Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 02:32:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bfu_7094/04_2023/6bfu_7094.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bfu_7094/04_2023/6bfu_7094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bfu_7094/04_2023/6bfu_7094.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bfu_7094/04_2023/6bfu_7094.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bfu_7094/04_2023/6bfu_7094.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bfu_7094/04_2023/6bfu_7094.pdb" } resolution = 3.5 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= 0.005 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 15255 2.51 5 N 3864 2.21 5 O 5232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 707": "OD1" <-> "OD2" Residue "A TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 725": "OD1" <-> "OD2" Residue "A PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 294": "NH1" <-> "NH2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 572": "OE1" <-> "OE2" Residue "B PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 707": "OD1" <-> "OD2" Residue "B TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 725": "OD1" <-> "OD2" Residue "B PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 294": "NH1" <-> "NH2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 572": "OE1" <-> "OE2" Residue "C PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 669": "NH1" <-> "NH2" Residue "C PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 707": "OD1" <-> "OD2" Residue "C TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 725": "OD1" <-> "OD2" Residue "C PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 24480 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 7442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7442 Classifications: {'peptide': 964} Link IDs: {'PTRANS': 34, 'TRANS': 929} Chain breaks: 1 Chain: "B" Number of atoms: 7442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7442 Classifications: {'peptide': 964} Link IDs: {'PTRANS': 34, 'TRANS': 929} Chain breaks: 1 Chain: "C" Number of atoms: 7442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7442 Classifications: {'peptide': 964} Link IDs: {'PTRANS': 34, 'TRANS': 929} Chain breaks: 1 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: 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: "F" 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: "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: 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: "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: 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: "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: 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: "N" 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: "O" 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: "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: 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: "R" 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: "S" 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: "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: 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: "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: 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: "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: 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: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" 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: "b" 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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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: 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: "f" 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: "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: 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: "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: 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: "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: 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: "n" 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: "o" 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: "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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 12.27, per 1000 atoms: 0.50 Number of scatterers: 24480 At special positions: 0 Unit cell: (122.36, 125.02, 159.6, 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 5232 8.00 N 3864 7.00 C 15255 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 116 " distance=2.04 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 181 " distance=2.05 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 378 " distance=2.04 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 352 " distance=2.01 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS A 433 " - pdb=" SG CYS A 484 " distance=2.04 Simple disulfide: pdb=" SG CYS A 532 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS A 597 " - pdb=" SG CYS A 619 " distance=2.08 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 608 " distance=2.04 Simple disulfide: pdb=" SG CYS A 699 " - pdb=" SG CYS A 710 " distance=2.04 Simple disulfide: pdb=" SG CYS A 901 " - pdb=" SG CYS A 912 " distance=2.01 Simple disulfide: pdb=" SG CYS A 951 " - pdb=" SG CYS A 997 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 116 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 181 " distance=2.05 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 335 " - pdb=" SG CYS B 378 " distance=2.05 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 352 " distance=2.01 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 484 " distance=2.04 Simple disulfide: pdb=" SG CYS B 532 " - pdb=" SG CYS B 545 " distance=2.03 Simple disulfide: pdb=" SG CYS B 597 " - pdb=" SG CYS B 619 " distance=2.08 