) REVERT: B 400 PHE cc_start: 0.7567 (p90) cc_final: 0.7162 (p90) REVERT: B 455 LEU cc_start: 0.8287 (mt) cc_final: 0.8021 (mt) REVERT: B 516 GLU cc_start: 0.7163 (tp30) cc_final: 0.6835 (tp30) REVERT: B 571 ASP cc_start: 0.8495 (t0) cc_final: 0.7981 (t0) REVERT: B 654 GLU cc_start: 0.7672 (tt0) cc_final: 0.7398 (tt0) REVERT: B 773 GLU cc_start: 0.7925 (tt0) cc_final: 0.7703 (tt0) REVERT: B 790 LYS cc_start: 0.8876 (mtmt) cc_final: 0.8581 (mtmm) REVERT: B 957 GLN cc_start: 0.8510 (tt0) cc_final: 0.8286 (tm-30) REVERT: B 995 ARG cc_start: 0.8168 (mtt-85) cc_final: 0.7751 (mtt-85) outliers start: 123 outliers final: 91 residues processed: 554 average time/residue: 0.4181 time to fit residues: 361.1254 Evaluate side-chains 566 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 466 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 839 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1149 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 198 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 218 optimal weight: 0.5980 chunk 158 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 chunk 252 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 613 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN B 66 HIS B 804 GLN B1125 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 28467 Z= 0.225 Angle : 0.733 12.860 38709 Z= 0.350 Chirality : 0.048 0.487 4695 Planarity : 0.004 0.036 4842 Dihedral : 11.132 104.977 5888 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.44 % Allowed : 17.08 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.33 (0.14), residues: 3333 helix: 1.40 (0.20), residues: 777 sheet: 0.32 (0.19), residues: 654 loop : -1.14 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 436 HIS 0.005 0.001 HIS C 954 PHE 0.016 0.001 PHE C 338 TYR 0.022 0.001 TYR C 380 ARG 0.007 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 483 time to evaluate : 3.097 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: C 41 LYS cc_start: 0.8806 (mmmm) cc_final: 0.8391 (mmmm) REVERT: C 105 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8676 (mp) REVERT: C 129 LYS cc_start: 0.7853 (tttt) cc_final: 0.7629 (ptmm) REVERT: C 377 PHE cc_start: 0.6753 (OUTLIER) cc_final: 0.6372 (t80) REVERT: C 398 ASP cc_start: 0.7243 (m-30) cc_final: 0.6646 (t0) REVERT: C 434 ILE cc_start: 0.7495 (mp) cc_final: 0.7202 (mt) REVERT: C 465 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7247 (tp30) REVERT: C 586 ASP cc_start: 0.7955 (m-30) cc_final: 0.7690 (m-30) REVERT: C 649 CYS cc_start: 0.6588 (t) cc_final: 0.6136 (t) REVERT: C 654 GLU cc_start: 0.7591 (tt0) cc_final: 0.7253 (tt0) REVERT: C 675 GLN cc_start: 0.7453 (pp30) cc_final: 0.6980 (pp30) REVERT: C 690 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7696 (mm-40) REVERT: C 820 ASP cc_start: 0.8417 (t0) cc_final: 0.8045 (m-30) REVERT: C 828 LEU cc_start: 0.8909 (tp) cc_final: 0.8690 (tt) REVERT: C 977 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8160 (mp) REVERT: C 1072 GLU cc_start: 0.8615 (pm20) cc_final: 0.8408 (pm20) REVERT: A 100 ILE cc_start: 0.9028 (mp) cc_final: 0.8788 (mp) REVERT: A 116 SER cc_start: 0.8663 (m) cc_final: 0.8405 (p) REVERT: A 129 LYS cc_start: 0.7935 (tttt) cc_final: 0.7554 (ptmm) REVERT: A 137 ASN cc_start: 0.8302 (m110) cc_final: 0.7747 (p0) REVERT: A 186 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: A 187 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8563 (mmmm) REVERT: A 239 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7880 (tm-30) REVERT: A 353 TRP cc_start: 0.8367 (p-90) cc_final: 0.7948 (p-90) REVERT: A 377 PHE cc_start: 0.6737 (OUTLIER) cc_final: 