Starting phenix.real_space_refine on Sat Feb 17 23:43:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx3_23565/02_2024/7lx3_23565.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx3_23565/02_2024/7lx3_23565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx3_23565/02_2024/7lx3_23565.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx3_23565/02_2024/7lx3_23565.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx3_23565/02_2024/7lx3_23565.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx3_23565/02_2024/7lx3_23565.pdb" } resolution = 3.45 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= 0.004 sd= 0.144 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 376": "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 "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 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 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 PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 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 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 "P TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 10.70, per 1000 atoms: 0.53 Number of scatterers: 20196 At special positions: 0 Unit cell: (144.2, 153.47, 152.44, 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=2.14 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=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 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=2.05 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=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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=2.15 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.09 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.02 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.18 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.05 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 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=2.15 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.09 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.18 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.05 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 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: 9.52 Conformation dependent library (CDL) restraints added in 3.2 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: 52 helices and 45 sheets defined 20.8% alpha, 39.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.292A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) 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: 3.993A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.803A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 528 removed outlier: 4.305A 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 546 removed outlier: 3.806A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU A 545 " --> pdb=" O ALA A 541 " (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 Processing helix chain 'A' and resid 638 through 650 removed outlier: 4.259A pdb=" N SER A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100D through 100H Processing helix chain 'B' and resid 98 through 116 removed outlier: 4.288A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.997A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.807A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.453A 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 546 removed outlier: 3.783A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (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 Processing helix chain 'B' and resid 638 through 650 removed outlier: 4.199A pdb=" N SER B 644 " --> pdb=" O ASP B 640 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 100D through 100H Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.295A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) 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: 4.008A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.828A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 528 removed outlier: 4.444A 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 546 removed outlier: 3.801A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU C 544 " --> pdb=" O GLN C 540 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 597 Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 650 removed outlier: 4.255A pdb=" N SER C 644 " --> pdb=" O ASP C 640 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 52 through 56 removed outlier: 4.103A pdb=" N GLY P 55 " --> pdb=" O HIS P 52 " (cutoff:3.500A) 