Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 14:31:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5szs_8331/04_2023/5szs_8331.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5szs_8331/04_2023/5szs_8331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5szs_8331/04_2023/5szs_8331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5szs_8331/04_2023/5szs_8331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5szs_8331/04_2023/5szs_8331.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5szs_8331/04_2023/5szs_8331.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 129 5.16 5 C 19089 2.51 5 N 4743 2.21 5 O 6345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 484": "OD1" <-> "OD2" Residue "A PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 922": "OD1" <-> "OD2" Residue "A PHE 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1081": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1137": "OD1" <-> "OD2" Residue "A TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 484": "OD1" <-> "OD2" Residue "B PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 922": "OD1" <-> "OD2" Residue "B PHE 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1081": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1137": "OD1" <-> "OD2" Residue "B TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 484": "OD1" <-> "OD2" Residue "C PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 922": "OD1" <-> "OD2" Residue "C PHE 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1081": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1137": "OD1" <-> "OD2" Residue "C TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1165": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 30306 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 9141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9141 Classifications: {'peptide': 1177} Link IDs: {'PTRANS': 41, 'TRANS': 1135} Chain breaks: 3 Chain: "B" Number of atoms: 9141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9141 Classifications: {'peptide': 1177} Link IDs: {'PTRANS': 41, 'TRANS': 1135} Chain breaks: 3 Chain: "C" Number of atoms: 9141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9141 Classifications: {'peptide': 1177} Link IDs: {'PTRANS': 41, 'TRANS': 1135} Chain breaks: 3 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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 chiralities: 2 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" 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 chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" 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 chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "r" 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 chiralities: 2 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "4" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "8" 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 chiralities: 2 Chain: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "AA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "BA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "CA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "DA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen 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 chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 15.41, per 1000 atoms: 0.51 Number of scatterers: 30306 At special positions: 0 Unit cell: (150.96, 141.44, 178.16, 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 129 16.00 O 6345 8.00 N 4743 7.00 C 19089 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 126 " distance=2.04 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 181 " distance=2.02 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 210 " distance=2.21 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 351 " distance=2.04 Simple disulfide: pdb=" SG CYS A 438 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS A 497 " - pdb=" SG CYS A 500 " distance=2.04 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 567 " distance=2.05 Simple disulfide: pdb=" SG CYS A 550 " - pdb=" SG CYS A 577 " distance=2.02 Simple disulfide: pdb=" SG CYS A 627 " - pdb=" SG CYS A 678 " distance=2.25 Simple disulfide: pdb=" SG CYS A 724 " - pdb=" SG CYS A 737 " distance=2.02 Simple disulfide: pdb=" SG CYS A 789 " - pdb=" SG CYS A 811 " distance=2.07 Simple disulfide: pdb=" SG CYS A 794 " - pdb=" SG CYS A 800 " distance=2.02 Simple disulfide: pdb=" SG CYS A 896 " - pdb=" SG CYS A 907 " distance=2.04 Simple disulfide: pdb=" SG CYS A1098 " - pdb=" SG CYS A1109 " distance=2.02 Simple disulfide: pdb=" SG CYS A1148 " - pdb=" SG CYS A1195 " distance=1.74 Simple disulfide: pdb=" SG CYS B 106 " - pdb=" SG CYS B 126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 181 " distance=2.02 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 210 " distance=2.21 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 351 " distance=2.04 Simple disulfide: pdb=" SG CYS B 438 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS B 497 " - pdb=" SG CYS B 500 " distance=2.04 Simple disulfide: pdb=" SG CYS B 516 " - pdb=" SG CYS B 567 " distance=2.05 Simple disulfide: pdb=" SG CYS B 550 " - pdb=" SG CYS B 577 " distance=2.02 Simple disulfide: pdb=" SG CYS B 627 " - pdb=" SG CYS B 678 " distance=2.25 Simple disulfide: pdb=" SG CYS B 724 " - pdb=" SG CYS B 737 " distance=2.02 Simple disulfide: pdb=" SG CYS B 789 " - pdb=" SG CYS B 811 " distance=2.07 Simple disulfide: pdb=" SG CYS B 794 " - pdb=" SG CYS B 800 " distance=2.02 Simple disulfide: pdb=" SG CYS B 896 " - pdb=" SG CYS B 907 " distance=2.04 Simple disulfide: pdb=" SG CYS B1098 " - pdb=" SG CYS B1109 " distance=2.02 Simple disulfide: pdb=" SG CYS B1148 " - pdb=" SG CYS B1195 " distance=1.74 Simple disulfide: pdb=" SG CYS C 106 " - pdb=" SG CYS C 126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 175 " - pdb=" SG CYS C 181 " distance=2.02 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 210 " distance=2.21 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 351 " distance=2.04 Simple disulfide: pdb=" SG CYS C 438 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS C 497 " - pdb=" SG CYS C 500 " distance=2.04 Simple disulfide: pdb=" SG CYS C 516 " - pdb=" SG CYS C 567 " distance=2.05 Simple disulfide: pdb=" SG CYS C 550 " - pdb=" SG CYS C 577 " distance=2.02 Simple disulfide: pdb=" SG CYS C 627 " - pdb=" SG CYS C 678 " distance=2.25 Simple disulfide: pdb=" SG CYS C 724 " - pdb=" SG CYS C 737 " distance=2.02 Simple disulfide: pdb=" SG CYS C 789 " - pdb=" SG CYS C 811 " distance=2.07 Simple disulfide: pdb=" SG CYS C 794 " - pdb=" SG CYS C 800 " distance=2.02 Simple disulfide: pdb=" SG CYS C 896 " - pdb=" SG CYS C 907 " distance=2.04 Simple disulfide: pdb=" SG CYS C1098 " - pdb=" SG CYS C1109 " distance=2.02 Simple disulfide: pdb=" SG CYS C1148 " - pdb=" SG CYS C1195 " distance=1.74 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM28675 O4 NAG g 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM27812 O4 NAG L 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM29538 O4 NAG 1 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 0 4 " - " MAN 0 5 " " MAN 0 5 " - " MAN 0 6 " " MAN D 4 " - " MAN D 5 " " MAN K 4 " - " MAN K 5 " " MAN K 5 " - " MAN K 6 " " MAN Y 4 " - " MAN Y 5 " " MAN f 4 " - " MAN f 5 " " MAN f 5 " - " MAN f 6 " " MAN t 4 " - " MAN t 5 