Starting phenix.real_space_refine on Sun Mar 24 23:06:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h05_0108/03_2024/6h05_0108.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h05_0108/03_2024/6h05_0108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h05_0108/03_2024/6h05_0108.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h05_0108/03_2024/6h05_0108.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h05_0108/03_2024/6h05_0108.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h05_0108/03_2024/6h05_0108.pdb" } resolution = 2.9 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.189 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 288 5.16 5 C 28080 2.51 5 N 8016 2.21 5 O 8160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 162": "NH1" <-> "NH2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 288": "NH1" <-> "NH2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 162": "NH1" <-> "NH2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B ARG 196": "NH1" <-> "NH2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 288": "NH1" <-> "NH2" Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 288": "NH1" <-> "NH2" Residue "C PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 288": "NH1" <-> "NH2" Residue "D PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 346": "NH1" <-> "NH2" Residue "D TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 164": "NH1" <-> "NH2" Residue "E ARG 196": "NH1" <-> "NH2" Residue "E PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 288": "NH1" <-> "NH2" Residue "E PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 346": "NH1" <-> "NH2" Residue "E TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 162": "NH1" <-> "NH2" Residue "F ARG 164": "NH1" <-> "NH2" Residue "F ARG 196": "NH1" <-> "NH2" Residue "F PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 288": "NH1" <-> "NH2" Residue "F PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 346": "NH1" <-> "NH2" Residue "F TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 164": "NH1" <-> "NH2" Residue "G ARG 196": "NH1" <-> "NH2" Residue "G PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 288": "NH1" <-> "NH2" Residue "G PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 346": "NH1" <-> "NH2" Residue "G TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 153": "NH1" <-> "NH2" Residue "H ARG 162": "NH1" <-> "NH2" Residue "H ARG 164": "NH1" <-> "NH2" Residue "H ARG 196": "NH1" <-> "NH2" Residue "H PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 288": "NH1" <-> "NH2" Residue "H PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 346": "NH1" <-> "NH2" Residue "H TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 153": "NH1" <-> "NH2" Residue "I ARG 162": "NH1" <-> "NH2" Residue "I ARG 164": "NH1" <-> "NH2" Residue "I ARG 196": "NH1" <-> "NH2" Residue "I PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 288": "NH1" <-> "NH2" Residue "I PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 346": "NH1" <-> "NH2" Residue "I TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 153": "NH1" <-> "NH2" Residue "J ARG 162": "NH1" <-> "NH2" Residue "J ARG 164": "NH1" <-> "NH2" Residue "J ARG 196": "NH1" <-> "NH2" Residue "J PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 288": "NH1" <-> "NH2" Residue "J PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 346": "NH1" <-> "NH2" Residue "J TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 153": "NH1" <-> "NH2" Residue "K ARG 162": "NH1" <-> "NH2" Residue "K ARG 164": "NH1" <-> "NH2" Residue "K ARG 196": "NH1" <-> "NH2" Residue "K PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 288": "NH1" <-> "NH2" Residue "K PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 346": "NH1" <-> "NH2" Residue "K TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 153": "NH1" <-> "NH2" Residue "L ARG 162": "NH1" <-> "NH2" Residue "L ARG 164": "NH1" <-> "NH2" Residue "L ARG 196": "NH1" <-> "NH2" Residue "L PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 288": "NH1" <-> "NH2" Residue "L PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 346": "NH1" <-> "NH2" Residue "L TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 153": "NH1" <-> "NH2" Residue "M ARG 162": "NH1" <-> "NH2" Residue "M ARG 164": "NH1" <-> "NH2" Residue "M ARG 196": "NH1" <-> "NH2" Residue "M PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 288": "NH1" <-> "NH2" Residue "M PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 346": "NH1" <-> "NH2" Residue "M TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 153": "NH1" <-> "NH2" Residue "N ARG 162": "NH1" <-> "NH2" Residue "N ARG 164": "NH1" <-> "NH2" Residue "N ARG 196": "NH1" <-> "NH2" Residue "N PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 288": "NH1" <-> "NH2" Residue "N PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 346": "NH1" <-> "NH2" Residue "N TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 153": "NH1" <-> "NH2" Residue "O ARG 162": "NH1" <-> "NH2" Residue "O ARG 164": "NH1" <-> "NH2" Residue "O ARG 196": "NH1" <-> "NH2" Residue "O PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 288": "NH1" <-> "NH2" Residue "O PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 346": "NH1" <-> "NH2" Residue "O TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 153": "NH1" <-> "NH2" Residue "P ARG 162": "NH1" <-> "NH2" Residue "P ARG 164": "NH1" <-> "NH2" Residue "P ARG 196": "NH1" <-> "NH2" Residue "P PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 288": "NH1" <-> "NH2" Residue "P PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 346": "NH1" <-> "NH2" Residue "P TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 153": "NH1" <-> "NH2" Residue "Q ARG 162": "NH1" <-> "NH2" Residue "Q ARG 164": "NH1" <-> "NH2" Residue "Q ARG 196": "NH1" <-> "NH2" Residue "Q PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 288": "NH1" <-> "NH2" Residue "Q PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 346": "NH1" <-> "NH2" Residue "Q TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 153": "NH1" <-> "NH2" Residue "R ARG 162": "NH1" <-> "NH2" Residue "R ARG 164": "NH1" <-> "NH2" Residue "R ARG 196": "NH1" <-> "NH2" Residue "R PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 288": "NH1" <-> "NH2" Residue "R PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 346": "NH1" <-> "NH2" Residue "R TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 153": "NH1" <-> "NH2" Residue "S ARG 162": "NH1" <-> "NH2" Residue "S ARG 164": "NH1" <-> "NH2" Residue "S ARG 196": "NH1" <-> "NH2" Residue "S PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 288": "NH1" <-> "NH2" Residue "S PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 346": "NH1" <-> "NH2" Residue "S TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 153": "NH1" <-> "NH2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ARG 164": "NH1" <-> "NH2" Residue "T ARG 196": "NH1" <-> "NH2" Residue "T PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 288": "NH1" <-> "NH2" Residue "T PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 346": "NH1" <-> "NH2" Residue "T TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 153": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ARG 164": "NH1" <-> "NH2" Residue "U ARG 196": "NH1" <-> "NH2" Residue "U PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 288": "NH1" <-> "NH2" Residue "U PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 346": "NH1" <-> "NH2" Residue "U TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 153": "NH1" <-> "NH2" Residue "V ARG 162": "NH1" <-> "NH2" Residue "V ARG 164": "NH1" <-> "NH2" Residue "V ARG 196": "NH1" <-> "NH2" Residue "V PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 288": "NH1" <-> "NH2" Residue "V PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 346": "NH1" <-> "NH2" Residue "V TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 153": "NH1" <-> "NH2" Residue "W ARG 162": "NH1" <-> "NH2" Residue "W ARG 164": "NH1" <-> "NH2" Residue "W ARG 196": "NH1" <-> "NH2" Residue "W PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 288": "NH1" <-> "NH2" Residue "W PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 346": "NH1" <-> "NH2" Residue "W TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 153": "NH1" <-> "NH2" Residue "X ARG 162": "NH1" <-> "NH2" Residue "X ARG 164": "NH1" <-> "NH2" Residue "X ARG 196": "NH1" <-> "NH2" Residue "X PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 288": "NH1" <-> "NH2" Residue "X PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 346": "NH1" <-> "NH2" Residue "X TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 44544 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "B" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "C" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "D" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "E" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "F" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "G" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "H" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "I" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "J" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "K" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "L" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "M" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "N" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "O" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "P" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "Q" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "R" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "S" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "T" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "U" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "V" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "W" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain: "X" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1856 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Time building chain proxies: 22.64, per 1000 atoms: 0.51 Number of scatterers: 44544 At special positions: 0 Unit cell: (155.967, 158.089, 155.967, 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 288 16.00 O 8160 8.00 N 8016 7.00 C 28080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 15.82 Conformation dependent library (CDL) restraints added in 8.6 seconds 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10608 Finding SS restraints... Secondary structure from input PDB file: 264 helices and 72 sheets defined 44.1% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.49 Creating SS restraints... Processing helix chain 'A' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS A 199 " --> pdb=" O MET A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 208 Processing helix chain 'A' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 271 Processing helix chain 'A' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.689A pdb=" N LEU A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE B 167 " --> pdb=" O MET B 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 194 Processing helix chain 'B' and resid 194 through 199 removed outlier: 3.609A pdb=" N HIS B 199 " --> pdb=" O MET B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 208 Processing helix chain 'B' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 271 Processing helix chain 'B' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 378 removed outlier: 4.070A pdb=" N PHE B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL B 376 " --> pdb=" O ILE B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE C 167 " --> pdb=" O MET C 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'C' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 208 Processing helix chain 'C' and resid 214 through 228 removed outlier: 3.927A pdb=" N LEU C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 271 Processing helix chain 'C' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 289 " --> pdb=" O GLU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 298 removed outlier: 3.747A pdb=" N MET C 297 " --> pdb=" O ALA C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 378 removed outlier: 4.070A pdb=" N PHE C 368 " --> pdb=" O GLU C 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL C 376 " --> pdb=" O ILE C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 removed outlier: 3.689A pdb=" N LEU C 384 " --> pdb=" O ARG C 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE D 167 " --> pdb=" O MET D 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 194 Processing helix chain 'D' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS D 199 " --> pdb=" O MET D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 208 Processing helix chain 'D' and resid 214 through 228 removed outlier: 3.927A pdb=" N LEU D 225 " --> pdb=" O SER D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN D 232 " --> pdb=" O GLN D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 271 Processing helix chain 'D' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS D 289 " --> pdb=" O GLU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 298 removed outlier: 3.747A pdb=" N MET D 297 " --> pdb=" O ALA D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 378 removed outlier: 4.070A pdb=" N PHE D 368 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL D 376 " --> pdb=" O ILE D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU D 384 " --> pdb=" O ARG D 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE E 167 " --> pdb=" O MET E 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 194 Processing helix chain 'E' and resid 194 through 199 removed outlier: 3.611A pdb=" N HIS E 199 " --> pdb=" O MET E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 208 Processing helix chain 'E' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU E 225 " --> pdb=" O SER E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN E 232 " --> pdb=" O GLN E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 271 Processing helix chain 'E' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS E 286 " --> pdb=" O GLU E 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS E 289 " --> pdb=" O GLU E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET E 297 " --> pdb=" O ALA E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 378 removed outlier: 4.070A pdb=" N PHE E 368 " --> pdb=" O GLU E 364 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL E 376 " --> pdb=" O ILE E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 385 removed outlier: 3.689A pdb=" N LEU E 384 " --> pdb=" O ARG E 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE F 167 " --> pdb=" O MET F 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 194 Processing helix chain 'F' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS F 199 " --> pdb=" O MET F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 208 Processing helix chain 'F' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU F 225 " --> pdb=" O SER F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 233 removed outlier: 4.075A pdb=" N ASN F 232 " --> pdb=" O GLN F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 271 Processing helix chain 'F' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS F 286 " --> pdb=" O GLU F 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS F 289 " --> pdb=" O GLU F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET F 297 " --> pdb=" O ALA F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE F 368 " --> pdb=" O GLU F 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL F 376 " --> pdb=" O ILE F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 172 removed outlier: 3.871A pdb=" N ILE G 167 " --> pdb=" O MET G 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA G 168 " --> pdb=" O ARG G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 194 Processing helix chain 'G' and resid 194 through 199 removed outlier: 3.609A pdb=" N HIS G 199 " --> pdb=" O MET G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 208 Processing helix chain 'G' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU G 225 " --> pdb=" O SER G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN G 232 " --> pdb=" O GLN G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 271 Processing helix chain 'G' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS G 286 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS G 289 " --> pdb=" O GLU G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET G 297 " --> pdb=" O ALA G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE G 368 " --> pdb=" O GLU G 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL G 376 " --> pdb=" O ILE G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 385 removed outlier: 3.689A pdb=" N LEU G 384 " --> pdb=" O ARG G 380 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE H 167 " --> pdb=" O MET H 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA H 168 " --> pdb=" O ARG H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 194 Processing helix chain 'H' and resid 194 through 199 removed outlier: 3.611A pdb=" N HIS H 199 " --> pdb=" O MET H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 208 Processing helix chain 'H' and resid 214 through 228 removed outlier: 3.927A pdb=" N LEU H 225 " --> pdb=" O SER H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN H 232 " --> pdb=" O GLN H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 271 Processing helix chain 'H' and resid 274 through 289 removed outlier: 3.609A pdb=" N LYS H 286 " --> pdb=" O GLU H 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS H 289 " --> pdb=" O GLU H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET H 297 " --> pdb=" O ALA H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 378 removed outlier: 4.070A pdb=" N PHE H 368 " --> pdb=" O GLU H 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL H 376 " --> pdb=" O ILE H 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 385 removed outlier: 3.689A pdb=" N LEU H 384 " --> pdb=" O ARG H 380 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 172 removed outlier: 3.869A pdb=" N ILE I 167 " --> pdb=" O MET I 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA I 168 " --> pdb=" O ARG I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 194 Processing helix chain 'I' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS I 199 " --> pdb=" O MET I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 208 Processing helix chain 'I' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU I 225 " --> pdb=" O SER I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN I 232 " --> pdb=" O GLN I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 271 Processing helix chain 'I' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS I 286 " --> pdb=" O GLU I 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS I 289 " --> pdb=" O GLU I 285 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET I 297 " --> pdb=" O ALA I 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE I 368 " --> pdb=" O GLU I 