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 608 " distance=2.05 Simple disulfide: pdb=" SG CYS B 699 " - pdb=" SG CYS B 710 " distance=2.04 Simple disulfide: pdb=" SG CYS B 901 " - pdb=" SG CYS B 912 " distance=2.01 Simple disulfide: pdb=" SG CYS B 951 " - pdb=" SG CYS B 997 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 181 " distance=2.05 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 270 " distance=2.03 Simple disulfide: pdb=" SG CYS C 335 " - pdb=" SG CYS C 378 " distance=2.04 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 352 " distance=2.01 Simple disulfide: pdb=" SG CYS C 361 " - pdb=" SG CYS C 386 " distance=2.03 Simple disulfide: pdb=" SG CYS C 433 " - pdb=" SG CYS C 484 " distance=2.04 Simple disulfide: pdb=" SG CYS C 532 " - pdb=" SG CYS C 545 " distance=2.03 Simple disulfide: pdb=" SG CYS C 597 " - pdb=" SG CYS C 619 " distance=2.08 Simple disulfide: pdb=" SG CYS C 602 " - pdb=" SG CYS C 608 " distance=2.04 Simple disulfide: pdb=" SG CYS C 699 " - pdb=" SG CYS C 710 " distance=2.04 Simple disulfide: pdb=" SG CYS C 901 " - pdb=" SG CYS C 912 " distance=2.01 Simple disulfide: pdb=" SG CYS C 951 " - pdb=" SG CYS C 997 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN F 4 " - " MAN F 5 " " MAN O 4 " - " MAN O 5 " " MAN Q 4 " - " MAN Q 5 " " MAN S 4 " - " MAN S 5 " " MAN b 4 " - " MAN b 5 " " MAN d 4 " - " MAN d 5 " " MAN f 4 " - " MAN f 5 " " MAN o 4 " - " MAN o 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " " BMA I 3 " - " MAN I 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " " BMA V 3 " - " MAN V 4 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " BMA f 3 " - " MAN f 4 " " BMA i 3 " - " MAN i 4 " " BMA o 3 " - " MAN o 4 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " " BMA F 3 " - " MAN F 6 " " BMA I 3 " - " MAN I 5 " " BMA O 3 " - " MAN O 6 " " BMA Q 3 " - " MAN Q 6 " " BMA S 3 " - " MAN S 6 " " BMA V 3 " - " MAN V 5 " " BMA b 3 " - " MAN b 6 " " BMA d 3 " - " MAN d 6 " " BMA f 3 " - " MAN f 6 " " BMA i 3 " - " MAN i 5 " " BMA o 3 " - " MAN o 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " 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 K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " 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 k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " 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-ASN " NAG A1099 " - " ASN A 99 " " NAG A1162 " - " ASN A 162 " " NAG A1169 " - " ASN A 169 " " NAG A1331 " - " ASN A 331 " " NAG A1505 " - " ASN A 505 " " NAG A1531 " - " ASN A 531 " " NAG A1945 " - " ASN A 945 " " NAG A1970 " - " ASN A 970 " " NAG B1099 " - " ASN B 99 " " NAG B1162 " - " ASN B 162 " " NAG B1169 " - " ASN B 169 " " NAG B1331 " - " ASN B 331 " " NAG B1505 " - " ASN B 505 " " NAG B1531 " - " ASN B 531 " " NAG B1945 " - " ASN B 945 " " NAG B1970 " - " ASN B 970 " " NAG C1099 " - " ASN C 99 " " NAG C1162 " - " ASN C 162 " " NAG C1169 " - " ASN C 169 " " NAG C1331 " - " ASN C 331 " " NAG C1505 " - " ASN C 505 " " NAG C1531 " - " ASN C 531 " " NAG C1945 " - " ASN C 945 " " NAG C1970 " - " ASN C 970 " " NAG D 1 " - " ASN A 74 " " NAG E 1 " - " ASN A 184 " " NAG F 1 " - " ASN A 241 " " NAG G 1 " - " ASN A 251 " " NAG H 1 " - " ASN A 311 " " NAG I 1 " - " ASN A 472 " " NAG J 1 " - " ASN A 494 " " NAG K 1 " - " ASN A 526 " " NAG L 1 " - " ASN A 652 " " NAG M 1 " - " ASN A 661 " " NAG N 1 " - " ASN A 788 " " NAG O 1 " - " ASN A 914 " " NAG P 1 " - " ASN A1003 " " NAG Q 1 " - " ASN B 74 " " NAG R 1 " - " ASN B 184 " " NAG S 1 " - " ASN B 241 " " NAG T 1 " - " ASN B 251 " " NAG U 1 " - " ASN B 311 " " NAG V 1 " - " ASN B 472 " " NAG W 1 " - " ASN B 494 " " NAG X 1 " - " ASN B 526 " " NAG Y 1 " - " ASN B 652 " " NAG Z 1 " - " ASN B 661 " " NAG a 1 " - " ASN B 788 " " NAG b 1 " - " ASN B 914 " " NAG c 1 " - " ASN B1003 " " NAG d 1 " - " ASN C 74 " " NAG e 1 " - " ASN C 184 " " NAG f 1 " - " ASN C 241 " " NAG g 1 " - " ASN C 251 " " NAG h 1 " - " ASN C 311 " " NAG i 1 " - " ASN C 472 " " NAG j 1 " - " ASN C 494 " " NAG k 1 " - " ASN C 526 " " NAG l 1 " - " ASN C 652 " " NAG m 1 " - " ASN C 661 " " NAG n 1 " - " ASN C 788 " " NAG o 1 " - " ASN C 914 " " NAG p 1 " - " ASN C1003 " Time building additional restraints: 13.53 Conformation dependent library (CDL) restraints added in 3.5 seconds 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5484 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 48 sheets defined 28.5% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'A' and resid 285 through 288 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.560A pdb=" N VAL A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 369' Processing helix chain 'A' and resid 504 through 508 removed outlier: 4.040A pdb=" N THR A 507 " --> pdb=" O SER A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 603 Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 617 through 641 Processing helix chain 'A' and resid 645 through 651 Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.808A pdb=" N LYS A 657 " --> pdb=" O THR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 683 Processing helix chain 'A' and resid 695 through 701 Processing helix chain 'A' and resid 703 through 706 Processing helix chain 'A' and resid 707 through 714 Processing helix chain 'A' and resid 725 through 739 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 752 through 765 Processing helix chain 'A' and resid 774 through 795 Processing helix chain 'A' and resid 804 through 823 Processing helix chain 'A' and resid 825 through 834 Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 845 through 853 Processing helix chain 'A' and resid 854 through 901 removed outlier: 3.721A pdb=" N GLN A 860 " --> pdb=" O VAL A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 989 No H-bonds generated for 'chain 'A' and resid 987 through 989' Processing helix chain 'A' and resid 1008 through 1012 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 162 through 169 Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 285 through 288 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.560A pdb=" N VAL B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 369' Processing helix chain 'B' and resid 504 through 508 removed outlier: 4.039A pdb=" N THR B 507 " --> pdb=" O SER B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 603 Processing helix chain 'B' and resid 605 through 613 Processing helix chain 'B' and resid 617 through 641 Processing helix chain 'B' and resid 645 through 651 Processing helix chain 'B' and resid 652 through 657 removed outlier: 3.808A pdb=" N LYS B 657 " --> pdb=" O THR B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 683 Processing helix chain 'B' and resid 695 through 701 Processing helix chain 'B' and resid 703 through 706 Processing helix chain 'B' and resid 707 through 714 Processing helix chain 'B' and resid 725 through 739 Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 752 through 765 Processing helix chain 'B' and resid 774 through 795 Processing helix chain 'B' and resid 804 through 823 Processing helix chain 'B' and resid 825 through 834 Processing helix chain 'B' and resid 835 through 837 No H-bonds generated for 'chain 'B' and resid 835 through 837' Processing helix chain 'B' and resid 845 through 853 Processing helix chain 'B' and resid 854 through 901 removed outlier: 3.719A pdb=" N GLN B 860 " --> pdb=" O VAL B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 989 No H-bonds generated for 'chain 'B' and resid 987 through 989' Processing helix chain 'B' and resid 1008 through 1012 Processing helix chain 'C' and resid 118 through 123 Processing helix chain 'C' and resid 162 through 169 Processing helix chain 'C' and resid 263 through 272 Processing helix chain 'C' and resid 285 through 288 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.560A pdb=" N VAL C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASN C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 369' Processing helix chain 'C' and resid 504 through 508 removed outlier: 4.040A pdb=" N THR C 507 " --> pdb=" O SER C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 603 Processing helix chain 'C' and resid 605 through 613 Processing helix chain 'C' and resid 617 through 641 Processing helix chain 'C' and resid 645 through 651 Processing helix chain 'C' and resid 652 through 657 removed outlier: 3.806A pdb=" N LYS C 657 " --> pdb=" O THR C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 683 Processing helix chain 'C' and resid 695 through 701 Processing helix chain 'C' and resid 703 through 706 Processing helix chain 'C' and resid 707 through 714 Processing helix chain 'C' and resid 725 through 739 Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 752 through 765 Processing helix chain 'C' and resid 774 through 795 Processing helix chain 'C' and resid 804 through 823 Processing helix chain 'C' and resid 825 through 834 Processing helix chain 'C' and resid 835 through 837 No H-bonds generated for 'chain 'C' and resid 835 through 837' Processing helix chain 'C' and resid 845 through 853 Processing helix chain 'C' and resid 854 through 901 removed outlier: 3.720A pdb=" N GLN C 860 " --> pdb=" O VAL C 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 989 No H-bonds generated for 'chain 'C' and resid 987 through 989' Processing helix chain 'C' and resid 1008 through 1012 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 91 removed outlier: 3.542A pdb=" N LEU A 89 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN A 241 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU A 91 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU A 239 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N PHE A 206 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 removed outlier: 7.375A pdb=" N ASP A 244 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TYR A 259 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 246 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE A 257 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A 248 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 105 removed outlier: 3.531A pdb=" N GLY A 189 " --> pdb=" O CYS A 181 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR A 183 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N TYR A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 280 through 283 removed outlier: 3.595A pdb=" N GLY A 499 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE A 493 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 293 through 297 removed outlier: 3.658A pdb=" N GLN A 293 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR A 468 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE A 460 " --> pdb=" O TYR A 468 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 349 through 350 removed outlier: 7.247A pdb=" N THR A 350 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 314 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN A 309 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE A 328 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN A 311 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A 326 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER A 313 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 320 through 328 removed outlier: 6.494A pdb=" N SER A 313 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A 326 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN A 311 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE A 328 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN A 309 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TYR A 405 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU A 379 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR A 407 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 377 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 409 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER A 373 " --> pdb=" O GLY A 411 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 333 through 335 removed outlier: 4.692A pdb=" N SER A 373 " --> pdb=" O GLY A 411 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 409 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 377 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR A 407 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU A 379 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TYR A 405 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 397 through 399 Processing sheet with id=AB1, first strand: chain 'A' and resid 353 through 358 removed outlier: 7.247A pdb=" N THR A 350 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 314 " --> pdb=" O THR A 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 537 through 539 Processing sheet with id=AB3, first strand: chain 'A' and resid 556 through 557 Processing sheet with id=AB4, first strand: chain 'A' and resid 571 through 587 removed outlier: 6.946A pdb=" N GLU A 572 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG A 943 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE A 941 " --> pdb=" O PRO A 574 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA A 576 " --> pdb=" O ASN A 939 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY A 928 " --> pdb=" O THR A 924 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR A 924 " --> pdb=" O GLY A 928 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE A 930 " --> pdb=" O THR A 922 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR A 922 " --> pdb=" O PHE A 930 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N MET A 932 " --> pdb=" O SER A 920 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER A 920 " --> pdb=" O MET A 932 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA A 934 " --> pdb=" O ILE A 918 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 592 through 595 removed outlier: 4.173A pdb=" N GLN A 592 " --> pdb=" O LEU A 720 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 643 through 644 removed outlier: 5.865A pdb=" N THR A 643 " --> pdb=" O GLN B 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 991 through 994 Processing sheet with id=AB8, first strand: chain 'A' and resid 964 through 969 Processing sheet with id=AB9, first strand: chain 'B' and resid 81 through 91 removed outlier: 3.543A pdb=" N LEU B 89 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN B 241 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU B 91 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU B 239 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N PHE B 206 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 95 through 96 removed outlier: 7.377A pdb=" N ASP B 244 " --> pdb=" O TYR B 259 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TYR B 259 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU B 246 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE B 257 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR B 248 " --> pdb=" O SER B 255 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 101 through 105 removed outlier: 3.532A pdb=" N GLY B 189 " --> pdb=" O CYS B 181 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR B 183 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 280 through 283 removed outlier: 3.594A pdb=" N GLY B 499 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE B 493 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL B 497 " --> pdb=" O ILE B 493 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 293 through 297 removed outlier: 3.658A pdb=" N GLN B 293 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR B 468 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE B 460 " --> pdb=" O TYR B 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 349 through 350 removed outlier: 7.246A pdb=" N THR B 350 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA B 314 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN B 309 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE B 328 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN B 311 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 326 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER B 313 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 320 through 328 removed outlier: 6.494A pdb=" N SER B 313 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 326 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN B 311 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE B 328 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN B 309 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR B 405 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU B 379 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR B 407 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE B 377 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL B 409 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N SER B 373 " --> pdb=" O GLY B 411 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 333 through 335 removed outlier: 4.691A pdb=" N SER B 373 " --> pdb=" O GLY B 411 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL B 409 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE B 377 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR B 407 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU B 379 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR B 405 " --> pdb=" O LEU B 379 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 397 through 399 Processing sheet with id=AC9, first strand: chain 'B' and resid 353 through 358 removed outlier: 7.246A pdb=" N THR B 350 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA B 314 " --> pdb=" O THR B 350 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 537 through 539 Processing sheet with id=AD2, first strand: chain 'B' and resid 571 through 587 removed outlier: 6.944A pdb=" N GLU B 572 " --> pdb=" O ARG B 943 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ARG