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " MAN 0 7 " - " MAN 0 8 " " BMA 3 3 " - " MAN 3 4 " " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " " BMA K 3 " - " MAN K 4 " " MAN K 7 " - " MAN K 8 " " BMA N 3 " - " MAN N 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA Y 3 " - " MAN Y 4 " " BMA a 3 " - " MAN a 4 " " BMA f 3 " - " MAN f 4 " " MAN f 7 " - " MAN f 8 " " BMA i 3 " - " MAN i 4 " " BMA p 3 " - " MAN p 4 " " BMA q 3 " - " MAN q 4 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " " BMAAA 3 " - " MANAA 4 " " BMABA 3 " - " MANBA 4 " ALPHA1-6 " BMA 0 3 " - " MAN 0 7 " " BMA 3 3 " - " MAN 3 5 " " BMA D 3 " - " MAN D 6 " " BMA H 3 " - " MAN H 4 " " BMA K 3 " - " MAN K 7 " " BMA N 3 " - " MAN N 5 " " BMA V 3 " - " MAN V 5 " " BMA Y 3 " - " MAN Y 6 " " BMA c 3 " - " MAN c 4 " " BMA f 3 " - " MAN f 7 " " BMA i 3 " - " MAN i 5 " " BMA q 3 " - " MAN q 5 " " BMA t 3 " - " MAN t 6 " " BMA x 3 " - " MAN x 4 " " BMABA 3 " - " MANBA 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 9 1 " - " NAG 9 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG 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 p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " NAG-ASN " NAG 0 1 " - " ASN C 426 " " NAG 1 1 " - " ASN C 486 " " NAG 2 1 " - " ASN C 506 " " NAG 3 1 " - " ASN C 666 " " NAG 4 1 " - " ASN C 699 " " NAG 5 1 " - " ASN C 723 " " NAG 6 1 " - " ASN C 749 " " NAG 7 1 " - " ASN C 762 " " NAG 8 1 " - " ASN C 768 " " NAG 9 1 " - " ASN C 844 " " NAG A1401 " - " ASN A 155 " " NAG A1402 " - " ASN A 187 " " NAG A1403 " - " ASN A 193 " " NAG A1439 " - " ASN A 512 " " NAG A1440 " - " ASN A 626 " " NAG A1441 " - " ASN A 645 " " NAG A1474 " - " ASN A1218 " " NAG B1401 " - " ASN B 155 " " NAG B1402 " - " ASN B 187 " " NAG B1403 " - " ASN B 193 " " NAG B1439 " - " ASN B 512 " " NAG B1440 " - " ASN B 626 " " NAG B1441 " - " ASN B 645 " " NAG B1474 " - " ASN B1218 " " NAG C1401 " - " ASN C 155 " " NAG C1402 " - " ASN C 187 " " NAG C1403 " - " ASN C 193 " " NAG C1439 " - " ASN C 512 " " NAG C1440 " - " ASN C 626 " " NAG C1441 " - " ASN C 645 " " NAG C1474 " - " ASN C1218 " " NAG D 1 " - " ASN A 240 " " NAG E 1 " - " ASN A 276 " " NAG F 1 " - " ASN A 301 " " NAG G 1 " - " ASN A 330 " " NAG H 1 " - " ASN A 354 " " NAG I 1 " - " ASN A 358 " " NAG J 1 " - " ASN A 403 " " NAG K 1 " - " ASN A 426 " " NAG L 1 " - " ASN A 486 " " NAG M 1 " - " ASN A 506 " " NAG N 1 " - " ASN A 666 " " NAG O 1 " - " ASN A 699 " " NAG P 1 " - " ASN A 723 " " NAG Q 1 " - " ASN A 749 " " NAG R 1 " - " ASN A 762 " " NAG S 1 " - " ASN A 768 " " NAG T 1 " - " ASN A 844 " " NAG U 1 " - " ASN A 852 " " NAG V 1 " - " ASN A1111 " " NAG W 1 " - " ASN A1196 " " NAG X 1 " - " ASN A1201 " " NAG Y 1 " - " ASN B 240 " " NAG Z 1 " - " ASN B 276 " " NAG a 1 " - " ASN B 301 " " NAG b 1 " - " ASN B 330 " " NAG c 1 " - " ASN B 354 " " NAG d 1 " - " ASN B 358 " " NAG e 1 " - " ASN B 403 " " NAG f 1 " - " ASN B 426 " " NAG g 1 " - " ASN B 486 " " NAG h 1 " - " ASN B 506 " " NAG i 1 " - " ASN B 666 " " NAG j 1 " - " ASN B 699 " " NAG k 1 " - " ASN B 723 " " NAG l 1 " - " ASN B 749 " " NAG m 1 " - " ASN B 762 " " NAG n 1 " - " ASN B 768 " " NAG o 1 " - " ASN B 844 " " NAG p 1 " - " ASN B 852 " " NAG q 1 " - " ASN B1111 " " NAG r 1 " - " ASN B1196 " " NAG s 1 " - " ASN B1201 " " NAG t 1 " - " ASN C 240 " " NAG u 1 " - " ASN C 276 " " NAG v 1 " - " ASN C 301 " " NAG w 1 " - " ASN C 330 " " NAG x 1 " - " ASN C 354 " " NAG y 1 " - " ASN C 358 " " NAG z 1 " - " ASN C 403 " " NAGAA 1 " - " ASN C 852 " " NAGBA 1 " - " ASN C1111 " " NAGCA 1 " - " ASN C1196 " " NAGDA 1 " - " ASN C1201 " Time building additional restraints: 14.78 Conformation dependent library (CDL) restraints added in 3.9 seconds 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6612 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 51 sheets defined 25.1% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 26 through 31 Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.640A pdb=" N ASN A 216 " --> pdb=" O GLY A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.571A pdb=" N ARG A 225 " --> pdb=" O GLN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 308 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 440 through 450 Processing helix chain 'A' and resid 530 through 534 Processing helix chain 'A' and resid 536 through 539 Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 799 through 804 Processing helix chain 'A' and resid 807 through 833 removed outlier: 4.801A pdb=" N THR A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 815 " --> pdb=" O CYS A 811 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 832 " --> pdb=" O ASP A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 843 Processing helix chain 'A' and resid 844 through 852 removed outlier: 4.138A pdb=" N GLY A 849 " --> pdb=" O THR A 846 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP A 850 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 882 Processing helix chain 'A' and resid 892 through 898 removed outlier: 4.118A pdb=" N THR A 897 " --> pdb=" O LYS A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 911 Processing helix chain 'A' and resid 922 through 936 Processing helix chain 'A' and resid 949 through 960 Processing helix chain 'A' and resid 969 through 992 removed outlier: 4.482A pdb=" N LYS A 973 " --> pdb=" O GLN A 969 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1031 Processing helix chain 'A' and resid 1032 through 1034 No H-bonds generated for 'chain 'A' and resid 1032 through 1034' Processing helix chain 'A' and resid 1042 through 1048 Processing helix chain 'A' and resid 1051 through 1099 removed outlier: 5.115A pdb=" N GLN A1057 " --> pdb=" O ILE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1187 No H-bonds generated for 'chain 'A' and resid 1185 through 1187' Processing helix chain 'A' and resid 1205 through 1210 Processing helix chain 'A' and resid 1216 through 1224 Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 212 through 217 removed outlier: 3.640A pdb=" N ASN B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.572A pdb=" N ARG B 225 " --> pdb=" O GLN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 308 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 440 through 450 Processing helix chain 'B' and resid 530 through 534 Processing helix chain 'B' and resid 536 through 539 Processing helix chain 'B' and resid 553 through 557 Processing helix chain 'B' and resid 799 through 804 Processing helix chain 'B' and resid 807 through 833 removed outlier: 4.801A pdb=" N THR B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 815 " --> pdb=" O CYS B 811 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET B 832 " --> pdb=" O ASP B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 843 Processing helix chain 'B' and resid 844 through 852 removed outlier: 4.138A pdb=" N GLY B 849 " --> pdb=" O THR B 846 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP B 850 " --> pdb=" O SER B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 882 Processing helix chain 'B' and resid 892 through 898 removed outlier: 4.118A pdb=" N THR B 897 " --> pdb=" O LYS B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 911 Processing helix chain 'B' and resid 922 through 936 Processing helix chain 'B' and resid 949 through 960 Processing helix chain 'B' and resid 969 through 992 removed outlier: 4.482A pdb=" N LYS B 973 " --> pdb=" O