Starting phenix.real_space_refine on Wed Aug 7 14:52:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx2_23564/08_2024/7lx2_23564.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx2_23564/08_2024/7lx2_23564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx2_23564/08_2024/7lx2_23564.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx2_23564/08_2024/7lx2_23564.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx2_23564/08_2024/7lx2_23564.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx2_23564/08_2024/7lx2_23564.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.146 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 111 5.16 5 C 12645 2.51 5 N 3279 2.21 5 O 4161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 92": "OD1" <-> "OD2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 92": "OD1" <-> "OD2" Residue "P TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 20196 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 4232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4232 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 24, 'TRANS': 509} Chain breaks: 7 Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "H" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "B" Number of atoms: 4232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4232 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 24, 'TRANS': 509} Chain breaks: 7 Chain: "M" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "N" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "C" Number of atoms: 4232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4232 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 24, 'TRANS': 509} Chain breaks: 7 Chain: "O" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "P" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 12.36, per 1000 atoms: 0.61 Number of scatterers: 20196 At special positions: 0 Unit cell: (152.874, 144.666, 150.822, 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 111 16.00 O 4161 8.00 N 3279 7.00 C 12645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.27 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.10 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.08 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.23 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 605 " distance=2.07 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.08 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.27 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.11 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.08 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.04 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 605 " distance=2.07 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.07 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.27 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.08 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 605 " distance=2.07 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " 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 T 4 " - " MAN T 5 " " MAN T 5 " - " MAN T 6 " " MAN W 4 " - " MAN W 5 " " MAN h 4 " - " MAN h 5 " " MAN h 5 " - " MAN h 6 " " MAN k 4 " - " MAN k 5 " " MAN v 4 " - " MAN v 5 " " MAN v 5 " - " MAN v 6 " " MAN y 4 " - " MAN y 5 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 8 " " BMA W 3 " - " MAN W 4 " " BMA c 3 " - " MAN c 4 " " MAN c 4 " - " MAN c 5 " " BMA h 3 " - " MAN h 4 " " MAN h 7 " - " MAN h 8 " " BMA k 3 " - " MAN k 4 " " BMA q 3 " - " MAN q 4 " " MAN q 4 " - " MAN q 5 " " BMA v 3 " - " MAN v 4 " " MAN v 7 " - " MAN v 8 " " BMA y 3 " - " MAN y 4 " ALPHA1-6 " BMA J 3 " - " MAN J 6 " " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 9 " " BMA W 3 " - " MAN W 6 " " BMA c 3 " - " MAN c 6 " " BMA h 3 " - " MAN h 7 " " MAN h 7 " - " MAN h 9 " " BMA k 3 " - " MAN k 6 " " BMA q 3 " - " MAN q 6 " " BMA v 3 " - " MAN v 7 " " MAN v 7 " - " MAN v 9 " " BMA y 3 " - " MAN y 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " NAG-ASN " NAG A 701 " - " ASN A 160 " " NAG A 702 " - " ASN A 190 " " NAG A 703 " - " ASN A 289 " " NAG A 704 " - " ASN A 339 " " NAG A 705 " - " ASN A 611 " " NAG B 701 " - " ASN B 160 " " NAG B 702 " - " ASN B 190 " " NAG B 703 " - " ASN B 289 " " NAG B 704 " - " ASN B 339 " " NAG B 705 " - " ASN B 611 " " NAG C 701 " - " ASN C 160 " " NAG C 702 " - " ASN C 190 " " NAG C 703 " - " ASN C 289 " " NAG C 704 " - " ASN C 339 " " NAG C 705 " - " ASN C 611 " " NAG D 1 " - " ASN A 88 " " NAG E 1 " - " ASN A 130 " " NAG F 1 " - " ASN A 197 " " NAG G 1 " - " ASN A 276 " " NAG I 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 262 " " NAG K 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 392 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN A 295 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 234 " " NAG V 1 " - " ASN A 241 " " NAG W 1 " - " ASN A 138 " " NAG X 1 " - " ASN B 88 " " NAG Y 1 " - " ASN B 130 " " NAG Z 1 " - " ASN B 197 " " NAG a 