B 943 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE B 941 " --> pdb=" O PRO B 574 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA B 576 " --> pdb=" O ASN B 939 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY B 928 " --> pdb=" O THR B 924 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N THR B 924 " --> pdb=" O GLY B 928 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE B 930 " --> pdb=" O THR B 922 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR B 922 " --> pdb=" O PHE B 930 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N MET B 932 " --> pdb=" O SER B 920 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER B 920 " --> pdb=" O MET B 932 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA B 934 " --> pdb=" O ILE B 918 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 592 through 595 removed outlier: 4.172A pdb=" N GLN B 592 " --> pdb=" O LEU B 720 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 643 through 644 removed outlier: 5.865A pdb=" N THR B 643 " --> pdb=" O GLN C 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 991 through 994 Processing sheet with id=AD6, first strand: chain 'B' and resid 964 through 969 Processing sheet with id=AD7, first strand: chain 'C' and resid 81 through 91 removed outlier: 3.541A pdb=" N LEU C 89 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN C 241 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU C 91 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU C 239 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN C 205 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N PHE C 206 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 95 through 96 removed outlier: 7.377A pdb=" N ASP C 244 " --> pdb=" O TYR C 259 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TYR C 259 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU C 246 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE C 257 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR C 248 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.531A pdb=" N GLY C 189 " --> pdb=" O CYS C 181 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR C 183 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 280 through 283 removed outlier: 3.594A pdb=" N GLY C 499 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE C 493 " --> pdb=" O VAL C 497 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL C 497 " --> pdb=" O ILE C 493 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 293 through 297 removed outlier: 3.659A pdb=" N GLN C 293 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TYR C 468 " --> pdb=" O VAL C 481 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE C 460 " --> pdb=" O TYR C 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 349 through 350 removed outlier: 7.247A pdb=" N THR C 350 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA C 314 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN C 309 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE C 328 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASN C 311 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL C 326 " --> pdb=" O ASN C 311 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER C 313 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 320 through 328 removed outlier: 6.494A pdb=" N SER C 313 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL C 326 " --> pdb=" O ASN C 311 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASN C 311 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE C 328 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN C 309 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR C 405 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU C 379 " --> pdb=" O TYR C 405 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR C 407 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE C 377 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL C 409 " --> pdb=" O SER C 375 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N SER C 373 " --> pdb=" O GLY C 411 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 333 through 335 removed outlier: 4.691A pdb=" N SER C 373 " --> pdb=" O GLY C 411 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL C 409 " --> pdb=" O SER C 375 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE C 377 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR C 407 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU C 379 " --> pdb=" O TYR C 405 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR C 405 " --> pdb=" O LEU C 379 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 397 through 399 Processing sheet with id=AE7, first strand: chain 'C' and resid 353 through 358 removed outlier: 7.247A pdb=" N THR C 350 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA C 314 " --> pdb=" O THR C 350 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 537 through 539 Processing sheet with id=AE9, first strand: chain 'C' and resid 571 through 587 removed outlier: 6.946A pdb=" N GLU C 572 " --> pdb=" O ARG C 943 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ARG C 943 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE C 941 " --> pdb=" O PRO C 574 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA C 576 " --> pdb=" O ASN C 939 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY C 928 " --> pdb=" O THR C 924 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR C 924 " --> pdb=" O GLY C 928 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE C 930 " --> pdb=" O THR C 922 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR C 922 " --> pdb=" O PHE C 930 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N MET C 932 " --> pdb=" O SER C 920 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER C 920 " --> pdb=" O MET C 932 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA C 934 " --> pdb=" O ILE C 918 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 592 through 595 removed outlier: 4.173A pdb=" N GLN C 592 " --> pdb=" O LEU C 720 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 991 through 994 Processing sheet with id=AF3, first strand: chain 'C' and resid 964 through 969 1078 hydrogen bonds defined for protein. 