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL I 376 " --> pdb=" O ILE I 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU I 384 " --> pdb=" O ARG I 380 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 172 removed outlier: 3.871A pdb=" N ILE J 167 " --> pdb=" O MET J 163 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA J 168 " --> pdb=" O ARG J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 194 Processing helix chain 'J' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS J 199 " --> pdb=" O MET J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 208 Processing helix chain 'J' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU J 225 " --> pdb=" O SER J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN J 232 " --> pdb=" O GLN J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 271 Processing helix chain 'J' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS J 286 " --> pdb=" O GLU J 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS J 289 " --> pdb=" O GLU J 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 298 removed outlier: 3.747A pdb=" N MET J 297 " --> pdb=" O ALA J 293 " (cutoff:3.500A) Processing helix chain 'J' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE J 368 " --> pdb=" O GLU J 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL J 376 " --> pdb=" O ILE J 372 " (cutoff:3.500A) Processing helix chain 'J' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU J 384 " --> pdb=" O ARG J 380 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 172 removed outlier: 3.871A pdb=" N ILE K 167 " --> pdb=" O MET K 163 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA K 168 " --> pdb=" O ARG K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 194 Processing helix chain 'K' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS K 199 " --> pdb=" O MET K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 208 Processing helix chain 'K' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU K 225 " --> pdb=" O SER K 221 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN K 232 " --> pdb=" O GLN K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 268 through 271 Processing helix chain 'K' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS K 286 " --> pdb=" O GLU K 282 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS K 289 " --> pdb=" O GLU K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET K 297 " --> pdb=" O ALA K 293 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE K 368 " --> pdb=" O GLU K 364 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL K 376 " --> pdb=" O ILE K 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU K 384 " --> pdb=" O ARG K 380 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 172 removed outlier: 3.869A pdb=" N ILE L 167 " --> pdb=" O MET L 163 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA L 168 " --> pdb=" O ARG L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 194 Processing helix chain 'L' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS L 199 " --> pdb=" O MET L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 199 through 208 Processing helix chain 'L' and resid 214 through 228 removed outlier: 3.927A pdb=" N LEU L 225 " --> pdb=" O SER L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN L 232 " --> pdb=" O GLN L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 268 through 271 Processing helix chain 'L' and resid 274 through 289 removed outlier: 3.609A pdb=" N LYS L 286 " --> pdb=" O GLU L 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS L 289 " --> pdb=" O GLU L 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET L 297 " --> pdb=" O ALA L 293 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE L 368 " --> pdb=" O GLU L 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL L 376 " --> pdb=" O ILE L 372 " (cutoff:3.500A) Processing helix chain 'L' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU L 384 " --> pdb=" O ARG L 380 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 172 removed outlier: 3.871A pdb=" N ILE M 167 " --> pdb=" O MET M 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA M 168 " --> pdb=" O ARG M 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 194 Processing helix chain 'M' and resid 194 through 199 removed outlier: 3.611A pdb=" N HIS M 199 " --> pdb=" O MET M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 208 Processing helix chain 'M' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU M 225 " --> pdb=" O SER M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN M 232 " --> pdb=" O GLN M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 268 through 271 Processing helix chain 'M' and resid 274 through 289 removed outlier: 3.609A pdb=" N LYS M 286 " --> pdb=" O GLU M 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS M 289 " --> pdb=" O GLU M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 298 removed outlier: 3.747A pdb=" N MET M 297 " --> pdb=" O ALA M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 362 through 378 removed outlier: 4.070A pdb=" N PHE M 368 " --> pdb=" O GLU M 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL M 376 " --> pdb=" O ILE M 372 " (cutoff:3.500A) Processing helix chain 'M' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU M 384 " --> pdb=" O ARG M 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE N 167 " --> pdb=" O MET N 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA N 168 " --> pdb=" O ARG N 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 189 through 194 Processing helix chain 'N' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS N 199 " --> pdb=" O MET N 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 208 Processing helix chain 'N' and resid 214 through 228 removed outlier: 3.927A pdb=" N LEU N 225 " --> pdb=" O SER N 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN N 232 " --> pdb=" O GLN N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 268 through 271 Processing helix chain 'N' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS N 286 " --> pdb=" O GLU N 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS N 289 " --> pdb=" O GLU N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET N 297 " --> pdb=" O ALA N 293 " (cutoff:3.500A) Processing helix chain 'N' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE N 368 " --> pdb=" O GLU N 364 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL N 376 " --> pdb=" O ILE N 372 " (cutoff:3.500A) Processing helix chain 'N' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU N 384 " --> pdb=" O ARG N 380 " (cutoff:3.500A) Processing helix chain 'O' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE O 167 " --> pdb=" O MET O 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA O 168 " --> pdb=" O ARG O 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 189 through 194 Processing helix chain 'O' and resid 194 through 199 removed outlier: 3.611A pdb=" N HIS O 199 " --> pdb=" O MET O 195 " (cutoff:3.500A) Processing helix chain 'O' and resid 199 through 208 Processing helix chain 'O' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU O 225 " --> pdb=" O SER O 221 " (cutoff:3.500A) Processing helix chain 'O' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN O 232 " --> pdb=" O GLN O 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 268 through 271 Processing helix chain 'O' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS O 286 " --> pdb=" O GLU O 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS O 289 " --> pdb=" O GLU O 285 " (cutoff:3.500A) Processing helix chain 'O' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET O 297 " --> pdb=" O ALA O 293 " (cutoff:3.500A) Processing helix chain 'O' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE O 368 " --> pdb=" O GLU O 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL O 376 " --> pdb=" O ILE O 372 " (cutoff:3.500A) Processing helix chain 'O' and resid 380 through 385 removed outlier: 3.689A pdb=" N LEU O 384 " --> pdb=" O ARG O 380 " (cutoff:3.500A) Processing helix chain 'P' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE P 167 " --> pdb=" O MET P 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA P 168 " --> pdb=" O ARG P 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 189 through 194 Processing helix chain 'P' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS P 199 " --> pdb=" O MET P 195 " (cutoff:3.500A) Processing helix chain 'P' and resid 199 through 208 Processing helix chain 'P' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU P 225 " --> pdb=" O SER P 221 " (cutoff:3.500A) Processing helix chain 'P' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN P 232 " --> pdb=" O GLN P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 268 through 271 Processing helix chain 'P' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS P 286 " --> pdb=" O GLU P 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS P 289 " --> pdb=" O GLU P 285 " (cutoff:3.500A) Processing helix chain 'P' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET P 297 " --> pdb=" O ALA P 293 " (cutoff:3.500A) Processing helix chain 'P' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE P 368 " --> pdb=" O GLU P 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL P 376 " --> pdb=" O ILE P 372 " (cutoff:3.500A) Processing helix chain 'P' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU P 384 " --> pdb=" O ARG P 380 " (cutoff:3.500A) Processing helix chain 'Q' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE Q 167 " --> pdb=" O MET Q 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA Q 168 " --> pdb=" O ARG Q 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 189 through 194 Processing helix chain 'Q' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS Q 199 " --> pdb=" O MET Q 195 " (cutoff:3.500A) Processing helix chain 'Q' and resid 199 through 208 Processing helix chain 'Q' and resid 214 through 228 removed outlier: 3.927A pdb=" N LEU Q 225 " --> pdb=" O SER Q 221 " (cutoff:3.500A) Processing helix chain 'Q' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN Q 232 " --> pdb=" O GLN Q 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 268 through 271 Processing helix chain 'Q' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS Q 286 " --> pdb=" O GLU Q 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS Q 289 " --> pdb=" O GLU Q 285 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET Q 297 " --> pdb=" O ALA Q 293 " (cutoff:3.500A) Processing helix chain 'Q' and resid 362 through 378 removed outlier: 4.070A pdb=" N PHE Q 368 " --> pdb=" O GLU Q 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL Q 376 " --> pdb=" O ILE Q 372 " (cutoff:3.500A) Processing helix chain 'Q' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU Q 384 " --> pdb=" O ARG Q 380 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE R 167 " --> pdb=" O MET R 163 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA R 168 " --> pdb=" O ARG R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 189 through 194 Processing helix chain 'R' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS R 199 " --> pdb=" O MET R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 208 Processing helix chain 'R' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU R 225 " --> pdb=" O SER R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN R 232 " --> pdb=" O GLN R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 271 Processing helix chain 'R' and resid 274 through 289 removed outlier: 3.611A pdb=" N LYS R 286 " --> pdb=" O GLU R 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS R 289 " --> pdb=" O GLU R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 298 removed outlier: 3.747A pdb=" N MET R 297 " --> pdb=" O ALA R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE R 368 " --> pdb=" O GLU R 364 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL R 376 " --> pdb=" O ILE R 372 " (cutoff:3.500A) Processing helix chain 'R' and resid 380 through 385 removed outlier: 3.689A pdb=" N LEU R 384 " --> pdb=" O ARG R 380 " (cutoff:3.500A) Processing helix chain 'S' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE S 167 " --> pdb=" O MET S 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA S 168 " --> pdb=" O ARG S 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 189 through 194 Processing helix chain 'S' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS S 199 " --> pdb=" O MET S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 199 through 208 Processing helix chain 'S' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU S 225 " --> pdb=" O SER S 221 " (cutoff:3.500A) Processing helix chain 'S' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN S 232 " --> pdb=" O GLN S 228 " (cutoff:3.500A) Processing helix chain 'S' and resid 268 through 271 Processing helix chain 'S' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS S 286 " --> pdb=" O GLU S 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS S 289 " --> pdb=" O GLU S 285 " (cutoff:3.500A) Processing helix chain 'S' and resid 293 through 298 removed outlier: 3.747A pdb=" N MET S 297 " --> pdb=" O ALA S 293 " (cutoff:3.500A) Processing helix chain 'S' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE S 368 " --> pdb=" O GLU S 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL S 376 " --> pdb=" O ILE S 372 " (cutoff:3.500A) Processing helix chain 'S' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU S 384 " --> pdb=" O ARG S 380 " (cutoff:3.500A) Processing helix chain 'T' and resid 161 through 172 removed outlier: 3.871A pdb=" N ILE T 167 " --> pdb=" O MET T 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA T 168 " --> pdb=" O ARG T 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 189 through 194 Processing helix chain 'T' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS T 199 " --> pdb=" O MET T 195 " (cutoff:3.500A) Processing helix chain 'T' and resid 199 through 208 Processing helix chain 'T' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU T 225 " --> pdb=" O SER T 221 " (cutoff:3.500A) Processing helix chain 'T' and resid 228 through 233 removed outlier: 4.073A pdb=" N ASN T 232 " --> pdb=" O GLN T 228 " (cutoff:3.500A) Processing helix chain 'T' and resid 268 through 271 Processing helix chain 'T' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS T 286 " --> pdb=" O GLU T 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS T 289 " --> pdb=" O GLU T 285 " (cutoff:3.500A) Processing helix chain 'T' and resid 293 through 298 removed outlier: 3.747A pdb=" N MET T 297 " --> pdb=" O ALA T 293 " (cutoff:3.500A) Processing helix chain 'T' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE T 368 " --> pdb=" O GLU T 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL T 376 " --> pdb=" O ILE T 372 " (cutoff:3.500A) Processing helix chain 'T' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU T 384 " --> pdb=" O ARG T 380 " (cutoff:3.500A) Processing helix chain 'U' and resid 161 through 172 removed outlier: 3.871A pdb=" N ILE U 167 " --> pdb=" O MET U 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA U 168 " --> pdb=" O ARG U 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 189 through 194 Processing helix chain 'U' and resid 194 through 199 removed outlier: 3.611A pdb=" N HIS U 199 " --> pdb=" O MET U 195 " (cutoff:3.500A) Processing helix chain 'U' and resid 199 through 208 Processing helix chain 'U' and resid 214 through 228 removed outlier: 3.927A pdb=" N LEU U 225 " --> pdb=" O SER U 221 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 233 removed outlier: 4.073A pdb=" N ASN U 232 " --> pdb=" O GLN U 228 " (cutoff:3.500A) Processing helix chain 'U' and resid 268 through 271 Processing helix chain 'U' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS U 286 " --> pdb=" O GLU U 282 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS U 289 " --> pdb=" O GLU U 285 " (cutoff:3.500A) Processing helix chain 'U' and resid 293 through 298 removed outlier: 3.747A pdb=" N MET U 297 " --> pdb=" O ALA U 293 " (cutoff:3.500A) Processing helix chain 'U' and resid 362 through 378 removed outlier: 4.070A pdb=" N PHE U 368 " --> pdb=" O GLU U 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL U 376 " --> pdb=" O ILE U 372 " (cutoff:3.500A) Processing helix chain 'U' and resid 380 through 385 removed outlier: 3.689A pdb=" N LEU U 384 " --> pdb=" O ARG U 380 " (cutoff:3.500A) Processing helix chain 'V' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE V 167 " --> pdb=" O MET V 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA V 168 " --> pdb=" O ARG V 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 189 through 194 Processing helix chain 'V' and resid 194 through 199 removed outlier: 3.611A pdb=" N HIS V 199 " --> pdb=" O MET V 195 " (cutoff:3.500A) Processing helix chain 'V' and resid 199 through 208 Processing helix chain 'V' and resid 214 through 228 removed outlier: 3.927A pdb=" N LEU V 225 " --> pdb=" O SER V 221 " (cutoff:3.500A) Processing helix chain 'V' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN V 232 " --> pdb=" O GLN V 228 " (cutoff:3.500A) Processing helix chain 'V' and resid 268 through 271 Processing helix chain 'V' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS V 286 " --> pdb=" O GLU V 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS V 289 " --> pdb=" O GLU V 285 " (cutoff:3.500A) Processing helix chain 'V' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET V 297 " --> pdb=" O ALA V 293 " (cutoff:3.500A) Processing helix chain 'V' and resid 362 through 378 removed outlier: 4.070A pdb=" N PHE V 368 " --> pdb=" O GLU V 364 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL V 376 " --> pdb=" O ILE V 372 " (cutoff:3.500A) Processing helix chain 'V' and resid 380 through 385 removed outlier: 3.690A pdb=" N LEU V 384 " --> pdb=" O ARG V 380 " (cutoff:3.500A) Processing helix chain 'W' and resid 161 through 172 removed outlier: 3.870A pdb=" N ILE W 167 " --> pdb=" O MET W 163 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA W 168 " --> pdb=" O ARG W 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 189 through 194 Processing helix chain 'W' and resid 194 through 199 removed outlier: 3.611A pdb=" N HIS W 199 " --> pdb=" O MET W 195 " (cutoff:3.500A) Processing helix chain 'W' and resid 199 through 208 Processing helix chain 'W' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU W 225 " --> pdb=" O SER W 221 " (cutoff:3.500A) Processing helix chain 'W' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN W 232 " --> pdb=" O GLN W 228 " (cutoff:3.500A) Processing helix chain 'W' and resid 268 through 271 Processing helix chain 'W' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS W 286 " --> pdb=" O GLU W 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS W 289 " --> pdb=" O GLU W 285 " (cutoff:3.500A) Processing helix chain 'W' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET W 297 " --> pdb=" O ALA W 293 " (cutoff:3.500A) Processing helix chain 'W' and resid 362 through 378 removed outlier: 4.071A pdb=" N PHE W 368 " --> pdb=" O GLU W 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL W 376 " --> pdb=" O ILE W 372 " (cutoff:3.500A) Processing helix chain 'W' and resid 380 through 385 removed outlier: 3.689A pdb=" N LEU W 384 " --> pdb=" O ARG W 380 " (cutoff:3.500A) Processing helix chain 'X' and resid 161 through 172 removed outlier: 3.869A pdb=" N ILE X 167 " --> pdb=" O MET X 163 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA X 168 " --> pdb=" O ARG X 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 189 through 194 Processing helix chain 'X' and resid 194 through 199 removed outlier: 3.610A pdb=" N HIS X 199 " --> pdb=" O MET X 195 " (cutoff:3.500A) Processing helix chain 'X' and resid 199 through 208 Processing helix chain 'X' and resid 214 through 228 removed outlier: 3.928A pdb=" N LEU X 225 " --> pdb=" O SER X 221 " (cutoff:3.500A) Processing helix chain 'X' and resid 228 through 233 removed outlier: 4.074A pdb=" N ASN X 232 " --> pdb=" O GLN X 228 " (cutoff:3.500A) Processing helix chain 'X' and resid 268 through 271 Processing helix chain 'X' and resid 274 through 289 removed outlier: 3.610A pdb=" N LYS X 286 " --> pdb=" O GLU X 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS X 289 " --> pdb=" O GLU X 285 " (cutoff:3.500A) Processing helix chain 'X' and resid 293 through 298 removed outlier: 3.748A pdb=" N MET X 297 " --> pdb=" O ALA X 293 " (cutoff:3.500A) Processing helix chain 'X' and resid 362 through 378 removed outlier: 4.070A pdb=" N PHE X 368 " --> pdb=" O GLU X 364 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL X 376 " --> pdb=" O ILE X 372 " (cutoff:3.500A) Processing helix chain 'X' and resid 380 through 385 removed outlier: 3.689A pdb=" N LEU X 384 " --> pdb=" O ARG X 380 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR A 350 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY A 331 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA A 352 " --> pdb=" O MET A 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET A 329 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR A 354 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU A 327 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP A 356 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA A 325 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR A 303 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET A 329 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER A 305 " --> pdb=" O MET A 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY A 331 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE A 304 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER A 251 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN A 306 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 234 through 236 removed outlier: 3.970A pdb=" N GLU A 241 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 254 through 256 Processing sheet with id= 4, first strand: chain 'B' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR B 350 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY B 331 " --> pdb=" O TYR B 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA B 352 " --> pdb=" O MET B 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET B 329 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR B 354 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU B 327 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP B 356 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA B 325 " --> pdb=" O ASP B 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR B 303 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET B 329 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER B 305 " --> pdb=" O MET B 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY B 331 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE B 304 " --> pdb=" O ASP B 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER B 251 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN B 306 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU B 241 " --> pdb=" O ASP B 236 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 254 through 256 Processing sheet with id= 7, first strand: chain 'C' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR C 350 " --> pdb=" O GLY C 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY C 331 " --> pdb=" O TYR C 350 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA C 352 " --> pdb=" O MET C 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET C 329 " --> pdb=" O ALA C 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR C 354 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU C 327 " --> pdb=" O THR C 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP C 356 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA C 325 " --> pdb=" O ASP C 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR C 303 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET C 329 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER C 305 " --> pdb=" O MET C 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY C 331 " --> pdb=" O SER C 305 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N ILE C 304 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER C 251 " --> pdb=" O ILE C 304 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ASN C 306 " --> pdb=" O SER C 251 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU C 241 " --> pdb=" O ASP C 236 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 254 through 256 Processing sheet with id= 10, first strand: chain 'D' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR D 350 " --> pdb=" O GLY D 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY D 331 " --> pdb=" O TYR D 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA D 352 " --> pdb=" O MET D 329 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N MET D 329 " --> pdb=" O ALA D 352 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR D 354 " --> pdb=" O LEU D 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU D 327 " --> pdb=" O THR D 354 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP D 356 " --> pdb=" O ALA D 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA D 325 " --> pdb=" O ASP D 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR D 303 " --> pdb=" O LEU D 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET D 329 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER D 305 " --> pdb=" O MET D 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY D 331 " --> pdb=" O SER D 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE D 304 " --> pdb=" O ASP D 249 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER D 251 " --> pdb=" O ILE D 304 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ASN D 306 " --> pdb=" O SER D 251 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 234 through 236 removed outlier: 3.970A pdb=" N GLU D 241 " --> pdb=" O ASP D 236 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 254 through 256 Processing sheet with id= 13, first strand: chain 'E' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR E 350 " --> pdb=" O GLY E 331 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY E 331 " --> pdb=" O TYR E 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA E 352 " --> pdb=" O MET E 329 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N MET E 329 " --> pdb=" O ALA E 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR E 354 " --> pdb=" O LEU E 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU E 327 " --> pdb=" O THR E 354 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP E 356 " --> pdb=" O ALA E 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA E 325 " --> pdb=" O ASP E 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR E 303 " --> pdb=" O LEU E 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET E 329 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER E 305 " --> pdb=" O MET E 329 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY E 331 " --> pdb=" O SER E 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE E 304 " --> pdb=" O ASP E 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER E 251 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN E 306 " --> pdb=" O SER E 251 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 234 through 236 removed outlier: 3.970A pdb=" N GLU E 241 " --> pdb=" O ASP E 236 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 254 through 256 Processing sheet with id= 16, first strand: chain 'F' and resid 180 through 188 removed outlier: 4.338A pdb=" N TYR F 350 " --> pdb=" O GLY F 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY F 331 " --> pdb=" O TYR F 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA F 352 " --> pdb=" O MET F 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET F 329 " --> pdb=" O ALA F 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR F 354 " --> pdb=" O LEU F 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU F 327 " --> pdb=" O THR F 354 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASP F 356 " --> pdb=" O ALA F 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA F 325 " --> pdb=" O ASP F 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR F 303 " --> pdb=" O LEU F 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET F 329 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER F 305 " --> pdb=" O MET F 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY F 331 " --> pdb=" O SER F 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE F 304 " --> pdb=" O ASP F 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER F 251 " --> pdb=" O ILE F 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN F 306 " --> pdb=" O SER F 251 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU F 241 " --> pdb=" O ASP F 236 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'F' and resid 254 through 256 Processing sheet with id= 19, first strand: chain 'G' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR G 350 " --> pdb=" O GLY G 331 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY G 331 " --> pdb=" O TYR G 350 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA G 352 " --> pdb=" O MET G 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET G 329 " --> pdb=" O ALA G 352 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR G 354 " --> pdb=" O LEU G 327 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU G 327 " --> pdb=" O THR G 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP G 356 " --> pdb=" O ALA G 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA G 325 " --> pdb=" O ASP G 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR G 303 " --> pdb=" O LEU G 327 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N MET G 329 " --> pdb=" O THR G 303 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER G 305 " --> pdb=" O MET G 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY G 331 " --> pdb=" O SER G 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE G 304 " --> pdb=" O ASP G 249 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER G 251 " --> pdb=" O ILE G 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN G 306 " --> pdb=" O SER G 251 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU G 241 " --> pdb=" O ASP G 236 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'G' and resid 254 through 256 Processing sheet with id= 22, first strand: chain 'H' and resid 180 through 188 removed outlier: 4.338A pdb=" N TYR H 350 " --> pdb=" O GLY H 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY H 331 " --> pdb=" O TYR H 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA H 352 " --> pdb=" O MET H 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET H 329 " --> pdb=" O ALA H 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR H 354 " --> pdb=" O LEU H 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU H 327 " --> pdb=" O THR H 354 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP H 356 " --> pdb=" O ALA H 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA H 325 " --> pdb=" O ASP H 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR H 303 " --> pdb=" O LEU H 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET H 329 " --> pdb=" O THR H 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER H 305 " --> pdb=" O MET H 329 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY H 331 " --> pdb=" O SER H 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE H 304 " --> pdb=" O ASP H 249 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER H 251 " --> pdb=" O ILE H 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN H 306 " --> pdb=" O SER H 251 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 234 through 236 removed outlier: 3.970A pdb=" N GLU H 241 " --> pdb=" O ASP H 236 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'H' and resid 254 through 256 Processing sheet with id= 25, first strand: chain 'I' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR I 350 " --> pdb=" O GLY I 331 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY I 331 " --> pdb=" O TYR I 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA I 352 " --> pdb=" O MET I 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET I 329 " --> pdb=" O ALA I 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR I 354 " --> pdb=" O LEU I 327 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU I 327 " --> pdb=" O THR I 354 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP I 356 " --> pdb=" O ALA I 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA I 325 " --> pdb=" O ASP I 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR I 303 " --> pdb=" O LEU I 327 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N MET I 329 " --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER I 305 " --> pdb=" O MET I 329 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY I 331 " --> pdb=" O SER I 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE I 304 " --> pdb=" O ASP I 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER I 251 " --> pdb=" O ILE I 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN I 306 " --> pdb=" O SER I 251 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'I' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU I 241 " --> pdb=" O ASP I 236 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'I' and resid 254 through 256 Processing sheet with id= 28, first strand: chain 'J' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR J 350 " --> pdb=" O GLY J 331 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY J 331 " --> pdb=" O TYR J 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA J 352 " --> pdb=" O MET J 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET J 329 " --> pdb=" O ALA J 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR J 354 " --> pdb=" O LEU J 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU J 327 " --> pdb=" O THR J 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP J 356 " --> pdb=" O ALA J 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA J 325 " --> pdb=" O ASP J 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR J 303 " --> pdb=" O LEU J 327 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N MET J 329 " --> pdb=" O THR J 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER J 305 " --> pdb=" O MET J 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY J 331 " --> pdb=" O SER J 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE J 304 " --> pdb=" O ASP J 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER J 251 " --> pdb=" O ILE J 304 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ASN J 306 " --> pdb=" O SER J 251 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'J' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU J 241 " --> pdb=" O ASP J 236 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'J' and resid 254 through 256 Processing sheet with id= 31, first strand: chain 'K' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR K 350 " --> pdb=" O GLY K 331 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY K 331 " --> pdb=" O TYR K 350 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA K 352 " --> pdb=" O MET K 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET K 329 " --> pdb=" O ALA K 352 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR K 354 " --> pdb=" O LEU K 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU K 327 " --> pdb=" O THR K 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP K 356 " --> pdb=" O ALA K 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA K 325 " --> pdb=" O ASP K 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR K 303 " --> pdb=" O LEU K 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET K 329 " --> pdb=" O THR K 303 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER K 305 " --> pdb=" O MET K 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY K 331 " --> pdb=" O SER K 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE K 304 " --> pdb=" O ASP K 249 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER K 251 " --> pdb=" O ILE K 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN K 306 " --> pdb=" O SER K 251 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'K' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU K 241 " --> pdb=" O ASP K 236 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'K' and resid 254 through 256 Processing sheet with id= 34, first strand: chain 'L' and resid 180 through 188 removed outlier: 4.338A pdb=" N TYR L 350 " --> pdb=" O GLY L 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY L 331 " --> pdb=" O TYR L 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA L 352 " --> pdb=" O MET L 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET L 329 " --> pdb=" O ALA L 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR L 354 " --> pdb=" O LEU L 327 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU L 327 " --> pdb=" O THR L 354 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP L 356 " --> pdb=" O ALA L 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA L 325 " --> pdb=" O ASP L 356 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N THR L 303 " --> pdb=" O LEU L 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET L 329 " --> pdb=" O THR L 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER L 305 " --> pdb=" O MET L 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY L 331 " --> pdb=" O SER L 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE L 304 " --> pdb=" O ASP L 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER L 251 " --> pdb=" O ILE L 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN L 306 " --> pdb=" O SER L 251 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'L' and resid 234 through 236 removed outlier: 3.970A pdb=" N GLU L 241 " --> pdb=" O ASP L 236 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'L' and resid 254 through 256 Processing sheet with id= 37, first strand: chain 'M' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR M 350 " --> pdb=" O GLY M 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY M 331 " --> pdb=" O TYR M 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA M 352 " --> pdb=" O MET M 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET M 329 " --> pdb=" O ALA M 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR M 354 " --> pdb=" O LEU M 