GLN B 969 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1031 Processing helix chain 'B' and resid 1032 through 1034 No H-bonds generated for 'chain 'B' and resid 1032 through 1034' Processing helix chain 'B' and resid 1042 through 1048 Processing helix chain 'B' and resid 1051 through 1099 removed outlier: 5.115A pdb=" N GLN B1057 " --> pdb=" O ILE B1053 " (cutoff:3.500A) Processing helix chain 'B' and resid 1185 through 1187 No H-bonds generated for 'chain 'B' and resid 1185 through 1187' Processing helix chain 'B' and resid 1205 through 1210 Processing helix chain 'B' and resid 1216 through 1224 Processing helix chain 'C' and resid 26 through 31 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 176 through 180 Processing helix chain 'C' and resid 212 through 217 removed outlier: 3.640A pdb=" N ASN C 216 " --> pdb=" O GLY C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.571A pdb=" N ARG C 225 " --> pdb=" O GLN C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 308 Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 440 through 450 Processing helix chain 'C' and resid 530 through 534 Processing helix chain 'C' and resid 536 through 539 Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 799 through 804 Processing helix chain 'C' and resid 807 through 833 removed outlier: 4.802A pdb=" N THR C 813 " --> pdb=" O SER C 809 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE C 814 " --> pdb=" O ALA C 810 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU C 815 " --> pdb=" O CYS C 811 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET C 832 " --> pdb=" O ASP C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 843 Processing helix chain 'C' and resid 844 through 852 removed outlier: 4.137A pdb=" N GLY C 849 " --> pdb=" O THR C 846 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP C 850 " --> pdb=" O SER C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 882 Processing helix chain 'C' and resid 892 through 898 removed outlier: 4.117A pdb=" N THR C 897 " --> pdb=" O LYS C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 911 Processing helix chain 'C' and resid 922 through 936 Processing helix chain 'C' and resid 949 through 960 Processing helix chain 'C' and resid 969 through 992 removed outlier: 4.481A pdb=" N LYS C 973 " --> pdb=" O GLN C 969 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1031 Processing helix chain 'C' and resid 1032 through 1034 No H-bonds generated for 'chain 'C' and resid 1032 through 1034' Processing helix chain 'C' and resid 1042 through 1048 Processing helix chain 'C' and resid 1051 through 1099 removed outlier: 5.114A pdb=" N GLN C1057 " --> pdb=" O ILE C1053 " (cutoff:3.500A) Processing helix chain 'C' and resid 1185 through 1187 No H-bonds generated for 'chain 'C' and resid 1185 through 1187' Processing helix chain 'C' and resid 1205 through 1210 Processing helix chain 'C' and resid 1216 through 1224 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 42 removed outlier: 7.246A pdb=" N THR A 191 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL A 206 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR A 204 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR A 195 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 59 removed outlier: 6.147A pdb=" N ALA A 99 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR A 133 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL A 101 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU A 131 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU A 103 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN A 129 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE A 105 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP A 125 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 161 removed outlier: 3.720A pdb=" N GLY A 62 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 262 removed outlier: 5.505A pdb=" N VAL A 248 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A 427 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG A 250 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 425 " --> pdb=" O ARG A 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR A 252 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL A 423 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 421 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE A 417 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU A 260 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 415 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TRP A 413 " --> pdb=" O PRO A 262 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN A 299 " --> pdb=" O TRP A 413 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL A 415 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG A 297 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE A 417 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 295 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE A 384 " --> pdb=" O TYR A 391 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 247 through 262 removed outlier: 5.505A pdb=" N VAL A 248 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A 427 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG A 250 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 425 " --> pdb=" O ARG A 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR A 252 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL A 423 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 421 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE A 417 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU A 260 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 415 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TRP A 413 " --> pdb=" O PRO A 262 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ASP A 422 " --> pdb=" O TYR A 437 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR A 437 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A 424 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU A 435 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN A 426 " --> pdb=" O GLN A 433 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 360 through 368 removed outlier: 6.817A pdb=" N CYS A 351 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR A 356 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP A 323 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS A 328 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY A 313 " --> pdb=" O CYS A 328 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 360 through 368 removed outlier: 6.817A pdb=" N CYS A 351 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR A 356 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP A 323 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 13.239A pdb=" N PHE A 326 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA9, first strand: chain 'A' and resid 457 through 461 removed outlier: 6.618A pdb=" N GLN A 683 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA A 694 " --> pdb=" O GLN A 683 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA A 685 " --> pdb=" O ILE A 692 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 471 through 474 removed outlier: 5.032A pdb=" N LEU A 662 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR A 654 " --> pdb=" O LEU A 662 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 504 through 509 removed outlier: 6.457A