0.6196 (t80) REVERT: A 586 ASP cc_start: 0.8112 (m-30) cc_final: 0.7844 (m-30) REVERT: A 646 ARG cc_start: 0.8557 (mmm-85) cc_final: 0.8208 (mmm160) REVERT: A 654 GLU cc_start: 0.7737 (tt0) cc_final: 0.7329 (tt0) REVERT: A 675 GLN cc_start: 0.7297 (pp30) cc_final: 0.6998 (pp30) REVERT: A 755 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8441 (mp10) REVERT: A 790 LYS cc_start: 0.8875 (mtmt) cc_final: 0.8562 (mtpp) REVERT: A 811 LYS cc_start: 0.8477 (ttmm) cc_final: 0.7931 (ttmm) REVERT: A 820 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.7936 (m-30) REVERT: A 950 ASP cc_start: 0.8114 (m-30) cc_final: 0.7679 (m-30) REVERT: A 977 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8386 (mp) REVERT: A 1072 GLU cc_start: 0.8533 (pm20) cc_final: 0.8063 (pm20) REVERT: A 1125 ASN cc_start: 0.8507 (p0) cc_final: 0.8273 (p0) REVERT: B 41 LYS cc_start: 0.8766 (mmmm) cc_final: 0.8307 (mmmm) REVERT: B 81 ASN cc_start: 0.7852 (t0) cc_final: 0.7302 (t0) REVERT: B 129 LYS cc_start: 0.8061 (tttt) cc_final: 0.7725 (ptmm) REVERT: B 153 MET cc_start: 0.5355 (OUTLIER) cc_final: 0.4846 (tmm) REVERT: B 177 MET cc_start: 0.6793 (OUTLIER) cc_final: 0.6246 (mmm) REVERT: B 190 ARG cc_start: 0.8178 (mtt90) cc_final: 0.6775 (mpt90) REVERT: B 191 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7624 (mt-10) REVERT: B 239 GLN cc_start: 0.7894 (tt0) cc_final: 0.7460 (tt0) REVERT: B 317 ASN cc_start: 0.8296 (m110) cc_final: 0.8052 (m110) REVERT: B 377 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.6256 (t80) REVERT: B 400 PHE cc_start: 0.7525 (p90) cc_final: 0.7086 (p90) REVERT: B 455 LEU cc_start: 0.8247 (mt) cc_final: 0.7977 (mt) REVERT: B 516 GLU cc_start: 0.7133 (tp30) cc_final: 0.6771 (tp30) REVERT: B 571 ASP cc_start: 0.8497 (t0) cc_final: 0.7983 (t0) REVERT: B 654 GLU cc_start: 0.7679 (tt0) cc_final: 0.7401 (tt0) REVERT: B 740 MET cc_start: 0.8599 (tpp) cc_final: 0.8320 (tpp) REVERT: B 773 GLU cc_start: 0.7872 (tt0) cc_final: 0.7639 (tt0) REVERT: B 790 LYS cc_start: 0.8849 (mtmt) cc_final: 0.8549 (mtmm) REVERT: B 957 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8289 (tm-30) REVERT: B 995 ARG cc_start: 0.8045 (mtt-85) cc_final: 0.7651 (mtt-85) outliers start: 101 outliers final: 72 residues processed: 541 average time/residue: 0.4117 time to fit residues: 344.9063 Evaluate side-chains 551 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 467 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 839 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1155 TYR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain A residue 1155 TYR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1149 LYS 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: 0.0980 chunk 299 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 234 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 chunk 282 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 121 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 28467 Z= 0.319 Angle : 0.766 10.196 38709 Z= 0.366 Chirality : 0.050 0.560 4695 Planarity : 0.004 0.039 4842 Dihedral : 10.771 104.060 5888 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.75 % Allowed : 17.42 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.36 (0.14), residues: 3333 helix: 1.42 (0.20), residues: 777 sheet: 0.31 (0.19), residues: 654 loop : -1.19 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP A 436 HIS 0.004 0.001 HIS C1064 PHE 0.042 0.002 PHE C 32 TYR 0.022 0.002 TYR A 380 ARG 0.010 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 490 time to evaluate : 3.264 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: C 41 LYS