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU M 327 " --> pdb=" O THR M 354 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP M 356 " --> pdb=" O ALA M 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA M 325 " --> pdb=" O ASP M 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR M 303 " --> pdb=" O LEU M 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET M 329 " --> pdb=" O THR M 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER M 305 " --> pdb=" O MET M 329 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY M 331 " --> pdb=" O SER M 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE M 304 " --> pdb=" O ASP M 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER M 251 " --> pdb=" O ILE M 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN M 306 " --> pdb=" O SER M 251 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'M' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU M 241 " --> pdb=" O ASP M 236 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'M' and resid 254 through 256 Processing sheet with id= 40, first strand: chain 'N' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR N 350 " --> pdb=" O GLY N 331 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY N 331 " --> pdb=" O TYR N 350 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA N 352 " --> pdb=" O MET N 329 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N MET N 329 " --> pdb=" O ALA N 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR N 354 " --> pdb=" O LEU N 327 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU N 327 " --> pdb=" O THR N 354 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP N 356 " --> pdb=" O ALA N 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA N 325 " --> pdb=" O ASP N 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR N 303 " --> pdb=" O LEU N 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET N 329 " --> pdb=" O THR N 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER N 305 " --> pdb=" O MET N 329 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY N 331 " --> pdb=" O SER N 305 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ILE N 304 " --> pdb=" O ASP N 249 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER N 251 " --> pdb=" O ILE N 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN N 306 " --> pdb=" O SER N 251 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'N' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU N 241 " --> pdb=" O ASP N 236 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'N' and resid 254 through 256 Processing sheet with id= 43, first strand: chain 'O' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR O 350 " --> pdb=" O GLY O 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY O 331 " --> pdb=" O TYR O 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA O 352 " --> pdb=" O MET O 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET O 329 " --> pdb=" O ALA O 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR O 354 " --> pdb=" O LEU O 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU O 327 " --> pdb=" O THR O 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP O 356 " --> pdb=" O ALA O 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA O 325 " --> pdb=" O ASP O 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR O 303 " --> pdb=" O LEU O 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET O 329 " --> pdb=" O THR O 303 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER O 305 " --> pdb=" O MET O 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY O 331 " --> pdb=" O SER O 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE O 304 " --> pdb=" O ASP O 249 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER O 251 " --> pdb=" O ILE O 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN O 306 " --> pdb=" O SER O 251 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'O' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU O 241 " --> pdb=" O ASP O 236 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'O' and resid 254 through 256 Processing sheet with id= 46, first strand: chain 'P' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR P 350 " --> pdb=" O GLY P 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY P 331 " --> pdb=" O TYR P 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA P 352 " --> pdb=" O MET P 329 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N MET P 329 " --> pdb=" O ALA P 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR P 354 " --> pdb=" O LEU P 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU P 327 " --> pdb=" O THR P 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP P 356 " --> pdb=" O ALA P 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA P 325 " --> pdb=" O ASP P 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR P 303 " --> pdb=" O LEU P 327 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N MET P 329 " --> pdb=" O THR P 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER P 305 " --> pdb=" O MET P 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY P 331 " --> pdb=" O SER P 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE P 304 " --> pdb=" O ASP P 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER P 251 " --> pdb=" O ILE P 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN P 306 " --> pdb=" O SER P 251 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'P' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU P 241 " --> pdb=" O ASP P 236 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'P' and resid 254 through 256 Processing sheet with id= 49, first strand: chain 'Q' and resid 180 through 188 removed outlier: 4.338A pdb=" N TYR Q 350 " --> pdb=" O GLY Q 331 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY Q 331 " --> pdb=" O TYR Q 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA Q 352 " --> pdb=" O MET Q 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET Q 329 " --> pdb=" O ALA Q 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR Q 354 " --> pdb=" O LEU Q 327 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU Q 327 " --> pdb=" O THR Q 354 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP Q 356 " --> pdb=" O ALA Q 325 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA Q 325 " --> pdb=" O ASP Q 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR Q 303 " --> pdb=" O LEU Q 327 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N MET Q 329 " --> pdb=" O THR Q 303 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER Q 305 " --> pdb=" O MET Q 329 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY Q 331 " --> pdb=" O SER Q 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE Q 304 " --> pdb=" O ASP Q 249 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER Q 251 " --> pdb=" O ILE Q 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN Q 306 " --> pdb=" O SER Q 251 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'Q' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU Q 241 " --> pdb=" O ASP Q 236 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'Q' and resid 254 through 256 Processing sheet with id= 52, first strand: chain 'R' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR R 350 " --> pdb=" O GLY R 331 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY R 331 " --> pdb=" O TYR R 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA R 352 " --> pdb=" O MET R 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET R 329 " --> pdb=" O ALA R 352 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR R 354 " --> pdb=" O LEU R 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU R 327 " --> pdb=" O THR R 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP R 356 " --> pdb=" O ALA R 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA R 325 " --> pdb=" O ASP R 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR R 303 " --> pdb=" O LEU R 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET R 329 " --> pdb=" O THR R 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER R 305 " --> pdb=" O MET R 329 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY R 331 " --> pdb=" O SER R 305 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ILE R 304 " --> pdb=" O ASP R 249 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER R 251 " --> pdb=" O ILE R 304 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ASN R 306 " --> pdb=" O SER R 251 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'R' and resid 234 through 236 removed outlier: 3.970A pdb=" N GLU R 241 " --> pdb=" O ASP R 236 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'R' and resid 254 through 256 Processing sheet with id= 55, first strand: chain 'S' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR S 350 " --> pdb=" O GLY S 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY S 331 " --> pdb=" O TYR S 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA S 352 " --> pdb=" O MET S 329 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N MET S 329 " --> pdb=" O ALA S 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR S 354 " --> pdb=" O LEU S 327 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU S 327 " --> pdb=" O THR S 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP S 356 " --> pdb=" O ALA S 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA S 325 " --> pdb=" O ASP S 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR S 303 " --> pdb=" O LEU S 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET S 329 " --> pdb=" O THR S 303 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER S 305 " --> pdb=" O MET S 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY S 331 " --> pdb=" O SER S 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE S 304 " --> pdb=" O ASP S 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER S 251 " --> pdb=" O ILE S 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN S 306 " --> pdb=" O SER S 251 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'S' and resid 234 through 236 removed outlier: 3.970A pdb=" N GLU S 241 " --> pdb=" O ASP S 236 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'S' and resid 254 through 256 Processing sheet with id= 58, first strand: chain 'T' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR T 350 " --> pdb=" O GLY T 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY T 331 " --> pdb=" O TYR T 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA T 352 " --> pdb=" O MET T 329 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N MET T 329 " --> pdb=" O ALA T 352 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR T 354 " --> pdb=" O LEU T 327 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU T 327 " --> pdb=" O THR T 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP T 356 " --> pdb=" O ALA T 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA T 325 " --> pdb=" O ASP T 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR T 303 " --> pdb=" O LEU T 327 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N MET T 329 " --> pdb=" O THR T 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER T 305 " --> pdb=" O MET T 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY T 331 " --> pdb=" O SER T 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE T 304 " --> pdb=" O ASP T 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER T 251 " --> pdb=" O ILE T 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN T 306 " --> pdb=" O SER T 251 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'T' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU T 241 " --> pdb=" O ASP T 236 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'T' and resid 254 through 256 Processing sheet with id= 61, first strand: chain 'U' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR U 350 " --> pdb=" O GLY U 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY U 331 " --> pdb=" O TYR U 350 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA U 352 " --> pdb=" O MET U 329 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET U 329 " --> pdb=" O ALA U 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR U 354 " --> pdb=" O LEU U 327 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU U 327 " --> pdb=" O THR U 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP U 356 " --> pdb=" O ALA U 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA U 325 " --> pdb=" O ASP U 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR U 303 " --> pdb=" O LEU U 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET U 329 " --> pdb=" O THR U 303 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER U 305 " --> pdb=" O MET U 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY U 331 " --> pdb=" O SER U 305 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N ILE U 304 " --> pdb=" O ASP U 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER U 251 " --> pdb=" O ILE U 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN U 306 " --> pdb=" O SER U 251 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'U' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU U 241 " --> pdb=" O ASP U 236 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'U' and resid 254 through 256 Processing sheet with id= 64, first strand: chain 'V' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR V 350 " --> pdb=" O GLY V 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY V 331 " --> pdb=" O TYR V 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA V 352 " --> pdb=" O MET V 329 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N MET V 329 " --> pdb=" O ALA V 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR V 354 " --> pdb=" O LEU V 327 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU V 327 " --> pdb=" O THR V 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP V 356 " --> pdb=" O ALA V 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA V 325 " --> pdb=" O ASP V 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR V 303 " --> pdb=" O LEU V 327 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N MET V 329 " --> pdb=" O THR V 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER V 305 " --> pdb=" O MET V 329 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY V 331 " --> pdb=" O SER V 305 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ILE V 304 " --> pdb=" O ASP V 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER V 251 " --> pdb=" O ILE V 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN V 306 " --> pdb=" O SER V 251 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'V' and resid 234 through 236 removed outlier: 3.970A pdb=" N GLU V 241 " --> pdb=" O ASP V 236 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'V' and resid 254 through 256 Processing sheet with id= 67, first strand: chain 'W' and resid 180 through 188 removed outlier: 4.337A pdb=" N TYR W 350 " --> pdb=" O GLY W 331 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY W 331 " --> pdb=" O TYR W 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA W 352 " --> pdb=" O MET W 329 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N MET W 329 " --> pdb=" O ALA W 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR W 354 " --> pdb=" O LEU W 327 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU W 327 " --> pdb=" O THR W 354 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP W 356 " --> pdb=" O ALA W 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA W 325 " --> pdb=" O ASP W 356 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR W 303 " --> pdb=" O LEU W 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET W 329 " --> pdb=" O THR W 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER W 305 " --> pdb=" O MET W 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY W 331 " --> pdb=" O SER W 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE W 304 " --> pdb=" O ASP W 249 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER W 251 " --> pdb=" O ILE W 304 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ASN W 306 " --> pdb=" O SER W 251 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'W' and resid 234 through 236 removed outlier: 3.971A pdb=" N GLU W 241 " --> pdb=" O ASP W 236 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'W' and resid 254 through 256 Processing sheet with id= 70, first strand: chain 'X' and resid 180 through 188 removed outlier: 4.338A pdb=" N TYR X 350 " --> pdb=" O GLY X 331 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY X 331 " --> pdb=" O TYR X 350 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA X 352 " --> pdb=" O MET X 329 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N MET X 329 " --> pdb=" O ALA X 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR X 354 " --> pdb=" O LEU X 327 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU X 327 " --> pdb=" O THR X 354 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP X 356 " --> pdb=" O ALA X 325 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA X 325 " --> pdb=" O ASP X 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR X 303 " --> pdb=" O LEU X 327 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET X 329 " --> pdb=" O THR X 303 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER X 305 " --> pdb=" O MET X 329 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY X 331 " --> pdb=" O SER X 305 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE X 304 " --> pdb=" O ASP X 249 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER X 251 " --> pdb=" O ILE X 304 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASN X 306 " --> pdb=" O SER X 251 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'X' and resid 234 through 236 removed outlier: 3.970A pdb=" N GLU X 241 " --> pdb=" O ASP X 236 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'X' and resid 254 through 256 1752 hydrogen bonds defined for protein. 4968 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: 17.07 Time building geometry restraints manager: 17.