pdb=" N SER A 601 " --> pdb=" O LYS A 564 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY A 603 " --> pdb=" O LYS A 562 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS A 562 " --> pdb=" O GLY A 603 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 514 through 515 removed outlier: 4.184A pdb=" N SER A 589 " --> pdb=" O TRP A 585 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP A 585 " --> pdb=" O SER A 589 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 581 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA A 595 " --> pdb=" O PHE A 579 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE A 579 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TYR A 597 " --> pdb=" O CYS A 577 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N CYS A 577 " --> pdb=" O TYR A 597 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 727 through 731 removed outlier: 6.775A pdb=" N ILE A 736 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N THR A 730 " --> pdb=" O PHE A 734 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N PHE A 734 " --> pdb=" O THR A 730 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 761 through 779 removed outlier: 6.896A pdb=" N ASN A 762 " --> pdb=" O LYS A1142 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS A1142 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER A 764 " --> pdb=" O ASN A1140 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN A1140 " --> pdb=" O SER A 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR A1138 " --> pdb=" O PRO A 766 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN A 768 " --> pdb=" O THR A1136 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU A1133 " --> pdb=" O HIS A1114 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS A1114 " --> pdb=" O LEU A1133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 761 through 779 removed outlier: 6.896A pdb=" N ASN A 762 " --> pdb=" O LYS A1142 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS A1142 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER A 764 " --> pdb=" O ASN A1140 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN A1140 " --> pdb=" O SER A 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR A1138 " --> pdb=" O PRO A 766 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN A 768 " --> pdb=" O THR A1136 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LYS A1142 " --> pdb=" O SER A1166 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU A1164 " --> pdb=" O TRP A1144 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 785 through 787 Processing sheet with id=AB8, first strand: chain 'A' and resid 1189 through 1191 removed outlier: 4.065A pdb=" N ILE A1202 " --> pdb=" O CYS A1148 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 37 through 42 removed outlier: 7.246A pdb=" N THR B 191 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL B 206 " --> pdb=" O THR B 191 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR B 204 " --> pdb=" O ASN B 193 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR B 195 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 55 through 59 removed outlier: 6.147A pdb=" N ALA B 99 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR B 133 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 101 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU B 131 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 103 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN B 129 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 105 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP B 125 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 156 through 161 removed outlier: 3.719A pdb=" N GLY B 62 " --> pdb=" O VAL B 186 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 247 through 262 removed outlier: 5.506A pdb=" N VAL B 248 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL B 427 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG B 250 " --> pdb=" O VAL B 425 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 425 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR B 252 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL B 423 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 421 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE B 417 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU B 260 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 415 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N TRP B 413 " --> pdb=" O PRO B 262 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN B 299 " --> pdb=" O TRP B 413 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL B 415 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG B 297 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE B 417 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL B 295 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN B 383 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE B 384 " --> pdb=" O TYR B 391 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 247 through 262 removed outlier: 5.506A pdb=" N VAL B 248 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL B 427 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG B 250 " --> pdb=" O VAL B 425 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 425 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR B 252 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL B 423 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 421 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE B 417 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU B 260 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 415 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N TRP B 413 " --> pdb=" O PRO B 262 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ASP B 422 " --> pdb=" O TYR B 437 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N TYR B 437 " --> pdb=" O ASP B 422 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU B 424 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 435 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN B 426 " --> pdb=" O GLN B 433 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 360 through 368 removed outlier: 6.816A pdb=" N CYS B 351 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR B 356 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASP B 323 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS B 328 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY B 313 " --> pdb=" O CYS B 328 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 360 through 368 removed outlier: 6.816A pdb=" N CYS B 351 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR B 356 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASP B 323 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 13.239A pdb=" N PHE B 326 " --> pdb=" O PRO B 341 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AC8, first strand: chain 'B' and resid 457 through 461 removed outlier: 6.618A pdb=" N GLN B 683 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA B 694 " --> pdb=" O GLN B 683 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA B 685 " --> pdb=" O ILE B 692 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 471 through 474 removed outlier: 5.032A pdb=" N LEU B 662 " --> pdb=" O VAL B 675 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR B 654 " --> pdb=" O LEU B 662 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 