1 " - " ASN B 276 " " NAG b 1 " - " ASN B 301 " " NAG c 1 " - " ASN B 262 " " NAG d 1 " - " ASN B 386 " " NAG e 1 " - " ASN B 392 " " NAG f 1 " - " ASN B 448 " " NAG g 1 " - " ASN B 295 " " NAG h 1 " - " ASN B 332 " " NAG i 1 " - " ASN B 234 " " NAG j 1 " - " ASN B 241 " " NAG k 1 " - " ASN B 138 " " NAG l 1 " - " ASN C 88 " " NAG m 1 " - " ASN C 130 " " NAG n 1 " - " ASN C 197 " " NAG o 1 " - " ASN C 276 " " NAG p 1 " - " ASN C 301 " " NAG q 1 " - " ASN C 262 " " NAG r 1 " - " ASN C 386 " " NAG s 1 " - " ASN C 392 " " NAG t 1 " - " ASN C 448 " " NAG u 1 " - " ASN C 295 " " NAG v 1 " - " ASN C 332 " " NAG w 1 " - " ASN C 234 " " NAG x 1 " - " ASN C 241 " " NAG y 1 " - " ASN C 138 " Time building additional restraints: 10.56 Conformation dependent library (CDL) restraints added in 4.0 seconds 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4314 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 48 sheets defined 20.5% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.015A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.962A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 528 removed outlier: 4.267A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 removed outlier: 4.279A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 597 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.654A pdb=" N LYS A 633 " --> pdb=" O MET A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 651 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100D through 100H Processing helix chain 'B' and resid 99 through 116 Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 335 through 348 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.957A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.924A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.273A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.280A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 597 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.816A pdb=" N LYS B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 651 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 61 through 64 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 100D through 100H Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.959A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.935A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 528 removed outlier: 4.283A pdb=" N GLY C 527 " --> pdb=" O GLY C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 542 removed outlier: 4.283A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 597 removed outlier: 3.724A pdb=" N TYR C 586 " --> pdb=" O ALA C 582 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.652A pdb=" N LYS C 633 " --> pdb=" O MET C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 651 Processing helix chain 'O' and resid 79 through 83 Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 61 through 64 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 100D through 100H Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.874A pdb=" N VAL A 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.053A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.760A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 132 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.640A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.687A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.811A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.907A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.905A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.156A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 274 removed outlier: 11.156A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.905A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.907A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.811A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE A 359 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.602A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 8 through 13 removed outlier: 6.761A pdb=" N THR L 8 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE L 105 " --> pdb=" O THR L 8 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL L 11 " --> pdb=" O ILE L 105 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N CYS L 88 " --> pdb=" O GLY L 99 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY L 101 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR L 86 " --> pdb=" O GLY L 101 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB6, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.892A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR H 33 " --> pdb=" O THR H 95 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.892A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR H 33 " --> pdb=" O THR H 95 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 494 through 499 removed outlier: 4.872A pdb=" N VAL B 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.883A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.830A