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: 4.672A 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: 3.909A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 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: 6.659A 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: 3.621A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.892A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.007A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.931A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.749A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 315 through 323 removed outlier: 6.572A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 393 through 395 Processing sheet with id=AB2, first strand: chain 'L' and resid 8 through 13 removed outlier: 6.400A pdb=" N THR L 8 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE L 105 " --> pdb=" O THR L 8 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL L 11 " --> pdb=" O ILE L 105 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.597A 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 removed outlier: 3.821A pdb=" N TYR H 33 " --> pdb=" O THR H 95 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB7, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.307A pdb=" N VAL B 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL B 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR B 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N TYR B 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N CYS B 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.047A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AC3, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AC4, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.665A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.617A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY B 451 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N GLU B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 11.888A pdb=" N LEU B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 11.998A pdb=" N LEU B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 10.935A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 315 through 323 removed outlier: 6.568A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE B 322 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASN B 301 " --> pdb=" O ILE B 322 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLU B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER B 334 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 393 through 395 Processing sheet with id=AC8, first strand: chain 'M' and resid 8 through 13 removed outlier: 6.399A pdb=" N THR M 8 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE M 105 " --> pdb=" O THR M 8 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL M 11 " --> pdb=" O ILE M 105 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLU M 100 " --> pdb=" O CYS M 88 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N CYS M 88 " --> pdb=" O GLU M 100 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP M 35 " --> pdb=" O ILE M 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 19 through 23 Processing sheet with id=AD1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.820A pdb=" N TYR N 33 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AD4, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.641A pdb=" N VAL C 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.047A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AD9, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AE1, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.687A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.611A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.917A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 12.060A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.796A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 315 through 323 removed outlier: 6.572A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 393 through 395 Processing sheet with id=AE5, first strand: chain 'O' and resid 8 through 13 removed outlier: 6.388A pdb=" N THR O 8 " --> pdb=" O THR O 103 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE O 105 " --> pdb=" O THR O 8 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL O 11 " --> pdb=" O ILE O 105 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP O 35 " --> pdb=" O ILE O 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 19 through 23 Processing sheet with id=AE7, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'P' and resid 11 through 12 removed outlier: 3.782A pdb=" N TYR P 33 " --> pdb=" O THR P 95 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY P 49 " --> pdb=" O TRP P 36 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 11 through 12 732 hydrogen bonds defined for protein. 