504 through 509 removed outlier: 6.456A pdb=" N SER B 601 " --> pdb=" O LYS B 564 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY B 603 " --> pdb=" O LYS B 562 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS B 562 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 514 through 515 removed outlier: 4.183A pdb=" N SER B 589 " --> pdb=" O TRP B 585 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP B 585 " --> pdb=" O SER B 589 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 581 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA B 595 " --> pdb=" O PHE B 579 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE B 579 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR B 597 " --> pdb=" O CYS B 577 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N CYS B 577 " --> pdb=" O TYR B 597 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 727 through 731 removed outlier: 6.775A pdb=" N ILE B 736 " --> pdb=" O VAL B 728 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N THR B 730 " --> pdb=" O PHE B 734 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE B 734 " --> pdb=" O THR B 730 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 761 through 779 removed outlier: 6.895A pdb=" N ASN B 762 " --> pdb=" O LYS B1142 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS B1142 " --> pdb=" O ASN B 762 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER B 764 " --> pdb=" O ASN B1140 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN B1140 " --> pdb=" O SER B 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR B1138 " --> pdb=" O PRO B 766 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN B 768 " --> pdb=" O THR B1136 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU B1133 " --> pdb=" O HIS B1114 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS B1114 " --> pdb=" O LEU B1133 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 761 through 779 removed outlier: 6.895A pdb=" N ASN B 762 " --> pdb=" O LYS B1142 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS B1142 " --> pdb=" O ASN B 762 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER B 764 " --> pdb=" O ASN B1140 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN B1140 " --> pdb=" O SER B 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR B1138 " --> pdb=" O PRO B 766 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN B 768 " --> pdb=" O THR B1136 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LYS B1142 " --> pdb=" O SER B1166 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU B1164 " --> pdb=" O TRP B1144 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 785 through 787 Processing sheet with id=AD7, first strand: chain 'B' and resid 1189 through 1191 removed outlier: 4.065A pdb=" N ILE B1202 " --> pdb=" O CYS B1148 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 37 through 42 removed outlier: 7.246A pdb=" N THR C 191 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL C 206 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR C 204 " --> pdb=" O ASN C 193 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR C 195 " --> pdb=" O VAL C 202 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 55 through 59 removed outlier: 6.147A pdb=" N ALA C 99 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR C 133 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL C 101 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU C 131 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU C 103 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN C 129 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE C 105 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP C 125 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 156 through 161 removed outlier: 3.719A pdb=" N GLY C 62 " --> pdb=" O VAL C 186 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 247 through 262 removed outlier: 5.505A pdb=" N VAL C 248 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL C 427 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG C 250 " --> pdb=" O VAL C 425 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL C 425 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR C 252 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL C 423 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 421 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE C 417 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU C 260 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL C 415 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TRP C 413 " --> pdb=" O PRO C 262 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN C 299 " --> pdb=" O TRP C 413 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL C 415 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG C 297 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE C 417 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL C 295 " --> pdb=" O PHE C 417 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N PHE C 384 " --> pdb=" O TYR C 391 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 247 through 262 removed outlier: 5.505A pdb=" N VAL C 248 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL C 427 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG C 250 " --> pdb=" O VAL C 425 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL C 425 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR C 252 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL C 423 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 421 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE C 417 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU C 260 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL C 415 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TRP C 413 " --> pdb=" O PRO C 262 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ASP C 422 " --> pdb=" O TYR C 437 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR C 437 " --> pdb=" O ASP C 422 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU C 424 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU C 435 " --> pdb=" O LEU C 424 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN C 426 " --> pdb=" O GLN C 433 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 360 through 368 removed outlier: 6.817A pdb=" N CYS C 351 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR C 356 " --> pdb=" O ASP C 323 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP C 323 " --> pdb=" O THR C 356 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS C 328 " --> pdb=" O GLY C 313 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLY C 313 " --> pdb=" O CYS C 328 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 360 through 368 removed outlier: 6.817A pdb=" N CYS C 351 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR C 356 " --> pdb=" O ASP C 323 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP C 323 " --> pdb=" O THR C 356 " (cutoff:3.500A) removed outlier: 13.239A pdb=" N PHE C 326 " --> pdb=" O PRO C 341 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 343 through 344 Processing sheet with id=AE7, first strand: chain 'C' and resid 457 through 461 removed outlier: 6.618A pdb=" N GLN C 683 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA C 694 " --> pdb=" O GLN C 683 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA C 685 " --> pdb=" O ILE C 692 