pdb=" N VAL B 75 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AC4, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AC5, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.645A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 259 through 261 removed outlier: 6.709A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLY B 451 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 10.287A pdb=" N GLU B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 11.831A pdb=" N LEU B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 11.931A pdb=" N LEU B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 10.918A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.173A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N GLU B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER B 334 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 271 through 274 removed outlier: 11.173A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.918A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.931A pdb=" N LEU B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 11.831A pdb=" N LEU B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 10.287A pdb=" N GLU B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLY B 451 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE B 359 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 304 through 312 removed outlier: 6.582A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 8 through 13 removed outlier: 6.730A pdb=" N THR M 8 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE M 105 " --> pdb=" O THR M 8 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL M 11 " --> pdb=" O ILE M 105 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLU M 100 " --> pdb=" O CYS M 88 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N CYS M 88 " --> pdb=" O GLU M 100 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP M 35 " --> pdb=" O ILE M 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 19 through 23 Processing sheet with id=AD2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AD4, first strand: chain 'N' and resid 58 through 59 removed outlier: 6.919A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR N 50 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR N 33 " --> pdb=" O THR N 95 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 58 through 59 removed outlier: 6.919A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR N 50 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR N 33 " --> pdb=" O THR N 95 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.870A pdb=" N VAL C 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.859A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.774A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AE1, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AE2, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AE3, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.648A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.706A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.920A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 10.908A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 271 through 274 removed outlier: 11.171A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.908A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.920A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE C 359 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.611A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 8 through 13 removed outlier: 6.740A pdb=" N THR O 8 " --> pdb=" O THR O 103 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE O 105 " --> pdb=" O THR O 8 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL O 11 " --> pdb=" O ILE O 105 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP O 35 " --> pdb=" O ILE O 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 19 through 23 Processing sheet with id=AE9, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'P' and resid 11 through 12 Processing sheet with id=AF2, first strand: chain 'P' and resid 58 through 59 removed outlier: 6.891A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR P 50 " --> pdb=" O TRP P 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP P 34 " --> pdb=" O TYR P 50 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR P 33 " --> pdb=" O THR P 95 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 58 through 59 removed outlier: 6.891A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR P 50 " --> pdb=" O TRP P 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP P 34 " --> pdb=" O TYR P 50 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR P 33 " --> pdb=" O THR P 95 " (cutoff:3.500A) 767 hydrogen bonds defined for protein. 1941 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: 7.79 Time building geometry restraints manager: 11.