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 15034 1.33 - 1.45: 6647 1.45 - 1.57: 22983 1.57 - 1.69: 0 1.69 - 1.80: 552 Bond restraints: 45216 Sorted by residual: bond pdb=" CG LEU N 353 " pdb=" CD2 LEU N 353 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.51e+00 bond pdb=" CG LEU Q 353 " pdb=" CD2 LEU Q 353 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.49e+00 bond pdb=" CG LEU T 353 " pdb=" CD2 LEU T 353 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.48e+00 bond pdb=" CG LEU I 353 " pdb=" CD2 LEU I 353 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.46e+00 bond pdb=" CG LEU E 353 " pdb=" CD2 LEU E 353 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.46e+00 ... (remaining 45211 not shown) Histogram of bond angle deviations from ideal: 95.79 - 102.98: 462 102.98 - 110.17: 11081 110.17 - 117.36: 21945 117.36 - 124.55: 26537 124.55 - 131.74: 911 Bond angle restraints: 60936 Sorted by residual: angle pdb=" C HIS N 207 " pdb=" N ASN N 208 " pdb=" CA ASN N 208 " ideal model delta sigma weight residual 122.82 128.23 -5.41 1.42e+00 4.96e-01 1.45e+01 angle pdb=" C HIS M 207 " pdb=" N ASN M 208 " pdb=" CA ASN M 208 " ideal model delta sigma weight residual 122.82 128.23 -5.41 1.42e+00 4.96e-01 1.45e+01 angle pdb=" C HIS D 207 " pdb=" N ASN D 208 " pdb=" CA ASN D 208 " ideal model delta sigma weight residual 122.82 128.20 -5.38 1.42e+00 4.96e-01 1.44e+01 angle pdb=" C HIS J 207 " pdb=" N ASN J 208 " pdb=" CA ASN J 208 " ideal model delta sigma weight residual 122.82 128.20 -5.38 1.42e+00 4.96e-01 1.44e+01 angle pdb=" C HIS G 207 " pdb=" N ASN G 208 " pdb=" CA ASN G 208 " ideal model delta sigma weight residual 122.82 128.20 -5.38 1.42e+00 4.96e-01 1.44e+01 ... (remaining 60931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 26910 16.89 - 33.77: 858 33.77 - 50.65: 144 50.65 - 67.54: 0 67.54 - 84.42: 48 Dihedral angle restraints: 27960 sinusoidal: 11616 harmonic: 16344 Sorted by residual: dihedral pdb=" CA ASN C 320 " pdb=" C ASN C 320 " pdb=" N PRO C 321 " pdb=" CA PRO C 321 " ideal model delta harmonic sigma weight residual -180.00 -155.44 -24.56 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ASN K 320 " pdb=" C ASN K 320 " pdb=" N PRO K 321 " pdb=" CA PRO K 321 " ideal model delta harmonic sigma weight residual 180.00 -155.45 -24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ASN R 320 " pdb=" C ASN R 320 " pdb=" N PRO R 321 " pdb=" CA PRO R 321 " ideal model delta harmonic sigma weight residual 180.00 -155.45 -24.55 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 27957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4155 0.054 - 0.109: 2172 0.109 - 0.163: 441 0.163 - 0.218: 168 0.218 - 0.272: 48 Chirality restraints: 6984 Sorted by residual: chirality pdb=" CB VAL D 351 " pdb=" CA VAL D 351 " pdb=" CG1 VAL D 351 " pdb=" CG2 VAL D 351 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB VAL M 351 " pdb=" CA VAL M 351 " pdb=" CG1 VAL M 351 " pdb=" CG2 VAL M 351 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB VAL J 351 " pdb=" CA VAL J 351 " pdb=" CG1 VAL J 351 " pdb=" CG2 VAL J 351 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 6981 not shown) Planarity restraints: 7968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 262 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO R 263 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO R 263 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 263 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL U 262 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.81e+00 pdb=" N PRO U 263 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO U 263 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO U 263 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 262 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.81e+00 pdb=" N PRO H 263 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO H 263 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 263 " -0.033 5.00e-02 4.00e+02 ... (remaining 7965 not shown) Histogram of nonbonded interaction distances: 0.43 - 1.32: 84 1.32 - 2.22: 432 2.22 - 3.11: 37015 3.11 - 4.01: 108626 4.01 - 4.90: 211566 Warning: very small nonbonded interaction distances. Nonbonded interactions: 357723 Sorted by model distance: nonbonded pdb=" CD2 LEU L 383 " pdb=" CA LEU X 383 " model vdw 0.426 3.890 nonbonded pdb=" CD2 LEU F 383 " pdb=" CA LEU Q 383 " model vdw 0.426 3.890 nonbonded pdb=" CD2 LEU E 383 " pdb=" CA LEU K 383 " model vdw 0.426 3.890 nonbonded pdb=" CA LEU A 383 " pdb=" CD2 LEU G 383 " model vdw 0.426 3.890 nonbonded pdb=" CD2 LEU B 383 " pdb=" CA LEU T 383 " model vdw 0.426 3.890 ... (remaining 357718 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' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.450 Check model and map are aligned: 0.650 Set scattering table: 0.390 Process input model: 112.160 Find NCS groups from input model: 3.080 Set up NCS constraints: 0.410 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:10.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1339 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 : 0.016 0.096 45216 Z= 1.034 Angle : 1.093 11.108 60936 Z= 0.597 Chirality : 0.067 0.272 6984 Planarity : 0.007 0.060 7968 Dihedral : 9.736 84.423 17352 Min Nonbonded Distance : 0.426 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -5.50 (0.09), residues: 5616 helix: -4.41 (0.07), residues: 1992 sheet: -2.89 (0.13), residues: 1464 loop : -3.10 (0.10), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.004 HIS I 330 PHE 0.033 0.004 PHE W 314 TYR 0.020 0.003 TYR H 355 ARG 0.017 0.001 ARG I 258 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 4776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 838 time to evaluate : 4.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 242 VAL cc_start: 0.2363 (t) cc_final: 0.2132 (m) REVERT: J 163 MET cc_start: 0.1082 (mmt) cc_final: 0.0569 (tmt) REVERT: J 302 PHE cc_start: 0.0805 (t80) cc_final: -0.0366 (t80) REVERT: Q 169 GLN cc_start: 0.2398 (mm110) cc_final: 0.1728 (mp10) outliers start: 0 outliers final: 4 residues processed: 838 average time/residue: 1.6675 time to fit residues: 1686.3850 Evaluate side-chains 532 residues out of total 4776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 528 time to evaluate : 4.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 329 MET Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain K residue 175 GLN Chi-restraints excluded: chain V residue 188 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 466 optimal weight: 3.9990 chunk 418 optimal weight: 0.8980 chunk 232 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 282 optimal weight: 0.7980 chunk 223 optimal weight: 0.9990 chunk 432 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 263 optimal weight: 8.9990 chunk 322 optimal weight: 20.0000 chunk 501 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN B 207 HIS ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN C 207 HIS C 228 GLN ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS ** E 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN F 193 GLN F 207 HIS F 228 GLN ** F 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 HIS H 267 ASN I 207 HIS ** I 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 357 HIS J 193 GLN J 207 HIS J 228 GLN K 185 ASN L 207 HIS L 228 GLN ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 185 ASN ** M 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 GLN ** N 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 GLN P 207 HIS P 228 GLN ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 228 GLN ** Q 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 185 ASN ** S 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 228 GLN ** T 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 175 GLN U 199 HIS U 228 GLN ** U 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 357 HIS X 193 GLN X 207 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2066 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 45216 Z= 0.235 Angle : 0.786 17.807 60936 Z= 0.405 Chirality : 0.049 0.331 6984 Planarity : 0.006 0.053 7968 Dihedral : 7.719 111.762 6226 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.76 % Allowed : 9.99 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -3.63 (0.10), residues: 5616 helix: -2.55 (0.10), residues: 2064 sheet: -2.04 (0.14), residues: 1392 loop : -2.23 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS G 199 PHE 0.031 0.002 PHE I 273 TYR 0.027 0.002 TYR J 350 ARG 0.012 0.001 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 4776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 656 time to evaluate : 4.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.7142 (mm110) REVERT: A 170 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7244 (pmm-80) REVERT: A 223 PHE cc_start: 0.7532 (t80) cc_final: 0.6947 (t80) REVERT: A 249 ASP cc_start: 0.7586 (p0) cc_final: 0.7291 (p0) REVERT: A 297 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7324 (mpp) REVERT: B 228 GLN cc_start: 0.0945 (mm-40) cc_final: 0.0651 (mp10) REVERT: B 349 MET cc_start: 0.2152 (pmm) cc_final: 0.0991 (pmm) REVERT: C 355 TYR cc_start: 0.1118 (p90) cc_final: 0.0749 (p90) REVERT: F 163 MET cc_start: -0.0830 (tmm) cc_final: -0.1326 (mmt) REVERT: G 180 MET cc_start: 0.0607 (mmt) cc_final: 0.0082 (mpp) REVERT: H 160 MET cc_start: 0.2346 (mpt) cc_final: 0.1704 (mpt) REVERT: H 172 LYS cc_start: 0.4135 (mmmt) cc_final: 0.3161 (mmtt) REVERT: H 313 LEU cc_start: 0.7498 (tp) cc_final: 0.7257 (tp) REVERT: J 163 MET cc_start: 0.1597 (mmt) cc_final: 0.0646 (tmt) REVERT: J 244 TYR cc_start: 0.0799 (OUTLIER) cc_final: -0.1481 (m-80) REVERT: J 302 PHE cc_start: 0.0775 (t80) cc_final: -0.0850 (t80) REVERT: K 160 MET cc_start: -0.1586 (OUTLIER) cc_final: -0.3005 (ptp) REVERT: K 180 MET cc_start: 0.1195 (tmt) cc_final: 0.0893 (tmm) REVERT: K 214 MET cc_start: 0.3148 (tmm) cc_final: 0.2390 (ttt) REVERT: K 297 MET cc_start: 0.0460 (OUTLIER) cc_final: -0.0131 (mmm) REVERT: K 357 HIS cc_start: 0.2618 (OUTLIER) cc_final: 0.2408 (t-90) REVERT: L 348 MET cc_start: -0.1701 (ttp) cc_final: -0.3513 (mmt) REVERT: M 297 MET cc_start: 0.3633 (mpp) cc_final: 0.3419 (mmp) REVERT: P 155 GLU cc_start: -0.0408 (pt0) cc_final: -0.1110 (tp30) REVERT: Q 195 MET cc_start: 0.2813 (tpp) cc_final: 0.2571 (tpt) REVERT: Q 302 PHE cc_start: -0.1162 (t80) cc_final: -0.1731 (t80) REVERT: Q 348 MET cc_start: 0.0044 (mmt) cc_final: -0.1929 (mtp) REVERT: Q 349 MET cc_start: 0.0466 (ppp) cc_final: -0.0551 (ttt) REVERT: R 189 MET cc_start: 0.1867 (mmm) cc_final: 0.1376 (mtt) REVERT: R 203 PHE cc_start: 0.7018 (OUTLIER) cc_final: 0.5549 (m-80) REVERT: S 329 MET cc_start: 0.4647 (mpt) cc_final: 0.4438 (mpp) REVERT: T 163 MET cc_start: 0.0178 (OUTLIER) cc_final: -0.0105 (tpt) REVERT: T 297 MET cc_start: -0.0882 (ttt) cc_final: -0.1226 (ttp) REVERT: V 246 ASP cc_start: 0.6583 (OUTLIER) cc_final: 0.6340 (m-30) REVERT: V 385 ASP cc_start: 0.6506 (t70) cc_final: 0.6286 (t70) REVERT: X 160 MET cc_start: -0.3403 (OUTLIER) cc_final: -0.5303 (ptp) REVERT: X 269 GLU cc_start: -0.0076 (mm-30) cc_final: -0.0355 (mp0) REVERT: X 358 ARG cc_start: 0.0464 (mtm180) cc_final: -0.0116 (mpt180) outliers start: 132 outliers final: 33 residues processed: 728 average time/residue: 1.6038 time to fit residues: 1423.5251 Evaluate side-chains 548 residues out of total 4776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 504 time to evaluate : 4.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 258 ARG Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain H residue 261 VAL Chi-restraints excluded: chain H residue 275 ASP Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain H residue 382 LEU Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain J residue 244 TYR Chi-restraints excluded: chain K residue 160 MET Chi-restraints excluded: chain K residue 249 ASP Chi-restraints excluded: chain K residue 297 MET Chi-restraints excluded: chain K residue 357 HIS Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain M residue 348 MET Chi-restraints excluded: chain N residue 244 TYR Chi-restraints excluded: chain N residue 280 ILE Chi-restraints excluded: chain Q residue 345 VAL Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain S residue 195 MET Chi-restraints excluded: chain S residue 223 PHE Chi-restraints excluded: chain S residue 276 ILE Chi-restraints excluded: chain T residue 163 MET Chi-restraints excluded: chain T residue 235 ILE Chi-restraints excluded: chain V residue 188 ASP Chi-restraints excluded: chain V residue 246 ASP Chi-restraints excluded: chain V residue 326 ILE Chi-restraints excluded: chain W residue 195 MET Chi-restraints excluded: chain W residue 339 ILE Chi-restraints excluded: chain X residue 160 MET Chi-restraints excluded: chain X residue 228 GLN Chi-restraints excluded: chain X residue 354 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 278 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 417 optimal weight: 4.9990 chunk 341 optimal weight: 0.0970 chunk 138 optimal weight: 30.0000 chunk 502 optimal weight: 0.9980 chunk 542 optimal weight: 5.9990 chunk 447 optimal weight: 5.9990 chunk 497 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 402 optimal weight: 0.0270 overall best weight: 1.4240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 185 ASN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 ASN E 228 GLN E 357 HIS ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 ASN F 193 GLN F 199 HIS F 323 GLN ** F 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 ASN H 185 ASN H 228 GLN H 323 GLN I 165 GLN I 228 GLN J 193 GLN J 228 GLN L 161 ASN ** L 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 HIS ** M 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 207 HIS P 267 ASN P 357 HIS ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 193 GLN ** Q 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 228 GLN ** T 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 175 GLN U 228 GLN ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 330 HIS X 185 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3011 moved from start: 0.7508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 45216 Z= 0.255 Angle : 0.781 14.650 60936 Z= 0.403 Chirality : 0.049 0.269 6984 Planarity : 0.006 0.090 7968 Dihedral : 6.700 72.593 6218 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.06 % Allowed : 13.55 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.88 (0.10), residues: 5616 helix: -2.00 (0.10), residues: 2064 sheet: -1.84 (0.13), residues: 1416 loop : -1.55 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.002 HIS W 357 PHE 0.032 0.003 PHE M 302 TYR 0.030 0.002 TYR M 355 ARG 0.032 0.001 ARG E 258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 4776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 684 time to evaluate : 5.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.7164 (mp10) REVERT: B 297 MET cc_start: 0.2628 (mtm) cc_final: 0.1857 (mtm) REVERT: B 319 ILE cc_start: 0.1178 (OUTLIER) cc_final: -0.0182 (tt) REVERT: C 355 TYR cc_start: 0.1477 (p90) cc_final: 0.0775 (p90) REVERT: D 286 LYS cc_start: 0.3730 (ttmt) cc_final: 0.3442 (ptpt) REVERT: E 160 MET cc_start: 0.2063 (mpp) cc_final: 0.1735 (mpp) REVERT: E 361 ASP cc_start: 0.6241 (t70) cc_final: 0.6017 (m-30) REVERT: E 371 LYS cc_start: 0.7947 (mttt) cc_final: 0.7719 (mppt) REVERT: F 348 MET cc_start: 0.2873 (OUTLIER) cc_final: -0.0311 (mpm) REVERT: G 161 ASN cc_start: 0.2611 (OUTLIER) cc_final: 0.2363 (p0) REVERT: G 180 MET cc_start: 0.1390 (mmt) cc_final: 0.0766 (pmm) REVERT: H 160 MET cc_start: 0.2318 (mpt) cc_final: 0.2060 (mpt) REVERT: H 188 ASP cc_start: 0.6994 (p0) cc_final: 0.6641 (p0) REVERT: H 205 LYS cc_start: 0.7283 (pptt) cc_final: 0.7047 (ptpp) REVERT: J 163 MET cc_start: 0.2243 (mmt) cc_final: 0.0566 (tmt) REVERT: J 244 TYR cc_start: 0.0920 (OUTLIER) cc_final: -0.1387 (m-80) REVERT: J 302 PHE cc_start: 0.2636 (t80) cc_final: 0.0501 (t80) REVERT: J 336 PRO cc_start: 0.2845 (Cg_endo) cc_final: 0.2581 (Cg_exo) REVERT: K 297 MET cc_start: 0.1142 (mmm) cc_final: 0.0621 (mmm) REVERT: K 357 HIS cc_start: 0.3467 (OUTLIER) cc_final: 0.2440 (t-90) REVERT: L 349 MET cc_start: 0.1684 (tpt) cc_final: 0.1153 (mmm) REVERT: M 160 MET cc_start: 0.1887 (OUTLIER) cc_final: 0.1668 (mmt) REVERT: N 297 MET cc_start: 0.4502 (tpt) cc_final: 0.2523 (mpp) REVERT: N 378 ASP cc_start: 0.7769 (p0) cc_final: 0.7532 (p0) REVERT: O 169 GLN cc_start: 0.1835 (tp-100) cc_final: 0.1323 (mt0) REVERT: O 203 PHE cc_start: -0.0731 (OUTLIER) cc_final: -0.1302 (t80) REVERT: O 302 PHE cc_start: 0.1779 (t80) cc_final: -0.0472 (t80) REVERT: P 155 GLU cc_start: 0.0281 (pt0) cc_final: -0.0983 (tm-30) REVERT: P 189 MET cc_start: 0.3471 (mmm) cc_final: 0.3107 (mpp) REVERT: P 297 MET cc_start: -0.0721 (ttt) cc_final: -0.1038 (ttp) REVERT: Q 163 MET cc_start: 0.2849 (mmm) cc_final: 0.2500 (mmp) REVERT: R 160 MET cc_start: -0.1172 (OUTLIER) cc_final: -0.1456 (pmm) REVERT: R 180 MET cc_start: 0.1739 (OUTLIER) cc_final: 0.1213 (pmm) REVERT: R 205 LYS cc_start: 0.7889 (pttt) cc_final: 0.7576 (mmmt) REVERT: R 260 LEU cc_start: 0.1768 (OUTLIER) cc_final: 0.0890 (pp) REVERT: S 180 MET cc_start: 0.1066 (tmt) cc_final: 0.0169 (tmt) REVERT: T 163 MET cc_start: 0.1456 (OUTLIER) cc_final: 0.0991 (tpt) REVERT: T 189 MET cc_start: 0.3568 (mmm) cc_final: 0.2680 (mpp) REVERT: T 297 MET cc_start: -0.1273 (ttt) cc_final: -0.1681 (ttp) REVERT: U 163 MET cc_start: 0.4418 (mpm) cc_final: 0.3951 (mmm) REVERT: U 165 GLN cc_start: 0.2740 (pt0) cc_final: 0.2269 (mm110) REVERT: X 160 MET cc_start: -0.3485 (mtt) cc_final: -0.4666 (ptp) REVERT: X 163 MET cc_start: 0.2186 (tpt) cc_final: 0.0925 (ppp) REVERT: X 180 MET cc_start: 0.0333 (ttp) cc_final: -0.0068 (tmm) REVERT: X 358 ARG cc_start: -0.0278 (mtm180) cc_final: -0.0754 (mtp-110) outliers start: 194 outliers final: 56 residues processed: 796 average time/residue: 1.4852 time to fit residues: 1459.3555 Evaluate side-chains 581 residues out of total 4776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 513 time to evaluate : 4.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain E residue 275 ASP Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain G residue 161 ASN Chi-restraints excluded: chain G residue 348 MET Chi-restraints excluded: chain G residue 349 MET Chi-restraints excluded: chain H residue 261 VAL Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain H residue 369 LEU Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 251 SER Chi-restraints excluded: chain I residue 298 ASP Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain J residue 203 PHE Chi-restraints excluded: chain J residue 244 TYR Chi-restraints excluded: chain K residue 161 ASN Chi-restraints excluded: chain K residue 249 ASP Chi-restraints excluded: chain K residue 357 HIS Chi-restraints excluded: chain L residue 249 ASP Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 337 VAL Chi-restraints excluded: chain L residue 339 ILE Chi-restraints excluded: chain L residue 345 VAL Chi-restraints excluded: chain M residue 160 MET Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 205 LYS Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain M residue 348 MET Chi-restraints excluded: chain N residue 280 ILE Chi-restraints excluded: chain O residue 161 ASN Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain P residue 161 ASN Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 348 MET Chi-restraints excluded: chain P residue 357 HIS Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Q residue 345 VAL Chi-restraints excluded: chain R residue 160 MET Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 360 ILE Chi-restraints excluded: chain S residue 161 ASN Chi-restraints excluded: chain S residue 177 THR Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain S residue 276 ILE Chi-restraints excluded: chain T residue 163 MET Chi-restraints excluded: chain T residue 235 ILE Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain T residue 278 ARG Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 376 VAL Chi-restraints excluded: chain W residue 339 ILE Chi-restraints excluded: chain X residue 213 PHE Chi-restraints excluded: chain X residue 354 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 496 optimal weight: 10.0000 chunk 377 optimal weight: 10.0000 chunk 260 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 239 optimal weight: 0.5980 chunk 337 optimal weight: 3.9990 chunk 503 optimal weight: 3.9990 chunk 533 optimal weight: 6.9990 chunk 263 optimal weight: 0.6980 chunk 477 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS C 199 HIS C 330 HIS ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 ASN ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 161 ASN I 208 ASN ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 GLN ** M 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 267 ASN ** N 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 323 GLN ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 330 HIS R 175 GLN ** R 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 207 HIS S 357 HIS ** T 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 357 HIS U 175 GLN ** V 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 226 GLN X 199 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3069 moved from start: 0.8178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 45216 Z= 0.178 Angle : 0.654 10.148 60936 Z= 0.333 Chirality : 0.045 0.215 6984 Planarity : 0.005 0.057 7968 Dihedral : 5.977 73.106 6216 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.79 % Allowed : 17.29 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.30 (0.11), residues: 5616 helix: -1.37 (0.11), residues: 1992 sheet: -1.60 (0.13), residues: 1416 loop : -1.35 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.021 0.001 HIS E 207 PHE 0.026 0.002 PHE V 213 TYR 0.017 0.001 TYR X 350 ARG 0.009 0.000 ARG I 288 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 4776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 558 time to evaluate : 4.