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 471 through 474 removed outlier: 5.032A pdb=" N LEU C 662 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR C 654 " --> pdb=" O LEU C 662 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 504 through 509 removed outlier: 6.456A pdb=" N SER C 601 " --> pdb=" O LYS C 564 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY C 603 " --> pdb=" O LYS C 562 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS C 562 " --> pdb=" O GLY C 603 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 514 through 515 removed outlier: 4.184A pdb=" N SER C 589 " --> pdb=" O TRP C 585 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP C 585 " --> pdb=" O SER C 589 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU C 581 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA C 595 " --> pdb=" O PHE C 579 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N PHE C 579 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR C 597 " --> pdb=" O CYS C 577 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N CYS C 577 " --> pdb=" O TYR C 597 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 727 through 731 removed outlier: 6.774A pdb=" N ILE C 736 " --> pdb=" O VAL C 728 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N THR C 730 " --> pdb=" O PHE C 734 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE C 734 " --> pdb=" O THR C 730 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 761 through 779 removed outlier: 6.896A pdb=" N ASN C 762 " --> pdb=" O LYS C1142 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS C1142 " --> pdb=" O ASN C 762 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER C 764 " --> pdb=" O ASN C1140 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN C1140 " --> pdb=" O SER C 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR C1138 " --> pdb=" O PRO C 766 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN C 768 " --> pdb=" O THR C1136 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C1133 " --> pdb=" O HIS C1114 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS C1114 " --> pdb=" O LEU C1133 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 761 through 779 removed outlier: 6.896A pdb=" N ASN C 762 " --> pdb=" O LYS C1142 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS C1142 " --> pdb=" O ASN C 762 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER C 764 " --> pdb=" O ASN C1140 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN C1140 " --> pdb=" O SER C 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR C1138 " --> pdb=" O PRO C 766 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN C 768 " --> pdb=" O THR C1136 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LYS C1142 " --> pdb=" O SER C1166 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU C1164 " --> pdb=" O TRP C1144 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 785 through 787 Processing sheet with id=AF6, first strand: chain 'C' and resid 1189 through 1191 removed outlier: 4.065A pdb=" N ILE C1202 " --> pdb=" O CYS C1148 " (cutoff:3.500A) 1269 hydrogen bonds defined for protein. 3312 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: 16.00 Time building geometry restraints manager: 15.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 7568 1.33 - 1.47: 10479 1.47 - 1.61: 12694 1.61 - 1.75: 36 1.75 - 1.89: 141 Bond restraints: 30918 Sorted by residual: bond pdb=" C VAL B1190 " pdb=" N GLN B1191 " ideal model delta sigma weight residual 1.330 1.465 -0.135 1.42e-02 4.96e+03 9.05e+01 bond pdb=" C VAL C1190 " pdb=" N GLN C1191 " ideal model delta sigma weight residual 1.330 1.465 -0.135 1.42e-02 4.96e+03 8.99e+01 bond pdb=" C VAL A1190 " pdb=" N GLN A1191 " ideal model delta sigma weight residual 1.330 1.465 -0.135 1.42e-02 4.96e+03 8.99e+01 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.580 -0.174 2.00e-02 2.50e+03 7.59e+01 bond pdb=" C1 NAG u 2 " pdb=" O5 NAG u 2 " ideal model delta sigma weight residual 1.406 1.580 -0.174 2.00e-02 2.50e+03 7.58e+01 ... (remaining 30913 not shown) Histogram of bond angle deviations from ideal: 69.36 - 85.83: 75 85.83 - 102.31: 529 102.31 - 118.78: 24746 118.78 - 135.26: 16758 135.26 - 151.74: 51 Bond angle restraints: 42159 Sorted by residual: angle pdb=" C2 MAN 0 4 " pdb=" C3 MAN 0 4 " pdb=" O3 MAN 0 4 " ideal model delta sigma weight residual 107.58 151.74 -44.16 3.00e+00 1.11e-01 2.17e+02 angle pdb=" C2 MAN f 4 " pdb=" C3 MAN f 4 " pdb=" O3 MAN f 4 " ideal model delta sigma weight residual 107.58 151.73 -44.15 3.00e+00 1.11e-01 2.17e+02 angle pdb=" C2 MAN K 4 " pdb=" C3 MAN K 4 " pdb=" O3 MAN K 4 " ideal model delta sigma weight residual 107.58 151.70 -44.12 3.00e+00 1.11e-01 2.16e+02 angle pdb=" C4 MAN f 4 " pdb=" C3 MAN f 4 " pdb=" O3 MAN f 4 " ideal model delta sigma weight residual 111.95 70.52 41.43 3.00e+00 1.11e-01 1.91e+02 angle pdb=" C4 MAN 0 4 " pdb=" C3 MAN 0 4 " pdb=" O3 MAN 0 4 " ideal model delta sigma weight residual 111.95 70.53 41.42 3.00e+00 1.11e-01 1.91e+02 ... (remaining 42154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15735 17.99 - 35.97: 580 35.97 - 53.96: 143 53.96 - 71.94: 72 71.94 - 89.93: 18 Dihedral angle restraints: 16548 sinusoidal: 6225 harmonic: 10323 Sorted by residual: dihedral pdb=" C ALA B 810 " pdb=" N ALA B 810 " pdb=" CA ALA B 810 " pdb=" CB ALA B 810 " ideal model delta harmonic sigma weight residual -122.60 -146.41 23.81 0 2.50e+00 1.60e-01 9.07e+01 dihedral pdb=" C ALA C 810 " pdb=" N ALA C 810 " pdb=" CA ALA C 810 " pdb=" CB ALA C 810 " ideal model delta harmonic sigma weight residual -122.60 -146.40 23.80 0 2.50e+00 1.60e-01 9.06e+01 dihedral pdb=" C ALA A 810 " pdb=" N ALA A 810 " pdb=" CA ALA A 810 " pdb=" CB ALA A 810 " ideal model delta harmonic sigma weight residual -122.60 -146.37 23.77 0 2.50e+00 1.60e-01 9.04e+01 ... (remaining 16545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.264: 4966 0.264 - 0.528: 385 0.528 - 0.792: 109 0.792 - 1.056: 51 1.056 - 1.320: 27 Chirality restraints: 5538 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.40 2.00e-02 2.50e+03 3.91e+02 chirality pdb=" C1 NAG u 2 " pdb=" O4 NAG u 1 " pdb=" C2 NAG u 2 " pdb=" O5 NAG u 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.40 2.00e-02 2.50e+03 3.91e+02 chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.79 0.39 2.00e-02 2.50e+03 3.88e+02 ... (remaining 5535 not shown) Planarity restraints: 5148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 486 " -0.093 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" CG ASN B 486 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN B 486 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 486 " 0.157 2.00e-02 2.50e+03 pdb=" C1 NAG g 1 " -0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 486 " 0.093 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" CG ASN A 486 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN A 486 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 486 " -0.157 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " 0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 486 " -0.093 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" CG ASN C 486 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN C 486 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN C 486 " 0.157 2.00e-02 2.50e+03 pdb=" C1 NAG 1 1 " -0.120 2.00e-02 2.50e+03 ... (remaining 5145 