1866 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: 7.47 Time building geometry restraints manager: 10.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 5563 1.33 - 1.48: 6744 1.48 - 1.63: 8159 1.63 - 1.78: 58 1.78 - 1.93: 83 Bond restraints: 20607 Sorted by residual: bond pdb=" CB CYS C 247 " pdb=" SG CYS C 247 " ideal model delta sigma weight residual 1.808 1.587 0.221 3.30e-02 9.18e+02 4.49e+01 bond pdb=" CB CYS B 247 " pdb=" SG CYS B 247 " ideal model delta sigma weight residual 1.808 1.588 0.220 3.30e-02 9.18e+02 4.45e+01 bond pdb=" CB HIS L 89 " pdb=" CG HIS L 89 " ideal model delta sigma weight residual 1.497 1.411 0.086 1.40e-02 5.10e+03 3.75e+01 bond pdb=" NE1 TRP C 427 " pdb=" CE2 TRP C 427 " ideal model delta sigma weight residual 1.370 1.305 0.065 1.10e-02 8.26e+03 3.49e+01 bond pdb=" CB CYS M 88 " pdb=" SG CYS M 88 " ideal model delta sigma weight residual 1.808 1.614 0.194 3.30e-02 9.18e+02 3.44e+01 ... (remaining 20602 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.46: 565 105.46 - 112.63: 11263 112.63 - 119.81: 7299 119.81 - 126.99: 8614 126.99 - 134.16: 270 Bond angle restraints: 28011 Sorted by residual: angle pdb=" C VAL A 75 " pdb=" N PRO A 76 " pdb=" CA PRO A 76 " ideal model delta sigma weight residual 120.03 128.16 -8.13 9.90e-01 1.02e+00 6.74e+01 angle pdb=" C VAL C 75 " pdb=" N PRO C 76 " pdb=" CA PRO C 76 " ideal model delta sigma weight residual 120.03 128.04 -8.01 9.90e-01 1.02e+00 6.55e+01 angle pdb=" C VAL B 75 " pdb=" N PRO B 76 " pdb=" CA PRO B 76 " ideal model delta sigma weight residual 120.03 128.00 -7.97 9.90e-01 1.02e+00 6.49e+01 angle pdb=" C ALA C 219 " pdb=" N PRO C 220 " pdb=" CA PRO C 220 " ideal model delta sigma weight residual 120.52 127.81 -7.29 9.90e-01 1.02e+00 5.42e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.87 127.52 -7.65 1.04e+00 9.25e-01 5.41e+01 ... (remaining 28006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.19: 13633 22.19 - 44.37: 320 44.37 - 66.56: 109 66.56 - 88.74: 48 88.74 - 110.93: 38 Dihedral angle restraints: 14148 sinusoidal: 7464 harmonic: 6684 Sorted by residual: dihedral pdb=" CB CYS C 218 " pdb=" SG CYS C 218 " pdb=" SG CYS C 247 " pdb=" CB CYS C 247 " ideal model delta sinusoidal sigma weight residual 93.00 43.89 49.11 1 1.00e+01 1.00e-02 3.32e+01 dihedral pdb=" CB CYS B 218 " pdb=" SG CYS B 218 " pdb=" SG CYS B 247 " pdb=" CB CYS B 247 " ideal model delta sinusoidal sigma weight residual 93.00 43.92 49.08 1 1.00e+01 1.00e-02 3.31e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -132.14 46.14 1 1.00e+01 1.00e-02 2.95e+01 ... (remaining 14145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2524 0.108 - 0.217: 900 0.217 - 0.325: 133 0.325 - 0.433: 20 0.433 - 0.542: 2 Chirality restraints: 3579 Sorted by residual: 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 -2.61 0.21 2.00e-02 2.50e+03 1.08e+02 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 -2.60 0.20 2.00e-02 2.50e+03 9.96e+01 chirality pdb=" C1 BMA y 3 " pdb=" O4 NAG y 2 " pdb=" C2 BMA y 3 " pdb=" O5 BMA y 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.00e+01 ... (remaining 3576 not shown) Planarity restraints: 3393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 190 " 0.111 2.00e-02 2.50e+03 1.13e-01 1.61e+02 pdb=" CG ASN C 190 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN C 190 " -0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN C 190 " -0.175 2.00e-02 2.50e+03 pdb=" C1 NAG C 702 " 0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 190 " -0.107 2.00e-02 2.50e+03 1.09e-01 1.47e+02 pdb=" CG ASN A 190 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 190 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN A 190 " 0.167 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " -0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 190 " 0.106 2.00e-02 2.50e+03 1.08e-01 1.47e+02 pdb=" CG ASN B 190 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN B 190 " -0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN B 190 " -0.167 2.00e-02 2.50e+03 pdb=" C1 NAG B 702 " 0.130 2.00e-02 2.50e+03 ... (remaining 3390 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3190 2.74 - 3.28: 17887 3.28 - 3.82: 33184 3.82 - 4.36: 39825 4.36 - 4.90: 65381 Nonbonded interactions: 159467 Sorted by model distance: nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.198 