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.7665 (tpt170) cc_final: 0.7386 (tpm-80) REVERT: A 170 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7440 (pmm-80) REVERT: A 185 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8175 (m110) REVERT: A 249 ASP cc_start: 0.7767 (p0) cc_final: 0.7480 (p0) REVERT: B 163 MET cc_start: 0.3388 (OUTLIER) cc_final: 0.3017 (pp-130) REVERT: B 180 MET cc_start: 0.1946 (tpp) cc_final: 0.0315 (ttp) REVERT: B 217 PHE cc_start: -0.0485 (OUTLIER) cc_final: -0.0885 (t80) REVERT: B 319 ILE cc_start: 0.1174 (OUTLIER) cc_final: 0.0051 (tt) REVERT: B 386 LEU cc_start: 0.6363 (tp) cc_final: 0.6099 (tp) REVERT: C 180 MET cc_start: 0.2474 (tpp) cc_final: 0.2238 (tpt) REVERT: C 297 MET cc_start: 0.2777 (mpp) cc_final: 0.2020 (pmm) REVERT: C 335 ARG cc_start: 0.2458 (OUTLIER) cc_final: 0.1026 (mpp80) REVERT: C 355 TYR cc_start: 0.1212 (p90) cc_final: 0.0623 (p90) REVERT: D 349 MET cc_start: -0.0019 (ppp) cc_final: -0.1871 (ppp) REVERT: F 348 MET cc_start: 0.2800 (OUTLIER) cc_final: -0.0423 (mpm) REVERT: G 348 MET cc_start: 0.2066 (OUTLIER) cc_final: -0.0558 (mtp) REVERT: H 369 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8466 (tp) REVERT: I 163 MET cc_start: 0.5194 (mpt) cc_final: 0.4655 (ppp) REVERT: J 163 MET cc_start: 0.2247 (mmt) cc_final: 0.0501 (tmt) REVERT: J 244 TYR cc_start: 0.0941 (OUTLIER) cc_final: -0.1431 (m-80) REVERT: J 380 ARG cc_start: 0.5875 (OUTLIER) cc_final: 0.5325 (ptm160) REVERT: K 214 MET cc_start: 0.4008 (OUTLIER) cc_final: 0.2744 (ttm) REVERT: K 297 MET cc_start: 0.0836 (OUTLIER) cc_final: 0.0493 (mmm) REVERT: K 357 HIS cc_start: 0.3695 (OUTLIER) cc_final: 0.3350 (t-90) REVERT: L 195 MET cc_start: 0.2481 (tpp) cc_final: 0.1600 (tpt) REVERT: L 271 MET cc_start: 0.3682 (tpp) cc_final: 0.3428 (mmp) REVERT: L 348 MET cc_start: -0.1105 (OUTLIER) cc_final: -0.2966 (mmt) REVERT: M 160 MET cc_start: 0.2104 (OUTLIER) cc_final: 0.1818 (mmt) REVERT: O 160 MET cc_start: -0.1855 (OUTLIER) cc_final: -0.2701 (mtt) REVERT: O 163 MET cc_start: 0.1128 (OUTLIER) cc_final: 0.0211 (mmm) REVERT: O 189 MET cc_start: 0.1741 (tpp) cc_final: 0.0900 (ttp) REVERT: O 203 PHE cc_start: -0.0449 (OUTLIER) cc_final: -0.1070 (t80) REVERT: O 302 PHE cc_start: 0.1086 (t80) cc_final: -0.1039 (t80) REVERT: P 189 MET cc_start: 0.3872 (mmm) cc_final: 0.3051 (mpp) REVERT: Q 163 MET cc_start: 0.3579 (mmm) cc_final: 0.3182 (mmp) REVERT: Q 271 MET cc_start: 0.2156 (OUTLIER) cc_final: 0.1867 (mpt) REVERT: Q 329 MET cc_start: -0.1119 (OUTLIER) cc_final: -0.1793 (tmm) REVERT: R 160 MET cc_start: -0.1196 (OUTLIER) cc_final: -0.1581 (pmm) REVERT: R 180 MET cc_start: 0.1553 (OUTLIER) cc_final: -0.4155 (ttt) REVERT: R 205 LYS cc_start: 0.7845 (pttt) cc_final: 0.7499 (mmmt) REVERT: R 273 PHE cc_start: 0.6518 (OUTLIER) cc_final: 0.6273 (t80) REVERT: S 180 MET cc_start: 0.0687 (tmt) cc_final: 0.0129 (tmt) REVERT: S 329 MET cc_start: 0.4326 (mpt) cc_final: 0.4112 (mpp) REVERT: S 348 MET cc_start: 0.4491 (ppp) cc_final: 0.1865 (tpt) REVERT: T 163 MET cc_start: 0.1626 (mmp) cc_final: 0.1396 (tpt) REVERT: T 297 MET cc_start: -0.0824 (ttt) cc_final: -0.1097 (ttp) REVERT: V 329 MET cc_start: 0.8234 (mpp) cc_final: 0.8031 (mpp) REVERT: W 378 ASP cc_start: 0.7206 (p0) cc_final: 0.6655 (p0) REVERT: X 160 MET cc_start: -0.3443 (OUTLIER) cc_final: -0.3823 (ptp) REVERT: X 163 MET cc_start: 0.2075 (tpt) cc_final: 0.0915 (ppp) REVERT: X 180 MET cc_start: 0.0582 (ttp) cc_final: 0.0288 (tmm) REVERT: X 326 ILE cc_start: 0.6875 (OUTLIER) cc_final: 0.6587 (pt) REVERT: X 358 ARG cc_start: -0.0402 (mtm180) cc_final: -0.0960 (mtp180) outliers start: 181 outliers final: 51 residues processed: 658 average time/residue: 1.5290 time to fit residues: 1237.7910 Evaluate side-chains 563 residues out of total 4776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 486 time to evaluate : 4.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 348 MET Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 189 MET Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 348 MET Chi-restraints excluded: chain H residue 261 VAL Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain H residue 369 LEU Chi-restraints excluded: chain I residue 323 GLN Chi-restraints excluded: chain J residue 160 MET Chi-restraints excluded: chain J residue 188 ASP Chi-restraints excluded: chain J residue 244 TYR Chi-restraints excluded: chain J residue 380 ARG Chi-restraints excluded: chain K residue 189 MET Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 249 ASP Chi-restraints excluded: chain K residue 297 MET Chi-restraints excluded: chain K residue 348 MET Chi-restraints excluded: chain K residue 357 HIS Chi-restraints excluded: chain L residue 348 MET Chi-restraints excluded: chain M residue 160 MET Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain M residue 348 MET Chi-restraints excluded: chain N residue 221 SER Chi-restraints excluded: chain N residue 280 ILE Chi-restraints excluded: chain N residue 318 ILE Chi-restraints excluded: chain N residue 348 MET Chi-restraints excluded: chain O residue 160 MET Chi-restraints excluded: chain O residue 163 MET Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 251 SER Chi-restraints excluded: chain Q residue 271 MET Chi-restraints excluded: chain Q residue 329 MET Chi-restraints excluded: chain Q residue 339 ILE Chi-restraints excluded: chain Q residue 345 VAL Chi-restraints excluded: chain R residue 160 MET Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 273 PHE Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 348 MET Chi-restraints excluded: chain S residue 260 LEU Chi-restraints excluded: chain S residue 276 ILE Chi-restraints excluded: chain T residue 195 MET Chi-restraints excluded: chain T residue 378 ASP Chi-restraints excluded: chain U residue 171 LEU Chi-restraints excluded: chain U residue 188 ASP Chi-restraints excluded: chain U residue 337 VAL Chi-restraints excluded: chain V residue 204 LEU Chi-restraints excluded: chain V residue 221 SER Chi-restraints excluded: chain W residue 339 ILE Chi-restraints excluded: chain X residue 160 MET Chi-restraints excluded: chain X residue 324 SER Chi-restraints excluded: chain X residue 326 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 444 optimal weight: 0.9990 chunk 302 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 397 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 455 optimal weight: 0.0010 chunk 368 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 272 optimal weight: 6.9990 chunk 478 optimal weight: 0.0020 chunk 134 optimal weight: 0.8980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 HIS ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 ASN E 199 HIS E 226 GLN ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 357 HIS G 176 ASN ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 228 GLN ** N 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 169 GLN O 193 GLN P 323 GLN P 357 HIS Q 161 ASN ** R 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 165 GLN T 357 HIS U 161 ASN U 185 ASN ** V 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 228 GLN X 161 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3176 moved from start: 0.8815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 45216 Z= 0.166 Angle : 0.629 10.278 60936 Z= 0.318 Chirality : 0.044 0.211 6984 Planarity : 0.004 0.059 7968 Dihedral : 5.562 85.261 6216 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.43 % Allowed : 18.51 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.79 (0.11), residues: 5616 helix: -0.95 (0.12), residues: 1992 sheet: -1.20 (0.15), residues: 1128 loop : -1.22 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS N 330 PHE 0.047 0.002 PHE O 217 TYR 0.023 0.001 TYR F 247 ARG 0.011 0.000 ARG I 198 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 4776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 553 time to evaluate : 4.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7367 (mpp80) REVERT: A 249 ASP cc_start: 0.7760 (p0) cc_final: 0.7453 (p0) REVERT: B 163 MET cc_start: 0.3781 (OUTLIER) cc_final: 0.3185 (pp-130) REVERT: B 180 MET cc_start: 0.1773 (tpp) cc_final: 0.1125 (ttp) REVERT: B 214 MET cc_start: -0.0155 (mmm) cc_final: -0.0371 (mmm) REVERT: B 217 PHE cc_start: -0.0628 (OUTLIER) cc_final: -0.1036 (t80) REVERT: B 319 ILE cc_start: 0.1139 (OUTLIER) cc_final: 0.0081 (tt) REVERT: B 329 MET cc_start: 0.0860 (mpp) cc_final: 0.0465 (mpt) REVERT: B 349 MET cc_start: 0.2124 (OUTLIER) cc_final: 0.0686 (mpm) REVERT: C 160 MET cc_start: -0.3022 (ptt) cc_final: -0.3243 (ptt) REVERT: C 297 MET cc_start: 0.2481 (mpp) cc_final: 0.1739 (pmm) REVERT: C 355 TYR cc_start: 0.1216 (p90) cc_final: 0.0588 (p90) REVERT: D 170 ARG cc_start: 0.4036 (OUTLIER) cc_final: 0.3671 (mmt90) REVERT: F 327 LEU cc_start: 0.4488 (OUTLIER) cc_final: 0.4129 (tm) REVERT: F 348 MET cc_start: 0.2991 (OUTLIER) cc_final: -0.0214 (mpm) REVERT: G 163 MET cc_start: 0.4280 (OUTLIER) cc_final: 0.3055 (ttt) REVERT: G 195 MET cc_start: 0.3542 (OUTLIER) cc_final: 0.3195 (mpt) REVERT: G 295 GLU cc_start: 0.4224 (tp30) cc_final: 0.3058 (tm-30) REVERT: G 329 MET cc_start: 0.3378 (mpt) cc_final: 0.3031 (mpt) REVERT: G 348 MET cc_start: 0.1991 (tpp) cc_final: -0.0906 (mtt) REVERT: H 160 MET cc_start: 0.2503 (mpt) cc_final: 0.2119 (mpt) REVERT: H 369 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8431 (tp) REVERT: I 160 MET cc_start: -0.0558 (pmm) cc_final: -0.1806 (ttp) REVERT: I 163 MET cc_start: 0.5275 (mpt) cc_final: 0.4696 (ppp) REVERT: I 385 ASP cc_start: 0.5504 (m-30) cc_final: 0.5004 (m-30) REVERT: J 163 MET cc_start: 0.2260 (mmt) cc_final: 0.0577 (tmt) REVERT: J 217 PHE cc_start: 0.3221 (m-10) cc_final: 0.2864 (m-80) REVERT: J 350 TYR cc_start: 0.1887 (OUTLIER) cc_final: 0.1532 (m-80) REVERT: K 214 MET cc_start: 0.3488 (tmm) cc_final: 0.2590 (mtt) REVERT: K 297 MET cc_start: 0.0711 (OUTLIER) cc_final: 0.0426 (mmm) REVERT: L 195 MET cc_start: 0.2327 (tpp) cc_final: 0.1860 (tpp) REVERT: L 348 MET cc_start: -0.1136 (OUTLIER) cc_final: -0.2963 (mmt) REVERT: N 297 MET cc_start: 0.4779 (tpt) cc_final: 0.2726 (mpp) REVERT: O 163 MET cc_start: 0.0858 (OUTLIER) cc_final: 0.0178 (mmm) REVERT: O 169 GLN cc_start: 0.2751 (OUTLIER) cc_final: 0.0961 (mt0) REVERT: O 302 PHE cc_start: 0.1018 (t80) cc_final: -0.0962 (t80) REVERT: P 189 MET cc_start: 0.3768 (mmm) cc_final: 0.3029 (mpp) REVERT: Q 163 MET cc_start: 0.4021 (mmm) cc_final: 0.3725 (mmp) REVERT: Q 329 MET cc_start: -0.1127 (OUTLIER) cc_final: -0.2151 (tmm) REVERT: R 205 LYS cc_start: 0.7833 (pttt) cc_final: 0.7565 (mmmt) REVERT: R 260 LEU cc_start: 0.1510 (OUTLIER) cc_final: 0.0740 (pp) REVERT: R 273 PHE cc_start: 0.6690 (OUTLIER) cc_final: 0.6408 (t80) REVERT: S 180 MET cc_start: 0.0588 (tmt) cc_final: -0.0148 (tmt) REVERT: S 329 MET cc_start: 0.4287 (mpt) cc_final: 0.3836 (mpp) REVERT: S 348 MET cc_start: 0.4202 (ppp) cc_final: 0.1903 (tpp) REVERT: T 195 MET cc_start: 0.1383 (OUTLIER) cc_final: 0.1042 (mmp) REVERT: T 214 MET cc_start: 0.0995 (tpt) cc_final: 0.0440 (tmt) REVERT: T 297 MET cc_start: -0.0549 (ttt) cc_final: -0.0813 (ttp) REVERT: U 160 MET cc_start: 0.0639 (pmm) cc_final: -0.1878 (mmt) REVERT: W 330 HIS cc_start: 0.4546 (m170) cc_final: 0.4018 (m90) REVERT: W 378 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.6895 (p0) REVERT: X 160 MET cc_start: -0.3300 (mtt) cc_final: -0.4032 (ptp) REVERT: X 163 MET cc_start: 0.2309 (tpt) cc_final: 0.1082 (ppp) REVERT: X 214 MET cc_start: 0.4511 (tmt) cc_final: 0.4195 (tmm) REVERT: X 326 ILE cc_start: 0.6681 (OUTLIER) cc_final: 0.6343 (pt) outliers start: 164 outliers final: 52 residues processed: 639 average time/residue: 1.5377 time to fit residues: 1207.1541 Evaluate side-chains 561 residues out of total 4776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 487 time to evaluate : 4.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 348 MET Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 163 MET Chi-restraints excluded: chain G residue 189 MET Chi-restraints excluded: chain G residue 195 MET Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain H residue 226 GLN Chi-restraints excluded: chain H residue 261 VAL Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain H residue 369 LEU Chi-restraints excluded: chain I residue 323 GLN Chi-restraints excluded: chain J residue 185 ASN Chi-restraints excluded: chain J residue 350 TYR Chi-restraints excluded: chain K residue 161 ASN Chi-restraints excluded: chain K residue 189 MET Chi-restraints excluded: chain K residue 249 ASP Chi-restraints excluded: chain K residue 297 MET Chi-restraints excluded: chain L residue 348 MET Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain M residue 348 MET Chi-restraints excluded: chain N residue 280 ILE Chi-restraints excluded: chain N residue 318 ILE Chi-restraints excluded: chain O residue 163 MET Chi-restraints excluded: chain O residue 169 GLN Chi-restraints excluded: chain P residue 161 ASN Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain Q residue 231 VAL Chi-restraints excluded: chain Q residue 329 MET Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 273 PHE Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 348 MET Chi-restraints excluded: chain S residue 214 MET Chi-restraints excluded: chain S residue 260 LEU Chi-restraints excluded: chain S residue 276 ILE Chi-restraints excluded: chain T residue 195 MET Chi-restraints excluded: chain T residue 378 ASP Chi-restraints excluded: chain U residue 171 LEU Chi-restraints excluded: chain U residue 188 ASP Chi-restraints excluded: chain U residue 337 VAL Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 204 LEU Chi-restraints excluded: chain W residue 339 ILE Chi-restraints excluded: chain W residue 378 ASP Chi-restraints excluded: chain X residue 213 PHE Chi-restraints excluded: chain X residue 324 SER Chi-restraints excluded: chain X residue 326 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 179 optimal weight: 2.9990 chunk 480 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 313 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 534 optimal weight: 10.0000 chunk 443 optimal weight: 7.9990 chunk 247 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 280 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 ASN E 207 HIS E 226 GLN ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 HIS F 161 ASN ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 HIS H 191 ASN H 207 HIS I 208 ASN K 267 ASN ** K 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 HIS ** M 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 207 HIS ** N 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 GLN P 323 GLN ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 207 HIS R 267 ASN S 176 ASN S 199 HIS ** S 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 267 ASN U 193 GLN V 165 GLN V 199 HIS V 226 GLN ** V 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3994 moved from start: 1.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 45216 Z= 0.362 Angle : 0.901 13.986 60936 Z= 0.464 Chirality : 0.052 0.263 6984 Planarity : 0.006 0.071 7968 Dihedral : 6.787 89.705 6216 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.47 % Favored : 94.50 % Rotamer: Outliers : 4.46 % Allowed : 19.41 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.38 (0.10), residues: 5616 helix: -1.54 (0.11), residues: 2009 sheet: -1.58 (0.14), residues: 1188 loop : -1.41 (0.12), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.002 HIS N 330 PHE 0.066 0.004 PHE N 314 TYR 0.031 0.003 TYR L 350 ARG 0.017 0.001 ARG K 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 4776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 675 time to evaluate : 5.