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.34: 6252 1.34 - 1.50: 7021 1.50 - 1.65: 7193 1.65 - 1.81: 128 1.81 - 1.96: 13 Bond restraints: 20607 Sorted by residual: bond pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " ideal model delta sigma weight residual 1.808 1.582 0.226 3.30e-02 9.18e+02 4.71e+01 bond pdb=" NE1 TRP B 427 " pdb=" CE2 TRP B 427 " ideal model delta sigma weight residual 1.370 1.307 0.063 1.10e-02 8.26e+03 3.31e+01 bond pdb=" NE1 TRP A 427 " pdb=" CE2 TRP A 427 " ideal model delta sigma weight residual 1.370 1.307 0.063 1.10e-02 8.26e+03 3.24e+01 bond pdb=" CB CYS M 88 " pdb=" SG CYS M 88 " ideal model delta sigma weight residual 1.808 1.621 0.187 3.30e-02 9.18e+02 3.20e+01 bond pdb=" NE1 TRP C 427 " pdb=" CE2 TRP C 427 " ideal model delta sigma weight residual 1.370 1.308 0.062 1.10e-02 8.26e+03 3.14e+01 ... (remaining 20602 not shown) Histogram of bond angle deviations from ideal: 97.92 - 105.19: 494 105.19 - 112.45: 11091 112.45 - 119.72: 7239 119.72 - 126.98: 8903 126.98 - 134.24: 284 Bond angle restraints: 28011 Sorted by residual: angle pdb=" C ILE M 58 " pdb=" N PRO M 59 " pdb=" CA PRO M 59 " ideal model delta sigma weight residual 119.78 127.50 -7.72 1.03e+00 9.43e-01 5.62e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.87 127.65 -7.78 1.04e+00 9.25e-01 5.60e+01 angle pdb=" C ALA A 219 " pdb=" N PRO A 220 " pdb=" CA PRO A 220 " ideal model delta sigma weight residual 120.52 127.93 -7.41 9.90e-01 1.02e+00 5.59e+01 angle pdb=" C ALA B 219 " pdb=" N PRO B 220 " pdb=" CA PRO B 220 " ideal model delta sigma weight residual 120.31 127.63 -7.32 9.80e-01 1.04e+00 5.58e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.87 127.58 -7.71 1.04e+00 9.25e-01 5.50e+01 ... (remaining 28006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.33: 13615 22.33 - 44.66: 332 44.66 - 66.98: 111 66.98 - 89.31: 54 89.31 - 111.64: 36 Dihedral angle restraints: 14148 sinusoidal: 7464 harmonic: 6684 Sorted by residual: dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 24.08 68.92 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CB CYS B 54 " pdb=" SG CYS B 54 " pdb=" SG CYS B 74 " pdb=" CB CYS B 74 " ideal model delta sinusoidal sigma weight residual 93.00 24.58 68.42 1 1.00e+01 1.00e-02 6.07e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 25.20 67.80 1 1.00e+01 1.00e-02 5.97e+01 ... (remaining 14145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2608 0.115 - 0.231: 868 0.231 - 0.346: 95 0.346 - 0.462: 7 0.462 - 0.577: 1 Chirality restraints: 3579 Sorted by residual: chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.17e+01 chirality pdb=" C1 BMA h 3 " pdb=" O4 NAG h 2 " pdb=" C2 BMA h 3 " pdb=" O5 BMA h 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.12e+01 chirality pdb=" C1 BMA v 3 " pdb=" O4 NAG v 2 " pdb=" C2 BMA v 3 " pdb=" O5 BMA v 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.10e+01 ... (remaining 3576 not shown) Planarity restraints: 3393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 190 " 0.112 2.00e-02 2.50e+03 1.15e-01 1.64e+02 pdb=" CG ASN C 190 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN C 190 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN C 190 " -0.178 2.00e-02 2.50e+03 pdb=" C1 NAG C 702 " 0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 190 " 0.112 2.00e-02 2.50e+03 1.15e-01 1.64e+02 pdb=" CG ASN A 190 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A 190 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 190 " -0.178 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " 0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 190 " -0.109 2.00e-02 2.50e+03 1.12e-01 1.57e+02 pdb=" CG ASN B 190 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN B 190 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN B 190 " 0.174 2.00e-02 2.50e+03 pdb=" C1 NAG B 702 " -0.134 2.00e-02 2.50e+03 ... (remaining 3390 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3444 2.75 - 3.29: 17515 3.29 - 3.82: 32894 3.82 - 4.36: 39748 4.36 - 4.90: 65714 Nonbonded interactions: 159315 Sorted by model distance: nonbonded pdb=" OG1 THR B 37 " pdb=" OG1 THR B 499 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.212 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.212 3.040 nonbonded pdb=" O4 MAN T 5 " pdb=" O6 MAN T 5 " model vdw 2.260 3.040 nonbonded pdb=" O4 NAG b 2 " pdb=" O6 NAG b 2 " model vdw 2.267 3.040 ... (remaining 159310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'w' selection = chain 'x' } ncs_group { reference = chain 'H' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'J' selection = chain 'W' selection = chain 'c' selection = chain 'k' selection = chain 'q' selection = chain 'y' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'T' selection = chain 'h' selection = chain 'v' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.760 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 59.930 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.021 0.226 20607 Z= 1.335 Angle : 1.719 12.178 