2874 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: 11.58 Time building geometry restraints manager: 14.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5199 1.32 - 1.45: 6468 1.45 - 1.58: 12897 1.58 - 1.71: 144 1.71 - 1.83: 180 Bond restraints: 24888 Sorted by residual: bond pdb=" N PRO C 59 " pdb=" CA PRO C 59 " ideal model delta sigma weight residual 1.474 1.438 0.036 7.40e-03 1.83e+04 2.31e+01 bond pdb=" N PRO B 59 " pdb=" CA PRO B 59 " ideal model delta sigma weight residual 1.474 1.439 0.035 7.40e-03 1.83e+04 2.26e+01 bond pdb=" N PRO A 59 " pdb=" CA PRO A 59 " ideal model delta sigma weight residual 1.474 1.439 0.035 7.40e-03 1.83e+04 2.25e+01 bond pdb=" C2 NAG D 2 " pdb=" N2 NAG D 2 " ideal model delta sigma weight residual 1.439 1.353 0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C2 NAG d 2 " pdb=" N2 NAG d 2 " ideal model delta sigma weight residual 1.439 1.353 0.086 2.00e-02 2.50e+03 1.87e+01 ... (remaining 24883 not shown) Histogram of bond angle deviations from ideal: 98.65 - 105.67: 493 105.67 - 112.68: 14341 112.68 - 119.70: 6838 119.70 - 126.72: 12164 126.72 - 133.73: 103 Bond angle restraints: 33939 Sorted by residual: angle pdb=" CD1 LEU B 453 " pdb=" CG LEU B 453 " pdb=" CD2 LEU B 453 " ideal model delta sigma weight residual 110.80 132.02 -21.22 2.20e+00 2.07e-01 9.31e+01 angle pdb=" CD1 LEU A 453 " pdb=" CG LEU A 453 " pdb=" CD2 LEU A 453 " ideal model delta sigma weight residual 110.80 131.99 -21.19 2.20e+00 2.07e-01 9.28e+01 angle pdb=" CD1 LEU C 453 " pdb=" CG LEU C 453 " pdb=" CD2 LEU C 453 " ideal model delta sigma weight residual 110.80 131.96 -21.16 2.20e+00 2.07e-01 9.25e+01 angle pdb=" C LYS B 338 " pdb=" N PRO B 339 " pdb=" CA PRO B 339 " ideal model delta sigma weight residual 119.32 127.75 -8.43 1.14e+00 7.69e-01 5.46e+01 angle pdb=" C LYS A 338 " pdb=" N PRO A 339 " pdb=" CA PRO A 339 " ideal model delta sigma weight residual 119.32 127.71 -8.39 1.14e+00 7.69e-01 5.42e+01 ... (remaining 33934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 13112 17.51 - 35.01: 436 35.01 - 52.51: 108 52.51 - 70.02: 54 70.02 - 87.52: 12 Dihedral angle restraints: 13722 sinusoidal: 5223 harmonic: 8499 Sorted by residual: dihedral pdb=" CB CYS C 433 " pdb=" SG CYS C 433 " pdb=" SG CYS C 484 " pdb=" CB CYS C 484 " ideal model delta sinusoidal sigma weight residual -86.00 -164.50 78.50 1 1.00e+01 1.00e-02 7.69e+01 dihedral pdb=" CB CYS A 433 " pdb=" SG CYS A 433 " pdb=" SG CYS A 484 " pdb=" CB CYS A 484 " ideal model delta sinusoidal sigma weight residual -86.00 -164.50 78.50 1 1.00e+01 1.00e-02 7.69e+01 dihedral pdb=" CB CYS B 433 " pdb=" SG CYS B 433 " pdb=" SG CYS B 484 " pdb=" CB CYS B 484 " ideal model delta sinusoidal sigma weight residual -86.00 -164.48 78.48 1 1.00e+01 1.00e-02 7.68e+01 ... (remaining 13719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 4244 0.153 - 0.306: 151 0.306 - 0.458: 123 0.458 - 0.611: 45 0.611 - 0.764: 3 Chirality restraints: 4566 Sorted by residual: chirality pdb=" C1 BMA m 3 " pdb=" O4 NAG m 2 " pdb=" C2 BMA m 3 " pdb=" O5 BMA m 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.22e+02 chirality pdb=" C1 BMA Z 3 " pdb=" O4 NAG Z 2 " pdb=" C2 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.19e+02 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 ... (remaining 4563 not shown) Planarity restraints: 4167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 114 " 0.064 2.00e-02 2.50e+03 3.42e-02 2.34e+01 pdb=" CG TYR A 114 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 114 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 114 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR A 114 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 114 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR A 114 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 114 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 114 " 0.064 2.00e-02 2.50e+03 3.41e-02 2.32e+01 pdb=" CG TYR B 114 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 114 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR B 114 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR B 114 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR B 114 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR B 114 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 114 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 114 " -0.064 2.00e-02 2.50e+03 3.40e-02 2.32e+01 pdb=" CG TYR C 114 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR C 114 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR C 114 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR C 114 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR C 114 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR C 114 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 114 " -0.051 2.00e-02 2.50e+03 ... (remaining 4164 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 90 2.58 - 3.16: 22370 3.16 - 3.74: 36760 3.74 - 4.32: 54914 4.32 - 4.90: 87383 Nonbonded interactions: 201517 Sorted by model distance: nonbonded pdb=" O ASN A 169 " pdb=" OD1 ASN A 169 " model vdw 2.005 3.040 nonbonded pdb=" O ASN B 169 " pdb=" OD1 ASN B 169 " model vdw 2.006 3.040 nonbonded pdb=" O ASN C 169 " pdb=" OD1 ASN C 169 " model vdw 2.007 3.040 nonbonded pdb=" O ASN B 914 " pdb=" OD1 ASN B 914 " model vdw 2.060 3.040 nonbonded pdb=" O ASN A 914 " pdb=" OD1 ASN A 914 " model vdw 2.060 3.040 ... (remaining 201512 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'o' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'R' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' } ncs_group { reference = chain 'G' selection = chain 'P' selection = chain 'T' selection = chain 'c' selection = chain 'g' selection = chain 'p' } ncs_group { reference = chain 'I' selection = chain 'V' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.070 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 68.430 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.018 0.086 24888 Z= 1.155 Angle : 1.391 21.223 33939 Z= 0.814 Chirality : 0.108 0.764 4566 Planarity : 0.006 0.034 4104 Dihedral : 10.659 87.523 8121 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.23 % Favored : 96.56 % Rotamer Outliers : 0.35 % 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: 0.52 (0.16), residues: 2880 helix: 1.17 (0.19), residues: 693 sheet: 0.14 (0.18), residues: 675 loop : 0.18 (0.17), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 529 time to evaluate : 3.