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7504 (pmm-80) REVERT: A 349 MET cc_start: 0.8633 (ttm) cc_final: 0.8404 (ttm) REVERT: B 160 MET cc_start: -0.0803 (ptt) cc_final: -0.1323 (ptp) REVERT: B 214 MET cc_start: -0.0442 (mmm) cc_final: -0.0844 (mmm) REVERT: B 297 MET cc_start: 0.2329 (mtm) cc_final: 0.1617 (mtm) REVERT: B 314 PHE cc_start: 0.1182 (p90) cc_final: 0.0453 (p90) REVERT: B 344 GLU cc_start: 0.8085 (pm20) cc_final: 0.7854 (pm20) REVERT: B 349 MET cc_start: 0.2754 (pmm) cc_final: 0.1672 (mpp) REVERT: C 335 ARG cc_start: 0.3102 (OUTLIER) cc_final: 0.1592 (mpp80) REVERT: C 350 TYR cc_start: 0.2727 (m-80) cc_final: 0.2449 (m-80) REVERT: D 170 ARG cc_start: 0.3972 (OUTLIER) cc_final: 0.3619 (mmt90) REVERT: E 160 MET cc_start: 0.2320 (mpp) cc_final: 0.1732 (mtt) REVERT: F 348 MET cc_start: 0.2615 (OUTLIER) cc_final: -0.0226 (mpm) REVERT: G 348 MET cc_start: 0.2334 (OUTLIER) cc_final: -0.0311 (tpp) REVERT: H 369 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8526 (tp) REVERT: I 160 MET cc_start: -0.0163 (pmm) cc_final: -0.1567 (ttp) REVERT: I 163 MET cc_start: 0.4867 (mpt) cc_final: 0.4591 (ppp) REVERT: J 160 MET cc_start: -0.3438 (OUTLIER) cc_final: -0.3710 (ptt) REVERT: J 244 TYR cc_start: 0.1561 (OUTLIER) cc_final: -0.1054 (m-80) REVERT: K 170 ARG cc_start: -0.0810 (ptp-170) cc_final: -0.1040 (tpp-160) REVERT: K 214 MET cc_start: 0.3759 (tmm) cc_final: 0.2306 (mtt) REVERT: K 297 MET cc_start: 0.1217 (mmm) cc_final: 0.0786 (mmm) REVERT: L 271 MET cc_start: 0.3221 (mmp) cc_final: 0.2666 (mtm) REVERT: N 280 ILE cc_start: 0.5096 (OUTLIER) cc_final: 0.4786 (mt) REVERT: O 163 MET cc_start: 0.0722 (OUTLIER) cc_final: 0.0165 (mmm) REVERT: O 203 PHE cc_start: -0.0567 (OUTLIER) cc_final: -0.0990 (t80) REVERT: O 302 PHE cc_start: 0.2140 (t80) cc_final: 0.0364 (t80) REVERT: P 189 MET cc_start: 0.3925 (mmm) cc_final: 0.3298 (mpp) REVERT: P 297 MET cc_start: -0.0974 (ttt) cc_final: -0.1360 (ttp) REVERT: Q 183 THR cc_start: 0.1631 (OUTLIER) cc_final: 0.1171 (t) REVERT: Q 230 VAL cc_start: -0.0837 (OUTLIER) cc_final: -0.1255 (m) REVERT: Q 271 MET cc_start: 0.3721 (OUTLIER) cc_final: 0.2528 (pp-130) REVERT: R 163 MET cc_start: 0.4378 (OUTLIER) cc_final: 0.3952 (mmm) REVERT: R 172 LYS cc_start: 0.3416 (OUTLIER) cc_final: 0.2327 (mmtt) REVERT: R 180 MET cc_start: 0.1769 (OUTLIER) cc_final: -0.4261 (ttt) REVERT: R 205 LYS cc_start: 0.8219 (pttt) cc_final: 0.8004 (mmmt) REVERT: R 260 LEU cc_start: 0.0735 (OUTLIER) cc_final: -0.0013 (pp) REVERT: R 360 ILE cc_start: 0.5349 (OUTLIER) cc_final: 0.4469 (mt) REVERT: S 180 MET cc_start: 0.0531 (tmt) cc_final: -0.1784 (ttp) REVERT: S 195 MET cc_start: 0.3608 (mpt) cc_final: 0.3350 (mpt) REVERT: S 249 ASP cc_start: 0.4265 (p0) cc_final: 0.4055 (p0) REVERT: S 297 MET cc_start: 0.2694 (mmt) cc_final: 0.2361 (mmt) REVERT: T 163 MET cc_start: 0.2364 (tpt) cc_final: 0.1412 (mmm) REVERT: T 189 MET cc_start: 0.3960 (mmm) cc_final: 0.3282 (mpp) REVERT: T 214 MET cc_start: 0.1391 (tpt) cc_final: 0.1132 (tmm) REVERT: T 297 MET cc_start: -0.0992 (ttt) cc_final: -0.1408 (ttp) REVERT: T 329 MET cc_start: 0.1845 (OUTLIER) cc_final: 0.0053 (pmm) REVERT: U 160 MET cc_start: 0.0515 (pmm) cc_final: -0.1403 (mmt) REVERT: V 194 GLU cc_start: 0.7250 (pp20) cc_final: 0.7016 (pp20) REVERT: W 215 SER cc_start: 0.8351 (p) cc_final: 0.8095 (p) REVERT: W 258 ARG cc_start: 0.3325 (pmt170) cc_final: 0.2781 (tmm-80) REVERT: W 344 GLU cc_start: 0.7855 (pm20) cc_final: 0.7570 (pm20) REVERT: X 160 MET cc_start: -0.3210 (OUTLIER) cc_final: -0.4642 (ptp) REVERT: X 186 GLU cc_start: -0.0856 (OUTLIER) cc_final: -0.2768 (mm-30) REVERT: X 214 MET cc_start: 0.4270 (tmt) cc_final: 0.3976 (tmm) REVERT: X 326 ILE cc_start: 0.7153 (OUTLIER) cc_final: 0.6431 (pp) REVERT: X 361 ASP cc_start: 0.5346 (OUTLIER) cc_final: 0.5132 (m-30) outliers start: 213 outliers final: 61 residues processed: 800 average time/residue: 1.5079 time to fit residues: 1481.1250 Evaluate side-chains 623 residues out of total 4776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 538 time to evaluate : 4.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 348 MET Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain H residue 369 LEU Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 323 GLN Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain J residue 160 MET Chi-restraints excluded: chain J residue 244 TYR Chi-restraints excluded: chain J residue 339 ILE Chi-restraints excluded: chain K residue 249 ASP Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 192 ILE Chi-restraints excluded: chain L residue 200 LYS Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 314 PHE Chi-restraints excluded: chain L residue 349 MET Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 208 ASN Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain M residue 348 MET Chi-restraints excluded: chain N residue 249 ASP Chi-restraints excluded: chain N residue 280 ILE Chi-restraints excluded: chain N residue 318 ILE Chi-restraints excluded: chain O residue 161 ASN Chi-restraints excluded: chain O residue 163 MET Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 351 VAL Chi-restraints excluded: chain P residue 161 ASN Chi-restraints excluded: chain P residue 357 HIS Chi-restraints excluded: chain Q residue 183 THR Chi-restraints excluded: chain Q residue 230 VAL Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Q residue 271 MET Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 172 LYS Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 273 PHE Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 360 ILE Chi-restraints excluded: chain S residue 161 ASN Chi-restraints excluded: chain S residue 247 TYR Chi-restraints excluded: chain S residue 265 ILE Chi-restraints excluded: chain S residue 276 ILE Chi-restraints excluded: chain T residue 329 MET Chi-restraints excluded: chain T residue 357 HIS Chi-restraints excluded: chain T residue 378 ASP Chi-restraints excluded: chain U residue 188 ASP Chi-restraints excluded: chain U residue 327 LEU Chi-restraints excluded: chain U residue 351 VAL Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 221 SER Chi-restraints excluded: chain X residue 160 MET Chi-restraints excluded: chain X residue 186 GLU Chi-restraints excluded: chain X residue 326 ILE Chi-restraints excluded: chain X residue 361 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 514 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 304 optimal weight: 0.3980 chunk 390 optimal weight: 0.7980 chunk 302 optimal weight: 0.9980 chunk 449 optimal weight: 9.9990 chunk 298 optimal weight: 0.9990 chunk 532 optimal weight: 0.9990 chunk 332 optimal weight: 3.9990 chunk 324 optimal weight: 20.0000 chunk 245 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 ASN I 185 ASN ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 GLN N 228 GLN O 176 ASN O 228 GLN P 185 ASN P 323 GLN ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 323 GLN Q 357 HIS R 228 GLN ** R 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 226 GLN ** V 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 323 GLN ** W 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3869 moved from start: 1.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 45216 Z= 0.200 Angle : 0.696 11.047 60936 Z= 0.352 Chirality : 0.045 0.196 6984 Planarity : 0.005 0.063 7968 Dihedral : 5.904 86.430 6216 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.16 % Allowed : 23.07 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.82 (0.11), residues: 5616 helix: -0.97 (0.11), residues: 2014 sheet: -1.36 (0.14), residues: 1195 loop : -1.15 (0.12), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS N 207 PHE 0.039 0.002 PHE N 314 TYR 0.021 0.001 TYR B 350 ARG 0.013 0.001 ARG R 266 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 4776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 578 time to evaluate : 4.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.7254 (mmm160) cc_final: 0.6812 (tpt170) REVERT: A 170 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7438 (mpp80) REVERT: A 185 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8195 (m110) REVERT: B 160 MET cc_start: -0.0915 (ptt) cc_final: -0.1407 (ptp) REVERT: B 163 MET cc_start: 0.3952 (pp-130) cc_final: 0.3646 (tmt) REVERT: B 297 MET cc_start: 0.2097 (mtm) cc_final: 0.1566 (mtm) REVERT: B 314 PHE cc_start: 0.1409 (p90) cc_final: 0.0560 (p90) REVERT: C 297 MET cc_start: 0.2716 (mpp) cc_final: 0.1797 (pmm) REVERT: D 192 ILE cc_start: 0.7010 (mm) cc_final: 0.6668 (mm) REVERT: D 241 GLU cc_start: 0.1591 (tp30) cc_final: 0.0915 (mm-30) REVERT: D 286 LYS cc_start: 0.2519 (pttm) cc_final: 0.1963 (ttmt) REVERT: E 160 MET cc_start: 0.2063 (mpp) cc_final: 0.1658 (mtt) REVERT: E 297 MET cc_start: 0.5422 (tmm) cc_final: 0.4698 (tpt) REVERT: F 329 MET cc_start: 0.2928 (pmm) cc_final: 0.2578 (ppp) REVERT: F 348 MET cc_start: 0.2445 (OUTLIER) cc_final: -0.0582 (mpm) REVERT: F 357 HIS cc_start: 0.1385 (OUTLIER) cc_final: 0.0263 (t70) REVERT: F 382 LEU cc_start: 0.0940 (OUTLIER) cc_final: 0.0252 (pt) REVERT: G 163 MET cc_start: 0.4176 (OUTLIER) cc_final: 0.3352 (mmm) REVERT: G 189 MET cc_start: 0.3237 (mpt) cc_final: -0.0572 (tpp) REVERT: G 348 MET cc_start: 0.2358 (tpp) cc_final: 0.1067 (tpp) REVERT: I 160 MET cc_start: 0.0180 (OUTLIER) cc_final: -0.0974 (ptm) REVERT: J 160 MET cc_start: -0.3406 (OUTLIER) cc_final: -0.3663 (ptt) REVERT: J 163 MET cc_start: 0.2855 (tpt) cc_final: 0.1432 (tmt) REVERT: J 244 TYR cc_start: 0.1593 (OUTLIER) cc_final: -0.1202 (m-80) REVERT: K 180 MET cc_start: 0.0045 (tmt) cc_final: -0.1111 (tmt) REVERT: K 214 MET cc_start: 0.3478 (OUTLIER) cc_final: 0.2412 (mtt) REVERT: K 297 MET cc_start: 0.0970 (mmm) cc_final: 0.0692 (mmm) REVERT: K 348 MET cc_start: 0.2640 (mtp) cc_final: 0.2401 (mtp) REVERT: L 271 MET cc_start: 0.3092 (mmp) cc_final: 0.2682 (mtm) REVERT: L 314 PHE cc_start: 0.6322 (OUTLIER) cc_final: 0.6089 (p90) REVERT: M 271 MET cc_start: 0.7707 (ttm) cc_final: 0.7390 (mtp) REVERT: M 342 LYS cc_start: 0.8589 (ptmt) cc_final: 0.8351 (pptt) REVERT: N 297 MET cc_start: 0.5076 (tpt) cc_final: 0.3271 (mpm) REVERT: O 163 MET cc_start: 0.0952 (OUTLIER) cc_final: 0.0205 (mmm) REVERT: O 203 PHE cc_start: -0.0756 (OUTLIER) cc_final: -0.0985 (t80) REVERT: O 271 MET cc_start: 0.1030 (OUTLIER) cc_final: 0.0665 (ttp) REVERT: O 302 PHE cc_start: 0.1632 (t80) cc_final: -0.0110 (t80) REVERT: P 189 MET cc_start: 0.3913 (mmm) cc_final: 0.3688 (mpp) REVERT: P 277 GLU cc_start: 0.4867 (pt0) cc_final: 0.4211 (pp20) REVERT: P 297 MET cc_start: -0.0951 (ttt) cc_final: -0.1267 (ttp) REVERT: Q 201 GLU cc_start: 0.7050 (pm20) cc_final: 0.6821 (pm20) REVERT: R 163 MET cc_start: 0.4918 (mpm) cc_final: 0.4536 (mmm) REVERT: R 172 LYS cc_start: 0.3320 (OUTLIER) cc_final: 0.2429 (mmtt) REVERT: R 180 MET cc_start: 0.2069 (OUTLIER) cc_final: -0.4112 (ttt) REVERT: R 260 LEU cc_start: 0.1168 (OUTLIER) cc_final: 0.0586 (pp) REVERT: R 333 PHE cc_start: 0.5097 (m-10) cc_final: 0.4885 (m-80) REVERT: R 360 ILE cc_start: 0.4033 (OUTLIER) cc_final: 0.3034 (mt) REVERT: S 180 MET cc_start: 0.0329 (tmt) cc_final: -0.0913 (tmt) REVERT: S 195 MET cc_start: 0.3798 (mpt) cc_final: 0.3565 (mpt) REVERT: S 223 PHE cc_start: 0.1864 (m-80) cc_final: 0.1604 (p90) REVERT: S 297 MET cc_start: 0.2709 (mmt) cc_final: 0.2397 (mmt) REVERT: S 348 MET cc_start: 0.4634 (ppp) cc_final: 0.3979 (ppp) REVERT: T 195 MET cc_start: 0.2205 (OUTLIER) cc_final: 0.1726 (mmp) REVERT: T 214 MET cc_start: 0.1725 (tpt) cc_final: 0.1448 (tmm) REVERT: T 329 MET cc_start: 0.1619 (OUTLIER) cc_final: 0.0161 (pmm) REVERT: T 348 MET cc_start: 0.2605 (mtt) cc_final: 0.2096 (ttp) REVERT: U 160 MET cc_start: 0.0563 (OUTLIER) cc_final: -0.1222 (mmt) REVERT: U 302 PHE cc_start: 0.0931 (t80) cc_final: -0.0835 (t80) REVERT: W 160 MET cc_start: 0.2592 (mpp) cc_final: 0.1785 (mtp) REVERT: W 258 ARG cc_start: 0.3130 (pmt170) cc_final: 0.2879 (tmm-80) REVERT: X 160 MET cc_start: -0.2875 (mtt) cc_final: -0.4436 (ptp) REVERT: X 214 MET cc_start: 0.4455 (tmt) cc_final: 0.4179 (tmm) REVERT: X 297 MET cc_start: 0.1426 (OUTLIER) cc_final: 0.0555 (mpp) REVERT: X 326 ILE cc_start: 0.6950 (OUTLIER) cc_final: 0.6192 (pp) outliers start: 151 outliers final: 59 residues processed: 673 average time/residue: 1.5370 time to fit residues: 1268.6612 Evaluate side-chains 602 residues out of total 4776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 520 time to evaluate : 4.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 348 MET Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 357 HIS Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 163 MET Chi-restraints excluded: chain G residue 339 ILE Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 160 MET Chi-restraints excluded: chain J residue 160 MET Chi-restraints excluded: chain J residue 203 PHE Chi-restraints excluded: chain J residue 244 TYR Chi-restraints excluded: chain J residue 350 TYR Chi-restraints excluded: chain K residue 161 ASN Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 249 ASP Chi-restraints excluded: chain L residue 314 PHE Chi-restraints excluded: chain L residue 349 MET Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain N residue 182 THR Chi-restraints excluded: chain N residue 296 ASP Chi-restraints excluded: chain N residue 318 ILE Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain O residue 161 ASN Chi-restraints excluded: chain O residue 163 MET Chi-restraints excluded: chain O residue 195 MET Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 271 MET Chi-restraints excluded: chain O residue 323 GLN Chi-restraints excluded: chain P residue 161 ASN Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain Q residue 183 THR Chi-restraints excluded: chain Q residue 271 MET Chi-restraints excluded: chain R residue 160 MET Chi-restraints excluded: chain R residue 172 LYS Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 188 ASP Chi-restraints excluded: chain R residue 221 SER Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 360 ILE Chi-restraints excluded: chain S residue 161 ASN Chi-restraints excluded: chain S residue 260 LEU Chi-restraints excluded: chain S residue 276 ILE Chi-restraints excluded: chain T residue 160 MET Chi-restraints excluded: chain T residue 195 MET Chi-restraints excluded: chain T residue 329 MET Chi-restraints excluded: chain T residue 378 ASP Chi-restraints excluded: chain T residue 386 LEU Chi-restraints excluded: chain U residue 160 MET Chi-restraints excluded: chain U residue 188 ASP Chi-restraints excluded: chain U residue 312 SER Chi-restraints excluded: chain V residue 249 ASP Chi-restraints excluded: chain X residue 249 ASP Chi-restraints excluded: chain X residue 297 MET Chi-restraints excluded: chain X residue 326 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 329 optimal weight: 0.8980 chunk 212 optimal weight: 9.9990 chunk 317 optimal weight: 0.6980 chunk 160 optimal weight: 0.0370 chunk 104 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 338 optimal weight: 1.9990 chunk 362 optimal weight: 0.9990 chunk 263 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 418 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 ASN I 185 ASN I 323 GLN J 272 ASN ** K 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 GLN N 226 GLN O 193 GLN O 199 HIS O 228 GLN P 323 GLN ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 330 HIS ** U 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 165 GLN ** V 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 226 GLN V 228 GLN ** V 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 357 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3853 moved from start: 1.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 45216 Z= 0.188 Angle : 0.697 14.903 60936 Z= 0.349 Chirality : 0.045 0.293 6984 Planarity : 0.005 0.062 7968 Dihedral : 5.635 86.197 6216 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.53 % Allowed : 24.31 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.51 (0.11), residues: 5616 helix: -0.60 (0.11), residues: 2014 sheet: -1.25 (0.15), residues: 1110 loop : -1.06 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS N 207 PHE 0.036 0.002 PHE G 223 TYR 0.023 0.001 TYR U 350 ARG 0.016 0.000 ARG V 170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 4776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 566 time to evaluate : 5.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7620 (pmm-80) REVERT: A 249 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7757 (p0) REVERT: B 163 MET cc_start: 0.3749 (pp-130) cc_final: 0.3485 (tmt) REVERT: B 297 MET cc_start: 0.2121 (mtm) cc_final: 0.1549 (mtm) REVERT: B 314 PHE cc_start: 0.1289 (p90) cc_final: 0.0206 (p90) REVERT: C 297 MET cc_start: 0.2465 (mpp) cc_final: 0.1828 (pmm) REVERT: D 241 GLU cc_start: 0.2010 (tp30) cc_final: 0.1506 (mm-30) REVERT: D 286 LYS cc_start: 0.2488 (pttm) cc_final: 0.2098 (tmmt) REVERT: E 160 MET cc_start: 0.2126 (mpp) cc_final: 0.1646 (mtt) REVERT: E 297 MET cc_start: 0.5561 (tmm) cc_final: 0.5002 (tpt) REVERT: F 160 MET cc_start: -0.3367 (ptt) cc_final: -0.4683 (pmm) REVERT: F 348 MET cc_start: 0.2609 (OUTLIER) cc_final: -0.0583 (mpm) REVERT: G 163 MET cc_start: 0.3558 (OUTLIER) cc_final: 0.2945 (mmm) REVERT: G 189 MET cc_start: 0.3159 (mpt) cc_final: -0.0558 (tpp) REVERT: G 195 MET cc_start: 0.2826 (mpt) cc_final: 0.2365 (mpt) REVERT: G 228 GLN cc_start: 0.4209 (mt0) cc_final: 0.3702 (mt0) REVERT: G 348 MET cc_start: 0.2248 (tpp) cc_final: 0.0855 (tpp) REVERT: I 160 MET cc_start: 0.0233 (pmm) cc_final: -0.0852 (ptm) REVERT: J 160 MET cc_start: -0.3447 (OUTLIER) cc_final: -0.3712 (ptt) REVERT: J 163 MET cc_start: 0.2728 (tpt) cc_final: 0.1405 (tmt) REVERT: J 244 TYR cc_start: 0.1342 (OUTLIER) cc_final: -0.1321 (m-80) REVERT: K 180 MET cc_start: -0.0417 (tmt) cc_final: -0.0756 (tmt) REVERT: K 214 MET cc_start: 0.3464 (OUTLIER) cc_final: 0.2353 (mtt) REVERT: K 271 MET cc_start: 0.3935 (OUTLIER) cc_final: 0.2497 (tmt) REVERT: K 297 MET cc_start: 0.1143 (mmm) cc_final: 0.0875 (mmm) REVERT: L 163 MET cc_start: 0.2900 (mmm) cc_final: 0.2619 (mmp) REVERT: L 271 MET cc_start: 0.3303 (mmp) cc_final: 0.2702 (mtm) REVERT: L 342 LYS cc_start: 0.8362 (pptt) cc_final: 0.8127 (pptt) REVERT: M 271 MET cc_start: 0.7763 (ttm) cc_final: 0.7503 (mtp) REVERT: M 342 LYS cc_start: 0.8573 (ptmt) cc_final: 0.8369 (pptt) REVERT: N 297 MET cc_start: 0.4992 (tpt) cc_final: 0.4635 (mmm) REVERT: O 163 MET cc_start: 0.0815 (OUTLIER) cc_final: 0.0174 (mmm) REVERT: O 189 MET cc_start: 0.1287 (tpp) cc_final: 0.0741 (ttp) REVERT: O 297 MET cc_start: 0.0910 (mpt) cc_final: 0.0620 (mmt) REVERT: O 302 PHE cc_start: 0.1390 (t80) cc_final: -0.0316 (t80) REVERT: O 348 MET cc_start: 0.2373 (pmm) cc_final: 0.1673 (pmm) REVERT: P 189 MET cc_start: 0.4273 (mmm) cc_final: 0.3506 (mpp) REVERT: P 277 GLU cc_start: 0.4960 (pt0) cc_final: 0.4322 (pp20) REVERT: P 297 MET cc_start: -0.0515 (ttt) cc_final: -0.0902 (mmm) REVERT: Q 271 MET cc_start: 0.3958 (OUTLIER) cc_final: 0.3019 (pp-130) REVERT: Q 302 PHE cc_start: -0.0220 (t80) cc_final: -0.2007 (t80) REVERT: Q 329 MET cc_start: 0.0046 (mmt) cc_final: -0.3153 (tmm) REVERT: R 163 MET cc_start: 0.4620 (mpm) cc_final: 0.4330 (mmm) REVERT: R 260 LEU cc_start: 0.1041 (OUTLIER) cc_final: 0.0454 (pp) REVERT: R 333 PHE cc_start: 0.4885 (m-10) cc_final: 0.4546 (m-80) REVERT: R 360 ILE cc_start: 0.3699 (OUTLIER) cc_final: 0.2788 (mt) REVERT: S 180 MET cc_start: 0.0620 (tmt) cc_final: -0.0382 (tmt) REVERT: S 223 PHE cc_start: 0.1900 (m-80) cc_final: 0.1577 (p90) REVERT: S 297 MET cc_start: 0.2891 (mmt) cc_final: 0.2502 (mmt) REVERT: S 348 MET cc_start: 0.4716 (ppp) cc_final: 0.4368 (ppp) REVERT: T 195 MET cc_start: 0.2120 (OUTLIER) cc_final: 0.1701 (mmp) REVERT: T 278 ARG cc_start: 0.6866 (tmm-80) cc_final: 0.6055 (mpp-170) REVERT: T 292 LEU cc_start: 0.0358 (OUTLIER) cc_final: -0.0117 (mp) REVERT: T 329 MET cc_start: 0.1004 (OUTLIER) cc_final: -0.0250 (pmm) REVERT: U 160 MET cc_start: 0.0246 (pmm) cc_final: -0.1545 (mmt) REVERT: U 172 LYS cc_start: 0.7610 (tmmt) cc_final: 0.6877 (mmtt) REVERT: U 180 MET cc_start: 0.2513 (mmt) cc_final: -0.0406 (ptp) REVERT: U 302 PHE cc_start: 0.0805 (t80) cc_final: -0.0923 (t80) REVERT: W 160 MET cc_start: 0.2551 (mpp) cc_final: 0.1736 (mtp) REVERT: W 258 ARG cc_start: 0.3280 (pmt170) cc_final: 0.3022 (tmm-80) REVERT: X 160 MET cc_start: -0.2824 (mtt) cc_final: -0.4515 (ptp) REVERT: X 214 MET cc_start: 0.4553 (tmt) cc_final: 0.4248 (tmm) REVERT: X 297 MET cc_start: 0.1326 (OUTLIER) cc_final: 0.0942 (mpp) REVERT: X 326 ILE cc_start: 0.7084 (OUTLIER) cc_final: 0.6301 (pp) outliers start: 121 outliers final: 45 residues processed: 644 average time/residue: 1.5537 time to fit residues: 1246.6343 Evaluate side-chains 573 residues out of total 4776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 511 time to evaluate : 4.