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 42 2.16 - 2.85: 10971 2.85 - 3.53: 39555 3.53 - 4.22: 74296 4.22 - 4.90: 118793 Nonbonded interactions: 243657 Sorted by model distance: nonbonded pdb=" O4 NAG g 1 " pdb=" C1 NAG g 2 " model vdw 1.476 3.470 nonbonded pdb=" O4 NAG L 1 " pdb=" C1 NAG L 2 " model vdw 1.476 3.470 nonbonded pdb=" O4 NAG 1 1 " pdb=" C1 NAG 1 2 " model vdw 1.476 3.470 nonbonded pdb=" O ASN C1111 " pdb=" OD1 ASN C1111 " model vdw 1.738 3.040 nonbonded pdb=" O ASN A1111 " pdb=" OD1 ASN A1111 " model vdw 1.738 3.040 ... (remaining 243652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain 'K' selection = chain 'f' } ncs_group { reference = chain '1' selection = chain '4' selection = chain 'DA' selection = chain 'L' selection = chain 'O' selection = chain 'X' selection = chain 'g' selection = chain 'j' selection = chain 's' } ncs_group { reference = chain '2' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'CA' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'r' selection = chain 'u' selection = chain 'w' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain '3' selection = chain 'BA' selection = chain 'N' selection = chain 'V' selection = chain 'i' selection = chain 'q' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'AA' selection = chain 'F' selection = chain 'H' selection = chain 'U' selection = chain 'a' selection = chain 'c' selection = chain 'p' selection = chain 'v' selection = chain 'x' } ncs_group { reference = chain 'D' selection = chain 'Y' selection = chain 't' } 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: 1.830 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: 0.030 Extract box with map and model: 9.580 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 83.730 Find NCS groups from input model: 2.200 Set up NCS constraints: 0.840 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 : 0.024 0.174 30918 Z= 1.499 Angle : 3.036 44.157 42159 Z= 1.342 Chirality : 0.199 1.320 5538 Planarity : 0.012 0.113 5064 Dihedral : 11.587 89.931 9792 Min Nonbonded Distance : 1.476 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.70 % Favored : 93.70 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.09 % 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: -0.27 (0.14), residues: 3507 helix: 0.72 (0.19), residues: 708 sheet: 0.72 (0.18), residues: 852 loop : -0.95 (0.14), residues: 1947 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 468 time to evaluate : 3.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 489 average time/residue: 0.4517 time to fit residues: 344.8140 Evaluate side-chains 180 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 167 time to evaluate : 3.179 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.2860 time to fit residues: 11.1478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 0.8980 chunk 266 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 chunk 275 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 167 optimal weight: 0.9980 chunk 204 optimal weight: 0.9980 chunk 318 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 ASN C 433 GLN C1021 GLN C1054 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 30918 Z= 0.266 Angle : 0.872 13.361 42159 Z= 0.409 Chirality : 0.052 0.388 5538 Planarity : 0.006 0.073 5064 Dihedral : 5.903 37.951 3831 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.19 % Favored : 95.30 % Rotamer Outliers : 1.71 % 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: 0.07 (0.14), residues: 3507 helix: 1.53 (0.20), residues: 687 sheet: 0.78 (0.18), residues: 897 loop : -0.89 (0.14), residues: 1923 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 258 time to evaluate : 3.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 30 residues processed: 298 average time/residue: 0.4146 time to fit residues: 201.7625 Evaluate side-chains 189 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 159 time to evaluate : 3.398 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3284 time to fit residues: 21.4917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 177 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 265 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 319 optimal weight: 0.5980 chunk 344 optimal weight: 1.9990 chunk 284 optimal weight: 3.9990 chunk 316 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN A 657 ASN A 679 ASN ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS A1054 GLN ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 30918 Z= 0.375 Angle : 0.825 12.190 42159 Z= 0.391 Chirality : 0.052 0.454 5538 Planarity : 0.005 0.059 5064 Dihedral : 5.551 33.661 3831 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.39 % Favored : 94.01 % Rotamer Outliers : 1.84 % 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: -0.10 (0.14), residues: 3507 helix: 1.88 (0.20), residues: 663 sheet: 0.90 (0.17), residues: 918 loop : -1.33 (0.14), residues: 1926 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 182 time to evaluate : 3.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 38 residues processed: 222 average time/residue: 0.3976 time to fit residues: 151.9074 Evaluate side-chains 187 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 149 time to evaluate : 3.528 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.3350 time to fit residues: 28.2268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 315 optimal weight: 0.7980 chunk 240 optimal weight: 4.9990 chunk 165 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 320 optimal weight: 5.9990 chunk 339 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 303 optimal weight: 0.0050 chunk 91 optimal weight: 0.7980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1140 ASN B 383 GLN ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 30918 Z= 0.202 Angle : 0.688 11.485 42159 Z= 0.325 Chirality : 0.047 0.430 5538 Planarity : 0.004 0.050 5064 Dihedral : 5.170 30.173 3831 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.76 % Favored : 94.81 % Rotamer Outliers : 0.97 % 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: -0.11 (0.14), residues: 3507 helix: 1.69 (0.20), residues: 729 sheet: 0.74 (0.17), residues: 876 loop : -1.24 (0.14), residues: 1902 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 3.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 189 average time/residue: 0.3828 time to fit residues: 124.5682 Evaluate side-chains 167 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 3.362 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3542 time to fit residues: 14.4973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 282 optimal weight: 0.9980 chunk 192 optimal weight: 0.4980 chunk 4 optimal weight: 5.9990 chunk 252 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 289 optimal weight: 0.9980 chunk 234 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 304 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 HIS ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 30918 Z= 0.204 Angle : 0.660 11.342 42159 Z= 0.312 Chirality : 0.047 0.426 5538 Planarity : 0.004 0.048 5064 Dihedral : 4.944 30.151 3831 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.45 % Favored : 94.21 % Rotamer Outliers : 1.33 % 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: -0.11 (0.14), residues: 3507 helix: 1.84 (0.20), residues: 732 sheet: 0.72 (0.17), residues: 918 loop : -1.34 (0.14), residues: 1857 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 175 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 21 residues processed: 203 average time/residue: 0.3852 time to fit residues: 134.3962 Evaluate side-chains 168 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 3.317 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2970 time to fit residues: 15.9434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 114 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 339 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 HIS ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 30918 Z= 0.336 Angle : 0.711 11.726 42159 Z= 0.339 Chirality : 0.048 0.435 5538 Planarity : 0.004 0.047 5064 Dihedral : 5.077 29.244 3831 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.73 % Favored : 93.90 % Rotamer Outliers : 1.33 % 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: -0.22 (0.14), residues: 3507 helix: 1.77 (0.20), residues: 726 sheet: 0.59 (0.17), residues: 951 loop : -1.41 (0.14), residues: 1830 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 142 time to evaluate : 3.