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 538 average time/residue: 0.3640 time to fit residues: 305.4753 Evaluate side-chains 234 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 227 time to evaluate : 3.053 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 7 average time/residue: 0.2295 time to fit residues: 6.9892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 225 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 137 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 261 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 GLN A 621 ASN A 712 GLN A 808 ASN A 830 HIS A 988 GLN B 168 HIS B 621 ASN B 712 GLN B 808 ASN ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 HIS B 988 GLN C 168 HIS ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 GLN C 712 GLN C 808 ASN C 988 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 24888 Z= 0.251 Angle : 0.658 8.340 33939 Z= 0.338 Chirality : 0.044 0.194 4566 Planarity : 0.005 0.083 4104 Dihedral : 4.932 37.353 3117 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.60 % Favored : 97.36 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.16), residues: 2880 helix: 2.68 (0.20), residues: 669 sheet: 0.21 (0.19), residues: 666 loop : 0.24 (0.17), residues: 1545 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 276 time to evaluate : 2.793 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: 45 outliers final: 24 residues processed: 308 average time/residue: 0.3824 time to fit residues: 183.8764 Evaluate side-chains 222 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 198 time to evaluate : 2.689 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2386 time to fit residues: 14.3274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 262 optimal weight: 0.9980 chunk 283 optimal weight: 0.0870 chunk 233 optimal weight: 0.7980 chunk 259 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 210 optimal weight: 0.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS A 621 ASN A 923 GLN B 923 GLN ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 24888 Z= 0.234 Angle : 0.618 14.008 33939 Z= 0.308 Chirality : 0.044 0.335 4566 Planarity : 0.004 0.080 4104 Dihedral : 4.761 39.706 3117 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.16), residues: 2880 helix: 2.69 (0.20), residues: 693 sheet: 0.17 (0.20), residues: 651 loop : 0.15 (0.17), residues: 1536 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 221 time to evaluate : 2.964 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: 37 outliers final: 12 residues processed: 253 average time/residue: 0.3415 time to fit residues: 141.7884 Evaluate side-chains 186 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 174 time to evaluate : 3.003 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2286 time to fit residues: 9.2469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 262 optimal weight: 0.6980 chunk 278 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 249 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 ASN A 772 GLN B 823 GLN ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 24888 Z= 0.259 Angle : 0.599 11.178 33939 Z= 0.299 Chirality : 0.043 0.207 4566 Planarity : 0.004 0.081 4104 Dihedral : 4.718 38.572 3117 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.16), residues: 2880 helix: 2.66 (0.20), residues: 693 sheet: 0.04 (0.20), residues: 678 loop : 0.11 (0.17), residues: 1509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 208 average time/residue: 0.3550 time to fit residues: 120.4719 Evaluate side-chains 184 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 174 time to evaluate : 2.781 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2256 time to fit residues: 7.8799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 0.2980 chunk 158 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 0 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 ASN B 589 GLN B 621 ASN B 772 GLN ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 ASN C 176 ASN C 610 GLN C1011 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 24888 Z= 0.263 Angle : 0.581 10.375 33939 Z= 0.289 Chirality : 0.043 0.315 4566 Planarity : 0.004 0.085 4104 Dihedral : 4.669 38.192 3117 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.93 (0.16), residues: 2880 helix: 2.45 (0.20), residues: 714 sheet: 0.10 (0.21), residues: 657 loop : 0.02 (0.17), residues: 1509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 187 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 16 residues processed: 210 average time/residue: 0.3465 time to fit residues: 118.8958 Evaluate side-chains 175 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 159 time to evaluate : 2.821 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2183 time to fit residues: 10.2608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 1.9990 chunk 250 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 278 optimal weight: 0.9980 chunk 231 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 92 optimal weight: 0.5980 chunk 146 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 ASN A 627 HIS B 627 HIS ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 