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 258 ARG Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 163 MET Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 323 GLN Chi-restraints excluded: chain J residue 160 MET Chi-restraints excluded: chain J residue 244 TYR Chi-restraints excluded: chain K residue 161 ASN Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 249 ASP Chi-restraints excluded: chain K residue 271 MET Chi-restraints excluded: chain L residue 192 ILE Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 282 GLU Chi-restraints excluded: chain M residue 348 MET Chi-restraints excluded: chain N residue 182 THR Chi-restraints excluded: chain O residue 161 ASN Chi-restraints excluded: chain O residue 163 MET Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain O residue 323 GLN Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain Q residue 183 THR Chi-restraints excluded: chain Q residue 271 MET Chi-restraints excluded: chain R residue 160 MET Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 360 ILE Chi-restraints excluded: chain S residue 161 ASN Chi-restraints excluded: chain S residue 260 LEU Chi-restraints excluded: chain S residue 276 ILE Chi-restraints excluded: chain T residue 195 MET Chi-restraints excluded: chain T residue 292 LEU Chi-restraints excluded: chain T residue 329 MET Chi-restraints excluded: chain T residue 386 LEU Chi-restraints excluded: chain U residue 184 PHE Chi-restraints excluded: chain V residue 249 ASP Chi-restraints excluded: chain X residue 249 ASP Chi-restraints excluded: chain X residue 297 MET Chi-restraints excluded: chain X residue 326 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 483 optimal weight: 20.0000 chunk 509 optimal weight: 1.9990 chunk 465 optimal weight: 1.9990 chunk 495 optimal weight: 0.6980 chunk 298 optimal weight: 0.4980 chunk 215 optimal weight: 5.9990 chunk 389 optimal weight: 0.9980 chunk 152 optimal weight: 8.9990 chunk 448 optimal weight: 1.9990 chunk 468 optimal weight: 9.9990 chunk 494 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN A 323 GLN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN B 320 ASN ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 ASN H 226 GLN I 185 ASN I 228 GLN I 323 GLN ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 323 GLN ** M 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 GLN N 226 GLN N 228 GLN ** N 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 323 GLN ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 226 GLN V 228 GLN W 228 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4044 moved from start: 1.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 45216 Z= 0.230 Angle : 0.750 20.552 60936 Z= 0.375 Chirality : 0.046 0.526 6984 Planarity : 0.005 0.083 7968 Dihedral : 5.786 85.847 6216 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.83 % Allowed : 24.25 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.44 (0.11), residues: 5616 helix: -0.49 (0.11), residues: 1981 sheet: -0.85 (0.16), residues: 879 loop : -1.26 (0.11), residues: 2756 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS N 207 PHE 0.044 0.002 PHE G 223 TYR 0.028 0.002 TYR X 350 ARG 0.016 0.001 ARG V 170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 4776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 567 time to evaluate : 4.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.7344 (mmm160) cc_final: 0.6950 (tpt170) REVERT: A 185 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8162 (m110) REVERT: A 249 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7838 (p0) REVERT: B 160 MET cc_start: -0.0774 (ptt) cc_final: -0.1392 (ptp) REVERT: B 320 ASN cc_start: 0.0756 (OUTLIER) cc_final: 0.0547 (m-40) REVERT: B 344 GLU cc_start: 0.7796 (pm20) cc_final: 0.7468 (pm20) REVERT: B 349 MET cc_start: 0.2252 (OUTLIER) cc_final: 0.1821 (mpm) REVERT: B 378 ASP cc_start: 0.5876 (p0) cc_final: 0.5538 (p0) REVERT: C 180 MET cc_start: 0.2652 (OUTLIER) cc_final: 0.2297 (tpt) REVERT: C 297 MET cc_start: 0.2591 (mpp) cc_final: 0.1764 (pmm) REVERT: D 286 LYS cc_start: 0.2790 (pttm) cc_final: 0.2300 (tmmt) REVERT: E 160 MET cc_start: 0.2379 (mpp) cc_final: 0.1797 (mtt) REVERT: E 241 GLU cc_start: 0.4898 (tt0) cc_final: 0.4455 (mm-30) REVERT: E 297 MET cc_start: 0.5807 (tmm) cc_final: 0.5518 (tpt) REVERT: F 160 MET cc_start: -0.3552 (ptt) cc_final: -0.4823 (pmm) REVERT: F 348 MET cc_start: 0.2598 (OUTLIER) cc_final: -0.0302 (mpm) REVERT: F 350 TYR cc_start: -0.0098 (OUTLIER) cc_final: -0.0368 (m-80) REVERT: F 357 HIS cc_start: 0.1404 (OUTLIER) cc_final: 0.0326 (t70) REVERT: F 382 LEU cc_start: 0.1535 (OUTLIER) cc_final: 0.1216 (pt) REVERT: G 163 MET cc_start: 0.3884 (OUTLIER) cc_final: 0.3289 (mmm) REVERT: G 189 MET cc_start: 0.3325 (mpt) cc_final: -0.0675 (tpp) REVERT: G 228 GLN cc_start: 0.4078 (mt0) cc_final: 0.3607 (mt0) REVERT: G 348 MET cc_start: 0.2206 (tpp) cc_final: 0.0976 (tpp) REVERT: I 160 MET cc_start: 0.0397 (pmm) cc_final: -0.0778 (ptm) REVERT: J 217 PHE cc_start: 0.4101 (m-10) cc_final: 0.3855 (m-10) REVERT: J 244 TYR cc_start: 0.1359 (OUTLIER) cc_final: -0.1285 (m-80) REVERT: J 329 MET cc_start: 0.2702 (mpt) cc_final: 0.2347 (mmt) REVERT: K 214 MET cc_start: 0.2859 (OUTLIER) cc_final: 0.2285 (mtm) REVERT: K 271 MET cc_start: 0.4251 (OUTLIER) cc_final: 0.2963 (tmt) REVERT: K 297 MET cc_start: 0.1207 (mmm) cc_final: 0.0903 (mmm) REVERT: L 271 MET cc_start: 0.3231 (mmp) cc_final: 0.2898 (mtm) REVERT: M 271 MET cc_start: 0.7899 (ttm) cc_final: 0.7535 (mtp) REVERT: M 323 GLN cc_start: -0.0018 (OUTLIER) cc_final: -0.1449 (tp40) REVERT: N 297 MET cc_start: 0.5563 (tpt) cc_final: 0.5242 (mmm) REVERT: O 302 PHE cc_start: 0.2015 (t80) cc_final: 0.0338 (t80) REVERT: O 348 MET cc_start: 0.1882 (pmm) cc_final: 0.1438 (pmm) REVERT: P 172 LYS cc_start: 0.0907 (OUTLIER) cc_final: 0.0027 (mmpt) REVERT: P 189 MET cc_start: 0.4242 (mmm) cc_final: 0.3683 (mpp) REVERT: P 297 MET cc_start: -0.0583 (ttt) cc_final: -0.0850 (mmm) REVERT: P 385 ASP cc_start: -0.0250 (OUTLIER) cc_final: -0.0511 (m-30) REVERT: R 163 MET cc_start: 0.4481 (mpm) cc_final: 0.4277 (mmm) REVERT: R 360 ILE cc_start: 0.4700 (OUTLIER) cc_final: 0.3854 (mt) REVERT: S 180 MET cc_start: 0.0432 (tmt) cc_final: -0.0730 (tmt) REVERT: S 297 MET cc_start: 0.2901 (mmt) cc_final: 0.2567 (mmt) REVERT: S 348 MET cc_start: 0.5100 (ppp) cc_final: 0.4427 (ppp) REVERT: T 195 MET cc_start: 0.2362 (OUTLIER) cc_final: 0.1883 (mmp) REVERT: T 271 MET cc_start: 0.3145 (OUTLIER) cc_final: 0.1995 (tmt) REVERT: T 278 ARG cc_start: 0.6433 (tmm-80) cc_final: 0.6049 (mpp-170) REVERT: T 297 MET cc_start: 0.1516 (mpm) cc_final: -0.2142 (ttt) REVERT: T 329 MET cc_start: 0.1176 (OUTLIER) cc_final: -0.0378 (pmm) REVERT: U 160 MET cc_start: 0.0349 (OUTLIER) cc_final: -0.1408 (mmt) REVERT: U 172 LYS cc_start: 0.7855 (tmmt) cc_final: 0.7111 (mmtt) REVERT: U 180 MET cc_start: 0.2003 (mmt) cc_final: -0.0802 (mtt) REVERT: U 302 PHE cc_start: 0.1122 (t80) cc_final: -0.0501 (t80) REVERT: W 160 MET cc_start: 0.2814 (mpp) cc_final: 0.1940 (mtt) REVERT: W 217 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7475 (t80) REVERT: X 160 MET cc_start: -0.2651 (OUTLIER) cc_final: -0.4514 (ptp) REVERT: X 214 MET cc_start: 0.4372 (tmt) cc_final: 0.4111 (tmm) REVERT: X 297 MET cc_start: 0.1509 (OUTLIER) cc_final: 0.1156 (mpp) REVERT: X 348 MET cc_start: 0.3666 (ttm) cc_final: 0.3222 (ttm) outliers start: 135 outliers final: 53 residues processed: 654 average time/residue: 1.5275 time to fit residues: 1226.6040 Evaluate side-chains 592 residues out of total 4776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 515 time to evaluate : 4.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 350 TYR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 357 HIS Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 163 MET Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 323 GLN Chi-restraints excluded: chain J residue 232 ASN Chi-restraints excluded: chain J residue 244 TYR Chi-restraints excluded: chain K residue 161 ASN Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 249 ASP Chi-restraints excluded: chain K residue 271 MET Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 192 ILE Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 323 GLN Chi-restraints excluded: chain M residue 348 MET Chi-restraints excluded: chain N residue 182 THR Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain O residue 161 ASN Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain O residue 323 GLN Chi-restraints excluded: chain P residue 161 ASN Chi-restraints excluded: chain P residue 172 LYS Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 327 LEU Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain P residue 385 ASP Chi-restraints excluded: chain Q residue 183 THR Chi-restraints excluded: chain R residue 160 MET Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 221 SER Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 360 ILE Chi-restraints excluded: chain R residue 378 ASP Chi-restraints excluded: chain S residue 161 ASN Chi-restraints excluded: chain S residue 276 ILE Chi-restraints excluded: chain S residue 323 GLN Chi-restraints excluded: chain T residue 195 MET Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain T residue 271 MET Chi-restraints excluded: chain T residue 320 ASN Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 329 MET Chi-restraints excluded: chain T residue 386 LEU Chi-restraints excluded: chain U residue 160 MET Chi-restraints excluded: chain U residue 184 PHE Chi-restraints excluded: chain U residue 296 ASP Chi-restraints excluded: chain U residue 312 SER Chi-restraints excluded: chain U residue 327 LEU Chi-restraints excluded: chain V residue 249 ASP Chi-restraints excluded: chain W residue 217 PHE Chi-restraints excluded: chain X residue 160 MET Chi-restraints excluded: chain X residue 249 ASP Chi-restraints excluded: chain X residue 297 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 325 optimal weight: 0.9990 chunk 524 optimal weight: 0.0770 chunk 319 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 364 optimal weight: 0.9990 chunk 549 optimal weight: 5.9990 chunk 506 optimal weight: 10.0000 chunk 437 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 338 optimal weight: 0.9990 chunk 268 optimal weight: 0.2980 overall best weight: 0.6744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN A 323 GLN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 323 GLN H 191 ASN I 185 ASN I 228 GLN I 323 GLN J 176 ASN ** K 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 323 GLN ** M 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 GLN N 208 ASN N 226 GLN N 228 GLN O 228 GLN P 323 GLN Q 175 GLN Q 176 ASN V 228 GLN ** V 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3980 moved from start: 1.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 45216 Z= 0.194 Angle : 0.727 18.671 60936 Z= 0.360 Chirality : 0.045 0.528 6984 Planarity : 0.005 0.077 7968 Dihedral : 5.579 85.018 6216 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.78 % Allowed : 25.65 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.31 (0.11), residues: 5616 helix: -0.33 (0.12), residues: 2002 sheet: -0.81 (0.16), residues: 879 loop : -1.23 (0.11), residues: 2735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS N 207 PHE 0.044 0.002 PHE G 223 TYR 0.016 0.001 TYR B 350 ARG 0.019 0.000 ARG V 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 4776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 536 time to evaluate : 5.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7787 (p0) REVERT: B 160 MET cc_start: -0.0706 (ptt) cc_final: -0.1374 (ptp) REVERT: B 320 ASN cc_start: 0.1501 (OUTLIER) cc_final: 0.1219 (m-40) REVERT: B 329 MET cc_start: -0.0432 (mpp) cc_final: -0.0818 (ttm) REVERT: B 344 GLU cc_start: 0.7751 (pm20) cc_final: 0.7316 (pm20) REVERT: B 349 MET cc_start: 0.2051 (OUTLIER) cc_final: 0.1580 (mpm) REVERT: B 378 ASP cc_start: 0.5615 (p0) cc_final: 0.5375 (p0) REVERT: C 214 MET cc_start: 0.3901 (tpp) cc_final: 0.3648 (pp-130) REVERT: C 297 MET cc_start: 0.2414 (mpp) cc_final: 0.1728 (pmm) REVERT: D 286 LYS cc_start: 0.2472 (pttm) cc_final: 0.2206 (tmmt) REVERT: D 367 THR cc_start: 0.6567 (m) cc_final: 0.6336 (m) REVERT: E 160 MET cc_start: 0.2360 (mpp) cc_final: 0.1867 (mtt) REVERT: E 206 LYS cc_start: 0.5065 (ttpt) cc_final: 0.4487 (tptm) REVERT: E 241 GLU cc_start: 0.4969 (tt0) cc_final: 0.4534 (mm-30) REVERT: E 383 LEU cc_start: 0.3919 (tt) cc_final: 0.3622 (mt) REVERT: F 160 MET cc_start: -0.3395 (ptt) cc_final: -0.4736 (pmm) REVERT: F 297 MET cc_start: 0.1095 (pmm) cc_final: 0.0743 (pmm) REVERT: F 348 MET cc_start: 0.2573 (OUTLIER) cc_final: -0.0324 (mpm) REVERT: F 357 HIS cc_start: 0.1134 (OUTLIER) cc_final: 0.0348 (t70) REVERT: G 163 MET cc_start: 0.3831 (OUTLIER) cc_final: 0.3310 (mmm) REVERT: G 189 MET cc_start: 0.3078 (mpt) cc_final: -0.0651 (tpp) REVERT: G 228 GLN cc_start: 0.3991 (mt0) cc_final: 0.3534 (mt0) REVERT: G 348 MET cc_start: 0.1771 (tpp) cc_final: 0.0333 (tpp) REVERT: I 160 MET cc_start: 0.0147 (pmm) cc_final: -0.0454 (ptm) REVERT: J 163 MET cc_start: 0.2063 (tpt) cc_final: 0.1056 (tmt) REVERT: J 217 PHE cc_start: 0.4148 (m-10) cc_final: 0.3908 (m-10) REVERT: J 244 TYR cc_start: 0.1330 (OUTLIER) cc_final: -0.1282 (m-80) REVERT: J 329 MET cc_start: 0.2583 (mpt) cc_final: 0.2236 (mmt) REVERT: J 368 PHE cc_start: 0.1266 (OUTLIER) cc_final: 0.0926 (t80) REVERT: K 180 MET cc_start: -0.0995 (tmt) cc_final: -0.1255 (tmt) REVERT: K 189 MET cc_start: 0.3586 (mpp) cc_final: 0.3370 (mmm) REVERT: K 214 MET cc_start: 0.2946 (tmm) cc_final: 0.2319 (mtt) REVERT: K 271 MET cc_start: 0.4120 (OUTLIER) cc_final: 0.2691 (tmt) REVERT: K 297 MET cc_start: 0.0900 (mmm) cc_final: 0.0686 (mmm) REVERT: L 163 MET cc_start: 0.2774 (mmm) cc_final: 0.2495 (mmp) REVERT: L 271 MET cc_start: 0.3368 (mmp) cc_final: 0.2958 (mtm) REVERT: L 348 MET cc_start: -0.0635 (ptm) cc_final: -0.2191 (mmt) REVERT: M 323 GLN cc_start: 0.0483 (OUTLIER) cc_final: -0.1504 (tp-100) REVERT: N 297 MET cc_start: 0.5494 (tpt) cc_final: 0.5114 (tpt) REVERT: O 163 MET cc_start: 0.1073 (mmm) cc_final: 0.0507 (mmm) REVERT: O 169 GLN cc_start: 0.2773 (tp-100) cc_final: 0.1082 (mt0) REVERT: O 302 PHE cc_start: 0.1681 (t80) cc_final: 0.0013 (t80) REVERT: O 348 MET cc_start: 0.1433 (pmm) cc_final: 0.0927 (pmm) REVERT: P 172 LYS cc_start: 0.0921 (OUTLIER) cc_final: 0.0110 (mmpt) REVERT: P 189 MET cc_start: 0.4169 (mmm) cc_final: 0.3548 (mpp) REVERT: Q 191 ASN cc_start: 0.8253 (t0) cc_final: 0.8037 (m-40) REVERT: Q 329 MET cc_start: -0.0170 (mmp) cc_final: -0.2827 (tpp) REVERT: R 163 MET cc_start: 0.4367 (mpm) cc_final: 0.4132 (mmm) REVERT: R 360 ILE cc_start: 0.4113 (OUTLIER) cc_final: 0.3232 (mt) REVERT: S 297 MET cc_start: 0.2860 (mmt) cc_final: 0.2519 (mmt) REVERT: S 348 MET cc_start: 0.4726 (ppp) cc_final: 0.4099 (ppp) REVERT: T 195 MET cc_start: 0.2232 (OUTLIER) cc_final: 0.1844 (mmp) REVERT: T 297 MET cc_start: 0.1758 (mpm) cc_final: -0.1893 (ttp) REVERT: T 329 MET cc_start: 0.0917 (OUTLIER) cc_final: -0.0430 (pmm) REVERT: U 160 MET cc_start: 0.0174 (OUTLIER) cc_final: -0.1459 (mmt) REVERT: U 172 LYS cc_start: 0.7828 (tmmt) cc_final: 0.7182 (mmtt) REVERT: U 180 MET cc_start: 0.2102 (mmt) cc_final: -0.0727 (mtm) REVERT: V 194 GLU cc_start: 0.7466 (pp20) cc_final: 0.7159 (pp20) REVERT: W 160 MET cc_start: 0.2837 (mpp) cc_final: 0.1907 (OUTLIER) REVERT: W 277 GLU cc_start: 0.4238 (mm-30) cc_final: 0.3649 (mm-30) REVERT: W 329 MET cc_start: 0.7168 (mpp) cc_final: 0.6797 (mpp) REVERT: X 160 MET cc_start: -0.2627 (mtt) cc_final: -0.4629 (ptp) REVERT: X 214 MET cc_start: 0.4589 (tmt) cc_final: 0.4366 (tmm) REVERT: X 297 MET cc_start: 0.1378 (OUTLIER) cc_final: 0.1073 (mpp) outliers start: 85 outliers final: 43 residues processed: 586 average time/residue: 1.5139 time to fit residues: 1092.0158 Evaluate side-chains 572 residues out of total 4776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 514 time to evaluate : 4.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 357 HIS Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 163 MET Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain J residue 244 TYR Chi-restraints excluded: chain J residue 348 MET Chi-restraints excluded: chain J residue 368 PHE Chi-restraints excluded: chain K residue 161 ASN Chi-restraints excluded: chain K residue 249 ASP Chi-restraints excluded: chain K residue 271 MET Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 282 GLU Chi-restraints excluded: chain M residue 323 GLN Chi-restraints excluded: chain M residue 337 VAL Chi-restraints excluded: chain M residue 348 MET Chi-restraints excluded: chain N residue 182 THR Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain O residue 161 ASN Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain O residue 323 GLN Chi-restraints excluded: chain P residue 161 ASN Chi-restraints excluded: chain P residue 172 LYS Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain Q residue 183 THR Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 360 ILE Chi-restraints excluded: chain S residue 161 ASN Chi-restraints excluded: chain S residue 276 ILE Chi-restraints excluded: chain S residue 323 GLN Chi-restraints excluded: chain T residue 195 MET Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain T residue 329 MET Chi-restraints excluded: chain T residue 386 LEU Chi-restraints excluded: chain U residue 160 MET Chi-restraints excluded: chain U residue 184 PHE Chi-restraints excluded: chain U residue 327 LEU Chi-restraints excluded: chain V residue 249 ASP Chi-restraints excluded: chain W residue 337 VAL Chi-restraints excluded: chain X residue 249 ASP Chi-restraints excluded: chain X residue 297 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 347 optimal weight: 10.0000 chunk 466 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 403 optimal weight: 0.6980 chunk 64 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 chunk 438 optimal weight: 6.9990 chunk 183 optimal weight: 0.4980 chunk 450 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 ASN I 185 ASN I 323 GLN J 176 ASN ** K 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 208 ASN N 226 GLN N 228 GLN ** N 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 228 GLN V 228 GLN ** V 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 323 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5356 r_free = 0.5356 target = 0.294351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5113 r_free = 0.5113 target = 0.264131 restraints weight = 69163.902| |-----------------------------------------------------------------------------| r_work (start): 0.5071 rms_B_bonded: 3.23 r_work: 0.4974 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4478 moved from start: 1.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 45216 Z= 0.197 Angle : 0.716 19.173 60936 Z= 0.355 Chirality : 0.045 0.494 6984 Planarity : 0.005 0.076 7968 Dihedral : 5.494 84.887 6216 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.07 % Allowed : 25.77 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.19 (0.11), residues: 5616 helix: -0.14 (0.12), residues: 1982 sheet: -0.81 (0.16), residues: 894 loop : -1.21 (0.11), residues: 2740 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS N 207 PHE 0.042 0.002 PHE G 223 TYR 0.018 0.001 TYR U 350 ARG 0.015 0.000 ARG V 166 =============================================================================== Job complete usr+sys time: 18908.16 seconds wall clock time: 340 minutes 14.09 seconds (20414.09 seconds total)