2.440 nonbonded pdb=" O4 NAG C 704 " pdb=" O6 NAG C 704 " model vdw 2.248 2.440 nonbonded pdb=" O4 MAN T 9 " pdb=" O6 MAN T 9 " model vdw 2.265 2.440 nonbonded pdb=" O4 MAN h 9 " pdb=" O6 MAN h 9 " model vdw 2.269 2.440 nonbonded pdb=" O4 MAN v 9 " pdb=" O6 MAN v 9 " model vdw 2.299 2.440 ... (remaining 159462 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain '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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.520 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 56.550 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 0.221 20607 Z= 1.348 Angle : 1.740 11.420 28011 Z= 1.105 Chirality : 0.106 0.542 3579 Planarity : 0.009 0.047 3336 Dihedral : 12.953 110.925 9717 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.10 % Allowed : 0.34 % Favored : 99.56 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.17), residues: 2262 helix: -0.38 (0.25), residues: 354 sheet: 1.02 (0.19), residues: 684 loop : 1.01 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.009 TRP B 96 HIS 0.006 0.002 HIS C 216 PHE 0.039 0.007 PHE L 67C TYR 0.050 0.007 TYR N 100O ARG 0.010 0.001 ARG L 31 *********************** 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 393 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 391 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 26 GLU cc_start: 0.8309 (mp0) cc_final: 0.7655 (mp0) REVERT: L 78 VAL cc_start: 0.8548 (t) cc_final: 0.8316 (p) REVERT: H 3 HIS cc_start: 0.6698 (t70) cc_final: 0.6398 (t-90) REVERT: H 91 TYR cc_start: 0.7703 (m-80) cc_final: 0.7449 (m-80) REVERT: B 180 ASP cc_start: 0.6989 (m-30) cc_final: 0.6787 (m-30) REVERT: M 49 TYR cc_start: 0.8053 (p90) cc_final: 0.7739 (p90) REVERT: M 104 LEU cc_start: 0.7808 (tp) cc_final: 0.7414 (tp) REVERT: N 24 VAL cc_start: 0.7996 (t) cc_final: 0.7700 (t) REVERT: N 91 TYR cc_start: 0.7558 (m-80) cc_final: 0.6873 (m-80) REVERT: N 92 CYS cc_start: 0.6264 (t) cc_final: 0.6013 (t) REVERT: C 180 ASP cc_start: 0.6995 (m-30) cc_final: 0.6787 (m-30) REVERT: O 49 TYR cc_start: 0.8086 (p90) cc_final: 0.7668 (p90) REVERT: O 52 ASN cc_start: 0.8731 (t0) cc_final: 0.8465 (t0) REVERT: O 86 TYR cc_start: 0.8414 (m-80) cc_final: 0.7973 (m-80) REVERT: O 104 LEU cc_start: 0.7770 (tp) cc_final: 0.7424 (tp) REVERT: P 91 TYR cc_start: 0.7735 (m-80) cc_final: 0.7468 (m-80) outliers start: 2 outliers final: 2 residues processed: 393 average time/residue: 0.3905 time to fit residues: 220.7199 Evaluate side-chains 193 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 425 ASN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN B 422 GLN N 32 ASN C 422 GLN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20607 Z= 0.240 Angle : 0.672 7.001 28011 Z= 0.349 Chirality : 0.047 0.255 3579 Planarity : 0.004 0.055 3336 Dihedral : 10.800 86.355 5416 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.11 % Favored : 98.85 % Rotamer: Outliers : 1.90 % Allowed : 6.87 % Favored : 91.23 % 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: 1.01 (0.17), residues: 2262 helix: 1.07 (0.27), residues: 345 sheet: 0.83 (0.18), residues: 690 loop : 0.61 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP P 36 HIS 0.005 0.001 HIS P 3 PHE 0.020 0.002 PHE A 383 TYR 0.022 0.002 TYR H 33 ARG 0.006 0.001 ARG L 95 *********************** 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 291 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 252 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.7188 (mp0) cc_final: 0.6216 (mp0) REVERT: H 13 LYS cc_start: 0.9266 (ttpt) cc_final: 0.8938 (ptpp) REVERT: B 180 ASP cc_start: 0.6933 (m-30) cc_final: 0.6689 (m-30) REVERT: M 17 GLN cc_start: 0.7419 (mm-40) cc_final: 0.6520 (mt0) REVERT: M 49 TYR cc_start: 0.7903 (p90) cc_final: 0.7570 (p90) REVERT: N 13 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8634 (ttpt) REVERT: N 81 ARG cc_start: 0.8324 (ttp80) cc_final: 0.7692 (ttm-80) REVERT: C 69 TRP cc_start: 0.8117 (m-90) cc_final: 0.7580 (m-90) REVERT: C 180 ASP cc_start: 0.7108 (m-30) cc_final: 0.6867 (m-30) REVERT: O 17 GLN cc_start: 0.7180 (mm-40) cc_final: 0.6566 (mt0) REVERT: O 49 TYR cc_start: 0.7934 (p90) cc_final: 0.7427 (p90) REVERT: P 5 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8388 (tm-30) outliers start: 39 outliers final: 21 residues processed: 282 average time/residue: 0.3537 time to fit residues: 149.4468 Evaluate side-chains 222 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 200 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 18 LEU Chi-restraints excluded: chain P residue 53 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 140 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 205 optimal weight: 40.0000 chunk 70 optimal weight: 30.0000 chunk 166 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 302 ASN L 17 GLN H 97 HIS ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN B 422 GLN C 229 ASN C 422 GLN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 20607 Z= 0.477 Angle : 0.745 7.111 28011 Z= 0.373 Chirality : 0.049 0.188 3579 Planarity : 0.005 0.053 3336 Dihedral : 10.374 93.530 5412 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.07 % Allowed : 7.41 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.17), residues: 2262 helix: 1.05 (0.28), residues: 345 sheet: 0.48 (0.19), residues: 699 loop : 0.19 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 36 HIS 0.015 0.002 HIS B 72 PHE 0.024 0.002 PHE P 100K TYR 0.026 0.002 TYR H 33 ARG 0.007 0.001 ARG H 81 *********************** 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 277 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 214 time to evaluate : 2.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8139 (mp10) REVERT: H 81 ARG cc_start: 0.8447 (ttp80) cc_final: 0.8068 (ttm-80) REVERT: B 135 ASN cc_start: 0.7373 (m-40) cc_final: 0.7164 (m-40) REVERT: M 49 TYR cc_start: 0.8105 (p90) cc_final: 0.7703 (p90) REVERT: N 5 GLN cc_start: 0.8722 (tm-30) cc_final: 0.7975 (pm20) REVERT: N 6 GLU cc_start: 0.7494 (mp0) cc_final: 0.7141 (mp0) REVERT: N 56 ASP cc_start: 0.4971 (t70) cc_final: 0.4629 (t70) REVERT: N 81 ARG cc_start: 0.8330 (ttp80) cc_final: 0.7804 (ttm-80) REVERT: C 95 MET cc_start: 0.9139 (ptm) cc_final: 0.8602 (ttp) REVERT: O 49 TYR cc_start: 0.7970 (p90) cc_final: 0.7744 (p90) REVERT: P 13 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8648 (ttmt) REVERT: P 56 ASP cc_start: 0.5535 (t70) cc_final: 0.5097 (t70) REVERT: P 81 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7691 (ttm-80) outliers start: 63 outliers final: 42 residues processed: 253 average time/residue: 0.3535 time to fit residues: 135.1799 Evaluate side-chains 237 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 194 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 51 ASN Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 18 LEU Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 89 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 107 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 139 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20607 Z= 0.284 Angle : 0.617 6.691 28011 Z= 0.309 Chirality : 0.046 0.213 3579 Planarity : 0.004 0.048 3336 Dihedral : 9.438 89.145 5412 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.02 % Allowed : 8.48 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2262 helix: 1.28 (0.28), residues: 348 sheet: 0.40 (0.19), residues: 690 loop : 0.07 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP N 36 HIS 0.012 0.001 HIS P 97 PHE 0.017 0.002 PHE H 100K TYR 0.019 0.002 TYR N 33 ARG 0.006 0.001 ARG O 61 *********************** 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 268 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 206 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLN cc_start: 0.7745 (mm-40) cc_final: 0.6510 (pt0) REVERT: L 25 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7721 (tm-30) REVERT: L 26 GLU cc_start: 0.8316 (mp0) cc_final: 0.7874 (mp0) REVERT: H 5 GLN cc_start: 0.8553 (tm-30) cc_final: 0.7983 (mp10) REVERT: H 81 ARG cc_start: 0.8371 (ttp80) cc_final: 0.8056 (ttp-110) REVERT: M 17 GLN cc_start: 0.7959 (mm-40) cc_final: 0.6767 (pt0) REVERT: N 6 GLU cc_start: 0.7459 (mp0) cc_final: 0.6961 (mp0) REVERT: C 95 MET cc_start: 0.9140 (ptm) cc_final: 0.8611 (ttp) REVERT: P 46 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7718 (tp30) REVERT: P 81 ARG cc_start: 0.8300 (ttp80) cc_final: 0.7822 (ttm-80) outliers start: 62 outliers final: 37 residues processed: 246 average time/residue: 0.3597 time to fit residues: 131.5409 Evaluate side-chains 229 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 191 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 18 LEU Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 53 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 164 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 197 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 97 HIS C 105 HIS P 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20607 Z= 0.287 Angle : 0.604 6.685 28011 Z= 0.300 Chirality : 0.046 0.201 3579 Planarity : 0.004 0.047 3336 Dihedral : 8.877 88.125 5412 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.56 % Allowed : 8.14 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.44 (0.28), residues: 348 sheet: 0.32 (0.19), residues: 690 loop : 0.02 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP P 36 HIS 0.012 0.001 HIS P 97 PHE 0.017 0.002 PHE H 100K TYR 0.016 0.002 TYR H 33 ARG 0.005 0.001 ARG M 61 *********************** 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 276 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 203 time to evaluate : 2.