cc_start: 0.8834 (mmmm) cc_final: 0.8429 (mmmm) REVERT: C 105 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8665 (mp) REVERT: C 129 LYS cc_start: 0.7887 (tttt) cc_final: 0.7635 (ptmm) REVERT: C 351 TYR cc_start: 0.8552 (p90) cc_final: 0.8193 (p90) REVERT: C 377 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.6404 (t80) REVERT: C 398 ASP cc_start: 0.7249 (m-30) cc_final: 0.6676 (t0) REVERT: C 434 ILE cc_start: 0.7531 (mp) cc_final: 0.7256 (mt) REVERT: C 465 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7351 (tp30) REVERT: C 586 ASP cc_start: 0.7951 (m-30) cc_final: 0.7713 (m-30) REVERT: C 649 CYS cc_start: 0.6521 (t) cc_final: 0.6079 (t) REVERT: C 654 GLU cc_start: 0.7585 (tt0) cc_final: 0.7253 (tt0) REVERT: C 675 GLN cc_start: 0.7463 (pp30) cc_final: 0.6986 (pp30) REVERT: C 690 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7726 (mm-40) REVERT: C 811 LYS cc_start: 0.8618 (ttmm) cc_final: 0.8196 (ttmm) REVERT: C 820 ASP cc_start: 0.8423 (t0) cc_final: 0.8059 (m-30) REVERT: C 828 LEU cc_start: 0.8933 (tp) cc_final: 0.8733 (tt) REVERT: C 977 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8186 (mp) REVERT: C 1072 GLU cc_start: 0.8678 (pm20) cc_final: 0.8463 (pm20) REVERT: A 100 ILE cc_start: 0.9078 (mp) cc_final: 0.8793 (mp) REVERT: A 116 SER cc_start: 0.8662 (m) cc_final: 0.8422 (p) REVERT: A 137 ASN cc_start: 0.8350 (m110) cc_final: 0.7851 (p0) REVERT: A 186 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.6667 (m-80) REVERT: A 377 PHE cc_start: 0.6873 (OUTLIER) cc_final: 0.6341 (t80) REVERT: A 586 ASP cc_start: 0.8103 (m-30) cc_final: 0.7847 (m-30) REVERT: A 646 ARG cc_start: 0.8563 (mmm-85) cc_final: 0.8191 (mmm160) REVERT: A 654 GLU cc_start: 0.7691 (tt0) cc_final: 0.7276 (tt0) REVERT: A 675 GLN cc_start: 0.7318 (pp30) cc_final: 0.6972 (pp30) REVERT: A 755 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8455 (mp10) REVERT: A 776 LYS cc_start: 0.8795 (tttp) cc_final: 0.8505 (tttm) REVERT: A 790 LYS cc_start: 0.8896 (mtmt) cc_final: 0.8587 (mtpp) REVERT: A 804 GLN cc_start: 0.8318 (mt0) cc_final: 0.8082 (mt0) REVERT: A 811 LYS cc_start: 0.8495 (ttmm) cc_final: 0.7963 (ttmm) REVERT: A 820 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.7960 (m-30) REVERT: A 950 ASP cc_start: 0.8147 (m-30) cc_final: 0.7737 (m-30) REVERT: A 977 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8428 (mp) REVERT: B 41 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8323 (mmmm) REVERT: B 81 ASN cc_start: 0.7840 (t0) cc_final: 0.7320 (t0) REVERT: B 129 LYS cc_start: 0.8040 (tttt) cc_final: 0.7714 (ptmm) REVERT: B 153 MET cc_start: 0.5225 (OUTLIER) cc_final: 0.4696 (tmm) REVERT: B 177 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6307 (mmm) REVERT: B 190 ARG cc_start: 0.8178 (mtt90) cc_final: 0.6800 (mpt90) REVERT: B 191 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7661 (mt-10) REVERT: B 239 GLN cc_start: 0.7925 (tt0) cc_final: 0.7442 (tt0) REVERT: B 317 ASN cc_start: 0.8288 (m110) cc_final: 0.8047 (m110) REVERT: B 377 PHE cc_start: 0.6818 (OUTLIER) cc_final: 0.6281 (t80) REVERT: B 455 LEU cc_start: 0.8285 (mt) cc_final: 0.7992 (mt) REVERT: B 516 GLU cc_start: 0.7160 (tp30) cc_final: 0.6766 (tp30) REVERT: B 564 GLN cc_start: 0.8152 (tp-100) cc_final: 0.7951 (tp-100) REVERT: B 571 ASP cc_start: 0.8497 (t0) cc_final: 0.7990 (t0) REVERT: B 654 GLU cc_start: 0.7676 (tt0) cc_final: 0.7398 (tt0) REVERT: B 740 MET cc_start: 0.8741 (tpp) cc_final: 0.8398 (tpp) REVERT: B 773 GLU cc_start: 0.7914 (tt0) cc_final: 0.7685 (tt0) REVERT: B 790 LYS cc_start: 0.8861 (mtmt) cc_final: 0.8527 (mtmm) REVERT: B 825 LYS cc_start: 0.8783 (mmmt) cc_final: 