28011 Z= 1.092 Chirality : 0.104 0.577 3579 Planarity : 0.009 0.047 3336 Dihedral : 13.137 111.640 9717 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.15 % Allowed : 0.73 % Favored : 99.12 % Cbeta Deviations : 0.14 % 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: 0.73 (0.17), residues: 2262 helix: -1.22 (0.24), residues: 393 sheet: 1.00 (0.18), residues: 675 loop : 0.99 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.009 TRP A 96 HIS 0.007 0.002 HIS H 52 PHE 0.043 0.007 PHE B 353 TYR 0.053 0.007 TYR H 100O ARG 0.006 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 409 time to evaluate : 2.232 Fit side-chains revert: symmetry clash REVERT: A 68 VAL cc_start: 0.9181 (p) cc_final: 0.8954 (p) REVERT: B 173 TYR cc_start: 0.8034 (m-80) cc_final: 0.7809 (m-80) REVERT: N 100 LYS cc_start: 0.8460 (mttt) cc_final: 0.8219 (mmtt) outliers start: 3 outliers final: 3 residues processed: 412 average time/residue: 0.3501 time to fit residues: 213.0333 Evaluate side-chains 198 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 195 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain C residue 138 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 95 optimal weight: 0.0570 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 229 ASN A 362 ASN B 105 HIS B 625 ASN M 52 ASN C 105 HIS C 114 GLN C 362 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20607 Z= 0.216 Angle : 0.676 8.740 28011 Z= 0.347 Chirality : 0.048 0.310 3579 Planarity : 0.004 0.028 3336 Dihedral : 10.843 83.894 5418 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.06 % Favored : 98.81 % Rotamer: Outliers : 1.75 % Allowed : 5.56 % Favored : 92.69 % 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: 0.83 (0.17), residues: 2262 helix: 0.45 (0.27), residues: 384 sheet: 0.77 (0.18), residues: 687 loop : 0.62 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 479 HIS 0.007 0.001 HIS P 3 PHE 0.016 0.002 PHE B 382 TYR 0.019 0.001 TYR C 318 ARG 0.003 0.000 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 257 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7814 (tpp) cc_final: 0.7515 (mmt) REVERT: A 535 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8572 (mtp) REVERT: N 100 LYS cc_start: 0.8427 (mttt) cc_final: 0.8193 (mmtt) REVERT: N 100 MET cc_start: 0.8367 (mpp) cc_final: 0.7598 (mpp) outliers start: 36 outliers final: 13 residues processed: 286 average time/residue: 0.3249 time to fit residues: 141.7258 Evaluate side-chains 203 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 189 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 109 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 6.9990 chunk 64 optimal weight: 0.0770 chunk 172 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 57 optimal weight: 0.0670 chunk 207 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 205 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 overall best weight: 2.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN L 52 ASN N 3 HIS C 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20607 Z= 0.321 Angle : 0.643 7.830 28011 Z= 0.324 Chirality : 0.048 0.229 3579 Planarity : 0.004 0.052 3336 Dihedral : 9.871 81.506 5412 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.58 % Allowed : 7.70 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2262 helix: 0.71 (0.27), residues: 384 sheet: 0.47 (0.18), residues: 693 loop : 0.20 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 479 HIS 0.009 0.001 HIS A 72 PHE 0.014 0.002 PHE P 100K TYR 0.015 0.002 TYR H 100M ARG 0.003 0.001 ARG C 350 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 189 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.7776 (mtp) cc_final: 0.7561 (mtm) REVERT: A 475 MET cc_start: 0.7743 (tpp) cc_final: 0.7312 (mmt) REVERT: N 100 LYS cc_start: 0.8463 (mttt) cc_final: 0.8246 (mmmt) REVERT: N 100 MET cc_start: 0.8082 (mpp) cc_final: 0.7346 (mpp) REVERT: C 581 LEU cc_start: 0.8738 (mt) cc_final: 0.8492 (mt) outliers start: 53 outliers final: 33 residues processed: 228 average time/residue: 0.3223 time to fit residues: 111.9889 Evaluate side-chains 204 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 171 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 41 LEU Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.9990 chunk 155 optimal weight: 0.0670 chunk 107 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 208 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 197 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 246 GLN L 52 ASN B 246 GLN B 362 ASN C 246 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 20607 Z= 0.159 Angle : 0.551 7.668 28011 Z= 0.275 Chirality : 0.045 0.223 3579 Planarity : 0.003 0.033 3336 Dihedral : 8.926 76.480 5412 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.85 % Allowed : 8.58 % Favored : 89.57 % 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: 0.60 (0.17), residues: 2262 helix: 1.10 (0.28), residues: 384 sheet: 0.58 (0.18), residues: 693 loop : 0.17 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 479 HIS 0.009 0.001 HIS A 72 PHE 0.014 0.001 PHE B 53 TYR 0.011 0.001 TYR H 33 ARG 0.003 0.000 ARG O 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 193 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 80 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7700 (tp) REVERT: B 110 SER cc_start: 0.8912 (t) cc_final: 0.8671 (m) REVERT: N 100 LYS cc_start: 0.8449 (mttt) cc_final: 0.8210 (mmmt) REVERT: C 109 ILE cc_start: 0.8839 (mm) cc_final: 0.8425 (mt) outliers start: 38 outliers final: 17 residues processed: 222 average time/residue: 0.3294 time to fit residues: 112.3809 Evaluate side-chains 191 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 173 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain N residue 41 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 188 optimal weight: 0.9980 chunk 152 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 197 optimal weight: 0.0870 chunk 55 optimal weight: 10.0000 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20607 Z= 0.288 Angle : 0.586 6.400 28011 Z= 0.291 Chirality : 0.046 0.220 3579 Planarity : 0.004 0.040 3336 Dihedral : 8.593 79.566 5412 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.90 % Allowed : 8.67 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2262 helix: 1.09 (0.28), residues: 384 sheet: 0.39 (0.18), residues: 699 loop : 0.02 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 427 HIS 0.008 0.001 HIS A 72 PHE 0.015 0.002 PHE N 100K TYR 0.014 0.001 TYR P 100M ARG 0.004 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 178 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7374 (mmt) cc_final: 0.7150 (mmt) REVERT: A 620 ASP cc_start: 0.8040 (t0) cc_final: 0.7780 (t0) REVERT: N 100 LYS cc_start: 0.8500 (mttt) cc_final: 0.8226 (mmmt) outliers start: 39 outliers final: 30 residues processed: 205 average time/residue: 0.3139 time to fit residues: 100.8608 Evaluate side-chains 201 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 171 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 41 LEU Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.9990 chunk 198 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20607 Z= 0.218 Angle : 0.547 6.331 28011 Z= 0.272 Chirality : 0.045 0.212 3579 Planarity : 0.003 0.038 3336 Dihedral : 8.167 77.451 5412 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.24 % Allowed : 8.58 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.17), residues: 2262 helix: 1.21 (0.28), residues: 384 sheet: 0.45 (0.18), residues: 720 loop : -0.06 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 427 HIS 0.009 0.001 HIS A 72 PHE 0.013 0.002 PHE C 53 TYR 0.011 0.001 TYR H 100O ARG 0.003 0.000 ARG B 500 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 172 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7372 (mmt) cc_final: 0.7123 (mmp) REVERT: A 620 ASP cc_start: 0.8027 (t0) cc_final: 0.7729 (t0) REVERT: H 80 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7757 (tp) REVERT: N 100 LYS cc_start: 0.8507 (mttt) cc_final: 0.8226 (mmmt) outliers start: 46 outliers final: 30 residues processed: 205 average time/residue: 0.3073 time to fit residues: 98.1525 Evaluate side-chains 195 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 185 optimal weight: 0.0370 chunk 123 optimal weight: 0.7980 chunk 219 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 overall best weight: 2.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20607 Z= 0.261 Angle : 0.565 6.375 28011 Z= 0.281 Chirality : 0.045 0.201 3579 Planarity : 0.004 0.039 3336 Dihedral : 8.084 78.963 5412 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.24 % Allowed : 8.58 % Favored : 89.18 % 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: 0.37 (0.17), residues: 2262 helix: 1.21 (0.28), residues: 384 sheet: 0.40 (0.18), residues: 699 loop : -0.08 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 427 HIS 0.009 0.001 HIS A 72 PHE 0.016 0.002 PHE O 98 TYR 0.012 0.001 TYR N 100O ARG 0.005 0.000 ARG O 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 171 time to evaluate : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7393 (mmt) cc_final: 0.7132 (mmp) REVERT: A 620 ASP cc_start: 0.8027 (t0) cc_final: 0.7738 (t0) REVERT: H 80 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7834 (tp) REVERT: N 100 LYS cc_start: 0.8520 (mttt) cc_final: 0.8230 (mmmt) outliers start: 46 outliers final: 37 residues processed: 208 average time/residue: 0.3175 time to fit residues: 103.1990 Evaluate side-chains 206 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 168 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN C 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 20607 Z= 0.378 Angle : 0.625 6.451 28011 Z= 0.311 Chirality : 0.047 0.194 3579 Planarity : 0.004 0.046 3336 Dihedral : 8.373 81.989 5412 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.05 % Allowed : 9.06 % Favored : 88.89 % 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: 0.16 (0.17), residues: 2262 helix: 0.95 (0.28), residues: 387 sheet: 0.26 (0.19), residues: 705 loop : -0.19 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 36 HIS 0.009 0.001 HIS B 72 PHE 0.019 0.002 PHE O 98 TYR 0.018 0.002 TYR P 100M ARG 0.005 0.001 ARG O 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 175 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7494 (mmt) cc_final: 0.7233 (mmp) REVERT: A 620 ASP cc_start: 0.8076 (t0) cc_final: 0.7765 (t0) REVERT: H 80 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7871 (tp) REVERT: B 648 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: N 100 LYS cc_start: 0.8532 (mttt) cc_final: 0.8234 (mmmt) outliers start: 42 outliers final: 35 residues processed: 209 average time/residue: 0.3133 time to fit residues: 101.5991 Evaluate side-chains 205 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 168 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain P residue 109 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 0.8980 chunk 210 optimal weight: 9.9990 chunk 192 optimal weight: 0.6980 chunk 204 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 160 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 185 optimal weight: 0.0070 chunk 193 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20607 Z= 0.141 Angle : 0.527 6.230 28011 Z= 0.263 Chirality : 0.044 0.176 3579 Planarity : 0.003 0.035 3336 Dihedral : 7.743 75.857 5412 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.66 % Allowed : 9.89 % Favored : 88.45 % 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: 0.38 (0.17), residues: 2262 helix: 1.39 (0.28), residues: 384 sheet: 0.43 (0.19), residues: 708 loop : -0.17 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 34 HIS 0.008 0.001 HIS A 72 PHE 0.012 0.001 PHE B 53 TYR 0.012 0.001 TYR H 33 ARG 0.008 0.000 ARG O 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 176 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7308 (mmt) cc_final: 0.7039 (mmp) REVERT: A 620 ASP cc_start: 0.8026 (t0) cc_final: 0.7692 (t0) REVERT: H 80 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7855 (tp) REVERT: B 95 MET cc_start: 0.8913 (ptm) cc_final: 0.8704 (ptm) REVERT: M 36 TYR cc_start: 0.8487 (m-80) cc_final: 0.8285 (m-80) REVERT: N 100 LYS cc_start: 0.8516 (mttt) cc_final: 0.8269 (mmmt) outliers start: 34 outliers final: 28 residues processed: 206 average time/residue: 0.3297 time to fit residues: 104.1915 Evaluate side-chains 197 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 92 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.2161 > 50: distance: 9 - 13: 14.823 distance: 13 - 14: 9.481 distance: 13 - 144: 15.087 distance: 14 - 15: 17.298 distance: 14 - 17: 19.947 distance: 15 - 16: 8.589 distance: 15 - 25: 18.282 distance: 16 - 141: 11.263 distance: 17 - 18: 4.616 distance: 18 - 19: 22.343 distance: 18 - 20: 6.273 distance: 19 - 21: 5.974 distance: 20 - 22: 3.778 distance: 21 - 23: 4.325 distance: 22 - 23: 7.632 distance: 23 - 24: 6.257 distance: 25 - 26: 31.191 distance: 25 - 89: 17.425 distance: 26 - 27: 7.976 distance: 26 - 29: 33.577 distance: 27 - 28: 25.078 distance: 27 - 34: 7.658 distance: 28 - 86: 42.033 distance: 29 - 30: 14.651 distance: 30 - 31: 3.603 distance: 31 - 32: 19.367 distance: 31 - 33: 18.533 distance: 34 - 35: 14.290 distance: 34 - 127: 16.690 distance: 35 - 36: 8.787 distance: 35 - 38: 12.089 distance: 36 - 37: 18.195 distance: 36 - 43: 32.323 distance: 37 - 124: 29.238 distance: 38 - 39: 9.336 distance: 39 - 40: 23.951 distance: 40 - 41: 25.728 distance: 40 - 42: 21.654 distance: 43 - 44: 28.347 distance: 44 - 45: 26.581 distance: 44 - 47: 8.248 distance: 45 - 46: 15.375 distance: 45 - 54: 15.764 distance: 47 - 48: 28.276 distance: 48 - 49: 7.034 distance: 49 - 50: 10.003 distance: 50 - 51: 17.007 distance: 51 - 52: 16.305 distance: 51 - 53: 14.506 distance: 54 - 55: 31.638 distance: 54 - 60: 28.088 distance: 55 - 56: 15.810 distance: 55 - 58: 34.667 distance: 56 - 57: 39.151 distance: 56 - 61: 10.414 distance: 58 - 59: 14.155 distance: 59 - 60: 34.523 distance: 61 - 62: 19.682 distance: 62 - 63: 10.930 distance: 63 - 64: 16.739 distance: 63 - 65: 9.788 distance: 65 - 66: 7.116 distance: 66 - 67: 27.873 distance: 66 - 69: 14.518 distance: 67 - 68: 25.054 distance: 67 - 74: 12.439 distance: 69 - 70: 9.667 distance: 70 - 71: 21.048 distance: 71 - 72: 9.593 distance: 71 - 73: 6.162 distance: 74 - 75: 26.915 distance: 75 - 76: 17.245 distance: 75 - 78: 18.419 distance: 76 - 77: 11.526 distance: 76 - 79: 44.492 distance: 79 - 80: 15.933 distance: 79 - 85: 24.654 distance: 80 - 81: 11.949 distance: 80 - 83: 18.884 distance: 81 - 82: 35.605 distance: 81 - 86: 16.941 distance: 83 - 84: 7.964 distance: 84 - 85: 18.030 distance: 86 - 87: 12.525 distance: 87 - 88: 6.392 distance: 87 - 90: 11.424 distance: 88 - 89: 11.949 distance: 88 - 92: 27.442 distance: 90 - 91: 16.534