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8010 (mp10) REVERT: H 81 ARG cc_start: 0.8335 (ttp80) cc_final: 0.8093 (mtm110) REVERT: N 43 LYS cc_start: 0.8386 (mmmm) cc_final: 0.8176 (mmtp) REVERT: C 95 MET cc_start: 0.9170 (ptm) cc_final: 0.8665 (ttp) REVERT: O 17 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7809 (mp10) REVERT: P 5 GLN cc_start: 0.8496 (tm-30) cc_final: 0.7985 (mp10) REVERT: P 6 GLU cc_start: 0.7260 (mp0) cc_final: 0.6848 (mp0) REVERT: P 46 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7766 (tp30) REVERT: P 81 ARG cc_start: 0.8354 (ttp80) cc_final: 0.7809 (ttm-80) outliers start: 73 outliers final: 52 residues processed: 242 average time/residue: 0.3601 time to fit residues: 130.6981 Evaluate side-chains 237 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 184 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 97 HIS Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain O residue 13 VAL Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 18 LEU Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 53 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 3.9990 chunk 198 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 GLN N 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 20607 Z= 0.445 Angle : 0.680 7.203 28011 Z= 0.336 Chirality : 0.048 0.212 3579 Planarity : 0.005 0.054 3336 Dihedral : 9.017 93.436 5412 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.70 % Allowed : 8.92 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 2262 helix: 1.24 (0.28), residues: 348 sheet: 0.08 (0.19), residues: 702 loop : -0.15 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP H 36 HIS 0.035 0.002 HIS N 97 PHE 0.022 0.002 PHE P 100K TYR 0.020 0.002 TYR N 100M ARG 0.010 0.001 ARG M 61 *********************** 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 275 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 199 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7585 (mtp85) cc_final: 0.7272 (mmt180) REVERT: L 25 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7829 (tm-30) REVERT: L 26 GLU cc_start: 0.8316 (mp0) cc_final: 0.7926 (mp0) REVERT: H 5 GLN cc_start: 0.8562 (tm-30) cc_final: 0.7921 (mp10) REVERT: H 81 ARG cc_start: 0.8391 (ttp80) cc_final: 0.8119 (mtm110) REVERT: N 5 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8036 (mp10) REVERT: N 6 GLU cc_start: 0.6423 (mp0) cc_final: 0.5992 (mp0) REVERT: C 66 ARG cc_start: 0.7551 (mtp85) cc_final: 0.7319 (mmt180) REVERT: C 95 MET cc_start: 0.9226 (ptm) cc_final: 0.8728 (ttp) REVERT: P 5 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8057 (mp10) REVERT: P 6 GLU cc_start: 0.7348 (mp0) cc_final: 0.7109 (mp0) REVERT: P 46 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7835 (tp30) REVERT: P 81 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7720 (ttm-80) outliers start: 76 outliers final: 55 residues processed: 241 average time/residue: 0.3716 time to fit residues: 132.0949 Evaluate side-chains 242 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 186 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain O residue 13 VAL Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 89 ILE Chi-restraints excluded: chain P residue 92 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 161 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 219 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 133 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 20607 Z= 0.195 Angle : 0.587 11.483 28011 Z= 0.292 Chirality : 0.045 0.192 3579 Planarity : 0.004 0.049 3336 Dihedral : 8.325 84.545 5412 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.58 % Allowed : 10.62 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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 (0.18), residues: 2262 helix: 1.60 (0.28), residues: 348 sheet: 0.32 (0.19), residues: 684 loop : -0.07 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP N 36 HIS 0.013 0.001 HIS P 97 PHE 0.012 0.001 PHE H 100K TYR 0.016 0.001 TYR N 50 ARG 0.011 0.000 ARG M 61 *********************** 