0.8550 (mmmt) REVERT: B 995 ARG cc_start: 0.8121 (mtt-85) cc_final: 0.7717 (mtt-85) REVERT: B 1125 ASN cc_start: 0.8421 (p0) cc_final: 0.8153 (p0) outliers start: 110 outliers final: 87 residues processed: 551 average time/residue: 0.4171 time to fit residues: 356.5462 Evaluate side-chains 570 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 473 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 839 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain C residue 1155 TYR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1155 TYR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain B residue 1155 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 196 optimal weight: 0.9980 chunk 316 optimal weight: 0.3980 chunk 193 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 331 optimal weight: 0.9990 chunk 305 optimal weight: 2.9990 chunk 264 optimal weight: 0.0270 chunk 27 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN B 66 HIS ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.153 28467 Z= 0.326 Angle : 0.942 59.185 38709 Z= 0.501 Chirality : 0.050 0.545 4695 Planarity : 0.004 0.039 4842 Dihedral : 10.762 104.081 5888 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.37 % Allowed : 17.83 % Favored : 78.80 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.36 (0.14), residues: 3333 helix: 1.42 (0.20), residues: 777 sheet: 0.30 (0.19), residues: 654 loop : -1.20 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A 436 HIS 0.003 0.001 HIS C1064 PHE 0.031 0.002 PHE A 374 TYR 0.028 0.002 TYR C 396 ARG 0.014 0.001 ARG C 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 472 time to evaluate : 2.889 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: C 41 LYS cc_start: 0.8835 (mmmm) cc_final: 0.8425 (mmmm) REVERT: C 105 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8652 (mp) REVERT: C 129 LYS cc_start: 0.7882 (tttt) cc_final: 0.7630 (ptmm) REVERT: C 351 TYR cc_start: 0.8551 (p90) cc_final: 0.8194 (p90) REVERT: C 377 PHE cc_start: 0.6777 (OUTLIER) cc_final: 0.6408 (t80) REVERT: C 398 ASP cc_start: 0.7271 (m-30) cc_final: 0.6680 (t0) REVERT: C 434 ILE cc_start: 0.7530 (mp) cc_final: 0.7247 (mt) REVERT: C 465 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7208 (tp30) REVERT: C 586 ASP cc_start: 0.7943 (m-30) cc_final: 0.7710 (m-30) REVERT: C 649 CYS cc_start: 0.6519 (t) cc_final: 0.6076 (t) REVERT: C 654 GLU cc_start: 0.7582 (tt0) cc_final: 0.7240 (tt0) REVERT: C 675 GLN cc_start: 0.7452 (pp30) cc_final: 0.6977 (pp30) REVERT: C 690 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7629 (mm-40) REVERT: C 811 LYS cc_start: 0.8615 (ttmm) cc_final: 0.8192 (ttmm) REVERT: C 820 ASP cc_start: 0.8418 (t0) cc_final: 0.8056 (m-30) REVERT: C 828 LEU cc_start: 0.8935 (tp) cc_final: 0.8731 (tt) REVERT: C 955 ASN cc_start: 0.8520 (t0) cc_final: 0.7750 (t0) REVERT: C 977 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8188 (mp) REVERT: C 1072 GLU cc_start: 0.8675 (pm20) cc_final: 0.8464 (pm20) REVERT: A 100 ILE cc_start: 0.9076 (mp) cc_final: 0.8790 (mp) REVERT: A 116 SER cc_start: 0.8660 (m) cc_final: 0.8422 (p) REVERT: A 137 ASN cc_start: 0.8345 (m110) cc_final: 0.7849 (p0) REVERT: A 186 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.6664 (m-80) REVERT: A 239 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7846 (tm-30) REVERT: A 377 PHE cc_start: 0.6863 (OUTLIER) cc_final: 0.6333 (t80) REVERT: A 586 ASP cc_start: 0.8097 (m-30) cc_final: 0.7846 (m-30) REVERT: A 646 ARG cc_start: 0.8562 (mmm-85) cc_final: 0.8187 (mmm160) REVERT: A 654 GLU cc_start: 0.7689 (tt0) cc_final: 0.7275 (tt0) REVERT: A 675 GLN cc_start: 0.7316 (pp30) cc_final: 0.6967 (pp30) REVERT: A 755 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8454 (mp10) REVERT: A 790 LYS cc_start: 0.8894 (mtmt) cc_final: 0.8588 (mtpp) REVERT: A 804 GLN cc_start: 0.8317 (mt0) cc_final: 0.8084 (mt0) REVERT: A 811 LYS cc_start: 0.8495 (ttmm) cc_final: 0.7938 (ttmm) REVERT: A 820 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: A 950 ASP cc_start: 0.8144 (m-30) cc_final: 0.7733 (m-30) REVERT: A 977 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8427 (mp) REVERT: B 41 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8321 (mmmm) REVERT: B 81 ASN cc_start: 0.7847 (t0) cc_final: 0.7336 (t0) REVERT: B 129 LYS cc_start: 0.8036 (tttt) cc_final: 0.7709 (ptmm) REVERT: B 153 MET cc_start: 0.5222 (OUTLIER) cc_final: 0.4693 (tmm) REVERT: B 177 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6294 (mmm) REVERT: B 190 ARG cc_start: 0.8175 (mtt90) cc_final: 0.6798 (mpt90) REVERT: B 191 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7655 (mt-10) REVERT: B 239 GLN cc_start: 0.7930 (tt0) cc_final: 0.7437 (tt0) REVERT: B 317 ASN cc_start: 0.8287 (m110) cc_final: 0.8044 (m110) REVERT: B 377 PHE cc_start: 0.6798 (OUTLIER) cc_final: 0.6261 (t80) REVERT: B 400 PHE cc_start: 0.7568 (p90) cc_final: 0.7108 (p90) REVERT: B 455 LEU cc_start: 0.8282 (mt) cc_final: 0.8082 (tt) REVERT: B 516 GLU cc_start: 0.7151 (tp30) cc_final: 0.6759 (tp30) REVERT: B 571 ASP cc_start: 0.8498 (t0) cc_final: 0.7991 (t0) REVERT: B 654 GLU cc_start: 0.7674 (tt0) cc_final: 0.7397 (tt0) REVERT: B 740 MET cc_start: 0.8738 (tpp) cc_final: 0.8396 (tpp) REVERT: B 773 GLU cc_start: 0.7911 (tt0) cc_final: 0.7682 (tt0) REVERT: B 790 LYS cc_start: 0.8839 (mtmt) cc_final: 0.8534 (mtmm) REVERT: B 825 LYS cc_start: 0.8781 (mmmt) cc_final: 0.8548 (mmmt) REVERT: B 995 ARG cc_start: 0.8116 (mtt-85) cc_final: 0.7700 (mtt-85) REVERT: B 1125 ASN cc_start: 0.8420 (p0) cc_final: 0.8152 (p0) outliers start: 99 outliers final: 85 residues processed: 529 average time/residue: 0.4134 time to fit residues: 338.6138 Evaluate side-chains 563 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 468 time to evaluate : 3.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 839 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1155 TYR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain A residue 1155 TYR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain B residue 1155 TYR 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: 0.9990 chunk 80 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 264 optimal weight: 0.1980 chunk 110 optimal weight: 0.4980 chunk 271 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN B 66 HIS ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.106263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.084393 restraints weight = 61774.054| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.46 r_work: 0.3154 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.153 28467 Z= 0.326 Angle : 0.942 59.185 38709 Z= 0.501 Chirality : 0.050 0.545 4695 Planarity : 0.004 0.039 4842 Dihedral : 10.762 104.081 5888 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.24 % Allowed : 17.96 % Favored : 78.80 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.36 (0.14), residues: 3333 helix: 1.42 (0.20), residues: 777 sheet: 0.30 (0.19), residues: 654 loop : -1.20 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A 436 HIS 0.003 0.001 HIS C1064 PHE 0.031 0.002 PHE A 374 TYR 0.028 0.002 TYR C 396 ARG 0.014 0.001 ARG C 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7762.91 seconds wall clock time: 141 minutes 7.88 seconds (8467.88 seconds total)