24888 Z= 0.208 Angle : 0.564 9.510 33939 Z= 0.281 Chirality : 0.043 0.299 4566 Planarity : 0.004 0.083 4104 Dihedral : 4.621 37.434 3117 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.90 (0.16), residues: 2880 helix: 2.51 (0.20), residues: 714 sheet: 0.09 (0.21), residues: 657 loop : -0.03 (0.17), residues: 1509 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 189 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 203 average time/residue: 0.3634 time to fit residues: 119.6593 Evaluate side-chains 166 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 158 time to evaluate : 2.525 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2691 time to fit residues: 7.4673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 234 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 277 optimal weight: 1.9990 chunk 173 optimal weight: 0.4980 chunk 169 optimal weight: 0.6980 chunk 128 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 ASN ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 627 HIS C 769 ASN ** C 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 24888 Z= 0.222 Angle : 0.562 10.464 33939 Z= 0.280 Chirality : 0.043 0.291 4566 Planarity : 0.004 0.071 4104 Dihedral : 4.588 37.098 3117 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.90 (0.16), residues: 2880 helix: 2.48 (0.20), residues: 714 sheet: 0.11 (0.21), residues: 618 loop : -0.04 (0.17), residues: 1548 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 165 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 176 average time/residue: 0.3636 time to fit residues: 104.6116 Evaluate side-chains 165 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 157 time to evaluate : 2.731 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2210 time to fit residues: 6.8675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 769 ASN ** C 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 24888 Z= 0.288 Angle : 0.592 11.987 33939 Z= 0.295 Chirality : 0.043 0.240 4566 Planarity : 0.004 0.066 4104 Dihedral : 4.651 37.058 3117 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.73 (0.17), residues: 2880 helix: 2.39 (0.20), residues: 717 sheet: -0.04 (0.21), residues: 672 loop : -0.15 (0.17), residues: 1491 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 160 time to evaluate : 2.968 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 170 average time/residue: 0.3737 time to fit residues: 103.6417 Evaluate side-chains 151 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 146 time to evaluate : 3.022 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2387 time to fit residues: 6.1728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 1.9990 chunk 265 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 258 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 244 optimal weight: 0.5980 chunk 257 optimal weight: 0.3980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 ASN A 824 GLN ** B 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 769 ASN ** C 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 24888 Z= 0.240 Angle : 0.578 13.302 33939 Z= 0.286 Chirality : 0.043 0.240 4566 Planarity : 0.004 0.064 4104 Dihedral : 4.615 36.714 3117 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.68 (0.16), residues: 2880 helix: 2.27 (0.20), residues: 735 sheet: -0.06 (0.21), residues: 627 loop : -0.18 (0.17), residues: 1518 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 163 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 168 average time/residue: 0.3506 time to fit residues: 96.2361 Evaluate side-chains 157 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 153 time to evaluate : 2.668 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2346 time to fit residues: 5.3692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 0.7980 chunk 273 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 286 optimal weight: 0.8980 chunk 264 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 ASN B 769 ASN ** B 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 769 ASN ** C 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 24888 Z= 0.298 Angle : 0.604 13.928 33939 Z= 0.300 Chirality : 0.043 0.244 4566 Planarity : 0.004 0.064 4104 Dihedral : 4.665 36.784 3117 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.61 (0.16), residues: 2880 helix: 2.25 (0.20), residues: 735 sheet: -0.14 (0.22), residues: 612 loop : -0.23 (0.17), residues: 1533 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 158 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 161 average time/residue: 0.3636 time to fit residues: 95.1495 Evaluate side-chains 157 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 2.745 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2120 time to fit residues: 4.4665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 210 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 95 optimal weight: 0.0470 chunk 234 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 769 ASN ** B 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 769 ASN ** C 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.106687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.077010 restraints weight = 43471.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.080544 restraints weight = 21190.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.082828 restraints weight = 13950.503| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 24888 Z= 0.314 Angle : 0.608 13.778 33939 Z= 0.302 Chirality : 0.044 0.247 4566 Planarity : 0.004 0.062 4104 Dihedral : 4.704 37.004 3117 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.43 (0.16), residues: 2880 helix: 2.00 (0.19), residues: 753 sheet: -0.18 (0.22), residues: 612 loop : -0.35 (0.17), residues: 1515 =============================================================================== Job complete usr+sys time: 3886.34 seconds wall clock time: 73 minutes 43.21 seconds (4423.21 seconds total)