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 258 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 205 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7590 (mtp85) cc_final: 0.7288 (mmt180) REVERT: L 25 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7725 (tm-30) REVERT: L 26 GLU cc_start: 0.8065 (mp0) cc_final: 0.7801 (mp0) REVERT: H 5 GLN cc_start: 0.8575 (tm-30) cc_final: 0.7940 (mp10) REVERT: N 5 GLN cc_start: 0.8805 (tm-30) cc_final: 0.7918 (mp10) REVERT: N 6 GLU cc_start: 0.6275 (mp0) cc_final: 0.5654 (mp0) REVERT: C 66 ARG cc_start: 0.7589 (mtp85) cc_final: 0.7319 (mmt180) REVERT: C 82 GLN cc_start: 0.8416 (pt0) cc_final: 0.8175 (pm20) REVERT: C 95 MET cc_start: 0.9176 (ptm) cc_final: 0.8662 (ttp) REVERT: C 103 GLN cc_start: 0.8627 (tp40) cc_final: 0.8418 (tt0) REVERT: P 5 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8045 (mp10) REVERT: P 6 GLU cc_start: 0.7216 (mp0) cc_final: 0.6801 (mp0) REVERT: P 46 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7754 (tp30) REVERT: P 81 ARG cc_start: 0.8305 (ttp80) cc_final: 0.7865 (ttm-80) outliers start: 53 outliers final: 39 residues processed: 233 average time/residue: 0.4030 time to fit residues: 139.8364 Evaluate side-chains 229 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 189 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 89 ILE Chi-restraints excluded: chain P residue 92 CYS 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: 4.9990 chunk 131 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 149 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 97 HIS ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 20607 Z= 0.259 Angle : 0.604 8.989 28011 Z= 0.299 Chirality : 0.045 0.186 3579 Planarity : 0.004 0.066 3336 Dihedral : 8.125 84.301 5412 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.63 % Allowed : 11.21 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.18), residues: 2262 helix: 1.66 (0.28), residues: 348 sheet: 0.29 (0.19), residues: 690 loop : -0.13 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP P 36 HIS 0.011 0.001 HIS P 97 PHE 0.017 0.002 PHE P 100K TYR 0.016 0.002 TYR H 50 ARG 0.013 0.001 ARG O 61 *********************** 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 252 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 198 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7673 (mtp85) cc_final: 0.7342 (mmt180) REVERT: L 17 GLN cc_start: 0.7788 (mm-40) cc_final: 0.6655 (pt0) REVERT: H 5 GLN cc_start: 0.8486 (tm-30) cc_final: 0.7830 (mp10) REVERT: N 5 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8003 (mp10) REVERT: N 6 GLU cc_start: 0.6187 (mp0) cc_final: 0.5664 (mp0) REVERT: C 66 ARG cc_start: 0.7610 (mtp85) cc_final: 0.7381 (mmt180) REVERT: C 82 GLN cc_start: 0.8435 (pt0) cc_final: 0.8194 (pm20) REVERT: C 95 MET cc_start: 0.9213 (ptm) cc_final: 0.8696 (ttp) REVERT: P 5 GLN cc_start: 0.8590 (tm-30) cc_final: 0.7868 (mp10) REVERT: P 6 GLU cc_start: 0.7181 (mp0) cc_final: 0.6762 (mp0) REVERT: P 46 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7694 (tp30) REVERT: P 81 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7759 (ttm-80) outliers start: 54 outliers final: 43 residues processed: 228 average time/residue: 0.3631 time to fit residues: 123.0023 Evaluate side-chains 236 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 192 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 97 HIS Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain O residue 13 VAL Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 89 ILE Chi-restraints excluded: chain P residue 92 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 8.9990 chunk 210 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 160 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 185 optimal weight: 6.9990 chunk 193 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 HIS H 97 HIS ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 20607 Z= 0.340 Angle : 0.628 8.084 28011 Z= 0.311 Chirality : 0.046 0.192 3579 Planarity : 0.004 0.055 3336 Dihedral : 8.193 86.088 5412 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.58 % Allowed : 11.31 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.18), residues: 2262 helix: 1.86 (0.29), residues: 330 sheet: 0.14 (0.19), residues: 696 loop : -0.18 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP P 36 HIS 0.018 0.002 HIS N 97 PHE 0.021 0.002 PHE P 100K TYR 0.015 0.002 TYR H 100M ARG 0.012 0.001 ARG O 61 *********************** 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 247 