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 30 residues processed: 171 average time/residue: 0.3839 time to fit residues: 114.3084 Evaluate side-chains 162 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 3.410 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2950 time to fit residues: 20.7973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 327 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 193 optimal weight: 0.6980 chunk 248 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 285 optimal weight: 0.6980 chunk 189 optimal weight: 1.9990 chunk 338 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 HIS ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1034 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 30918 Z= 0.238 Angle : 0.664 12.334 42159 Z= 0.315 Chirality : 0.047 0.429 5538 Planarity : 0.004 0.043 5064 Dihedral : 4.922 29.635 3831 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.19 % Favored : 94.47 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3507 helix: 1.82 (0.20), residues: 729 sheet: 0.71 (0.17), residues: 936 loop : -1.44 (0.14), residues: 1842 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 3.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 168 average time/residue: 0.4422 time to fit residues: 127.5141 Evaluate side-chains 142 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 3.415 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.3363 time to fit residues: 11.1266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 209 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 230 optimal weight: 0.5980 chunk 167 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 265 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 HIS ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1034 HIS C 383 GLN ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 30918 Z= 0.210 Angle : 0.641 14.433 42159 Z= 0.304 Chirality : 0.047 0.420 5538 Planarity : 0.003 0.043 5064 Dihedral : 4.764 28.160 3831 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.36 % Favored : 94.33 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3507 helix: 1.94 (0.20), residues: 729 sheet: 0.71 (0.17), residues: 945 loop : -1.40 (0.15), residues: 1833 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 147 time to evaluate : 3.318 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 outliers start: 24 outliers final: 17 residues processed: 164 average time/residue: 0.3851 time to fit residues: 109.1082 Evaluate side-chains 146 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 3.293 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.3040 time to fit residues: 13.5483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 307 optimal weight: 1.9990 chunk 324 optimal weight: 6.9990 chunk 295 optimal weight: 4.9990 chunk 315 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 284 optimal weight: 5.9990 chunk 298 optimal weight: 0.6980 chunk 314 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 HIS ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.095 30918 Z= 0.255 Angle : 0.665 25.054 42159 Z= 0.315 Chirality : 0.047 0.468 5538 Planarity : 0.004 0.043 5064 Dihedral : 4.778 28.150 3831 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.22 % Favored : 94.47 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3507 helix: 1.93 (0.20), residues: 729 sheet: 0.68 (0.17), residues: 951 loop : -1.43 (0.15), residues: 1827 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 3.603 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 outliers start: 14 outliers final: 10 residues processed: 152 average time/residue: 0.3915 time to fit residues: 103.1933 Evaluate side-chains 141 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 3.177 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.3216 time to fit residues: 10.0441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 207 optimal weight: 0.0170 chunk 333 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 231 optimal weight: 1.9990 chunk 349 optimal weight: 0.9980 chunk 321 optimal weight: 0.0870 chunk 278 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 HIS C1191 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 30918 Z= 0.179 Angle : 0.626 17.791 42159 Z= 0.297 Chirality : 0.047 0.414 5538 Planarity : 0.003 0.042 5064 Dihedral : 4.647 28.746 3831 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.02 % Favored : 94.70 % Rotamer Outliers : 0.29 % 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: -0.04 (0.15), residues: 3507 helix: 2.00 (0.20), residues: 732 sheet: 0.71 (0.17), residues: 945 loop : -1.34 (0.15), residues: 1830 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 3.319 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 outliers start: 9 outliers final: 9 residues processed: 151 average time/residue: 0.4041 time to fit residues: 103.7624 Evaluate side-chains 140 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 3.054 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.3244 time to fit residues: 9.5111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 221 optimal weight: 1.9990 chunk 296 optimal weight: 0.4980 chunk 85 optimal weight: 0.6980 chunk 256 optimal weight: 0.6980 chunk 41 optimal weight: 0.1980 chunk 77 optimal weight: 0.9990 chunk 278 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 286 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 HIS ** C 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.113482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.086412 restraints weight = 59973.097| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.26 r_work: 0.3043 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 30918 Z= 0.180 Angle : 0.611 15.942 42159 Z= 0.291 Chirality : 0.046 0.409 5538 Planarity : 0.003 0.042 5064 Dihedral : 4.557 26.940 3831 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.19 % Favored : 94.53 % Rotamer Outliers : 0.29 % 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: 0.03 (0.15), residues: 3507 helix: 2.07 (0.20), residues: 732 sheet: 0.77 (0.17), residues: 960 loop : -1.34 (0.15), residues: 1815 =============================================================================== Job complete usr+sys time: 4923.35 seconds wall clock time: 92 minutes 26.87 seconds (5546.87 seconds total)