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 194 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7729 (mtp85) cc_final: 0.7366 (mmt180) REVERT: L 25 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7702 (tm-30) REVERT: H 81 ARG cc_start: 0.8052 (ttp-110) cc_final: 0.7819 (mtm110) REVERT: C 66 ARG cc_start: 0.7766 (mtp85) cc_final: 0.7477 (mmt180) REVERT: C 82 GLN cc_start: 0.8445 (pt0) cc_final: 0.8211 (pm20) REVERT: C 95 MET cc_start: 0.9236 (ptm) cc_final: 0.8724 (ttp) REVERT: P 5 GLN cc_start: 0.8581 (tm-30) cc_final: 0.7953 (mp10) REVERT: P 6 GLU cc_start: 0.7235 (mp0) cc_final: 0.6841 (mp0) REVERT: P 46 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7805 (tp30) REVERT: P 81 ARG cc_start: 0.8152 (ttp80) cc_final: 0.7740 (ttm-80) outliers start: 53 outliers final: 44 residues processed: 224 average time/residue: 0.3949 time to fit residues: 133.3949 Evaluate side-chains 234 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 189 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 97 HIS Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 89 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.0770 chunk 132 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 209 optimal weight: 20.0000 chunk 180 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 139 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 HIS H 97 HIS ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 97 HIS O 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 20607 Z= 0.157 Angle : 0.577 10.355 28011 Z= 0.286 Chirality : 0.045 0.188 3579 Planarity : 0.004 0.059 3336 Dihedral : 7.604 77.784 5412 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.24 % Allowed : 11.55 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.18), residues: 2262 helix: 2.08 (0.29), residues: 336 sheet: 0.35 (0.20), residues: 678 loop : -0.20 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP P 36 HIS 0.017 0.001 HIS N 97 PHE 0.010 0.001 PHE B 382 TYR 0.017 0.001 TYR N 50 ARG 0.011 0.000 ARG O 61 ********************** REFINEMENT MACRO_CYCLE 10 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 248 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 202 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8581 (ptm) cc_final: 0.7848 (ttp) REVERT: A 103 GLN cc_start: 0.8681 (tp40) cc_final: 0.8351 (tt0) REVERT: L 17 GLN cc_start: 0.7747 (mm-40) cc_final: 0.6775 (pt0) REVERT: H 5 GLN cc_start: 0.8448 (tm-30) cc_final: 0.7898 (mp10) REVERT: H 81 ARG cc_start: 0.7997 (ttp-110) cc_final: 0.7751 (mtm110) REVERT: B 475 MET cc_start: 0.8099 (mmm) cc_final: 0.7895 (mmm) REVERT: M 17 GLN cc_start: 0.8081 (mp-120) cc_final: 0.7117 (pt0) REVERT: N 5 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8030 (mp10) REVERT: C 66 ARG cc_start: 0.7721 (mtp85) cc_final: 0.7467 (mmt180) REVERT: C 82 GLN cc_start: 0.8421 (pt0) cc_final: 0.8194 (pm20) REVERT: C 95 MET cc_start: 0.9192 (ptm) cc_final: 0.8680 (ttp) REVERT: P 5 GLN cc_start: 0.8645 (tm-30) cc_final: 0.7864 (mp10) REVERT: P 6 GLU cc_start: 0.7117 (mp0) cc_final: 0.6734 (mp0) REVERT: P 46 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7727 (tp30) REVERT: P 81 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7956 (ttm-80) outliers start: 46 outliers final: 37 residues processed: 230 average time/residue: 0.3507 time to fit residues: 120.9352 Evaluate side-chains 231 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 193 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 97 HIS Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 89 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 159 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 HIS H 97 HIS ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.105994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.075685 restraints weight = 41467.517| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.89 r_work: 0.2890 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20607 Z= 0.223 Angle : 0.595 10.940 28011 Z= 0.292 Chirality : 0.045 0.198 3579 Planarity : 0.004 0.056 3336 Dihedral : 7.504 77.333 5412 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.24 % Allowed : 11.65 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.18), residues: 2262 helix: 2.08 (0.29), residues: 336 sheet: 0.35 (0.20), residues: 672 loop : -0.21 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP N 36 HIS 0.018 0.001 HIS N 97 PHE 0.025 0.001 PHE N 100N TYR 0.021 0.001 TYR N 50 ARG 0.011 0.000 ARG O 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3951.47 seconds wall clock time: 73 minutes 28.84 seconds (4408.84 seconds total)